Databases, Bibliographic: Extensive collections, reputedly complete, of references and citations to books, articles, publications, etc., generally on a single subject or specialized subject area. Databases can operate through automated files, libraries, or computer disks. The concept should be differentiated from DATABASES, FACTUAL which is used for collections of data and facts apart from bibliographic references to them.Databases, Factual: Extensive collections, reputedly complete, of facts and data garnered from material of a specialized subject area and made available for analysis and application. The collection can be automated by various contemporary methods for retrieval. The concept should be differentiated from DATABASES, BIBLIOGRAPHIC which is restricted to collections of bibliographic references.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.Databases as Topic: Organized collections of computer records, standardized in format and content, that are stored in any of a variety of computer-readable modes. They are the basic sets of data from which computer-readable files are created. (from ALA Glossary of Library and Information Science, 1983)Databases, Protein: Databases containing information about PROTEINS such as AMINO ACID SEQUENCE; PROTEIN CONFORMATION; and other properties.Databases, Nucleic Acid: Databases containing information about NUCLEIC ACIDS such as BASE SEQUENCE; SNPS; NUCLEIC ACID CONFORMATION; and other properties. Information about the DNA fragments kept in a GENE LIBRARY or GENOMIC LIBRARY is often maintained in DNA databases.Information Storage and Retrieval: Organized activities related to the storage, location, search, and retrieval of information.Internet: A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange.Enzymes: Biological molecules that possess catalytic activity. They may occur naturally or be synthetically created. Enzymes are usually proteins, however CATALYTIC RNA and CATALYTIC DNA molecules have also been identified.Kinetics: The rate dynamics in chemical or physical systems.Vanilla: A plant genus of the family ORCHIDACEAE that is the source of the familiar flavoring used in foods and medicines (FLAVORING AGENTS).Nitrophenylgalactosides: Includes ortho-, meta-, and para-nitrophenylgalactosides.Paeonia: A plant genus of the family Paeoniaceae, order Dilleniales, subclass Dilleniidae, class Magnoliopsida. These perennial herbs are up to 2 m (6') tall. Leaves are alternate and are divided into three lobes, each lobe being further divided into three smaller lobes. The large flowers are symmetrical, bisexual, have 5 sepals, 5 petals (sometimes 10), and many stamens.Models, Chemical: Theoretical representations that simulate the behavior or activity of chemical processes or phenomena; includes the use of mathematical equations, computers, and other electronic equipment.Solubility: The ability of a substance to be dissolved, i.e. to form a solution with another substance. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)Directories as Topic: Lists of persons or organizations, systematically arranged, usually in alphabetic or classed order, giving address, affiliations, etc., for individuals, and giving address, officers, functions, and similar data for organizations. (ALA Glossary of Library and Information Science, 1983)United States Department of Agriculture: A cabinet department in the Executive Branch of the United States Government concerned with improving and maintaining farm income and developing and expanding markets for agricultural products. Through inspection and grading services it safeguards and insures standards of quality in food supply and production.Cell Adhesion: Adherence of cells to surfaces or to other cells.Reference Standards: A basis of value established for the measure of quantity, weight, extent or quality, e.g. weight standards, standard solutions, methods, techniques, and procedures used in diagnosis and therapy.DirectoryCell Adhesion Molecules: Surface ligands, usually glycoproteins, that mediate cell-to-cell adhesion. Their functions include the assembly and interconnection of various vertebrate systems, as well as maintenance of tissue integration, wound healing, morphogenic movements, cellular migrations, and metastasis.Integrins: A family of transmembrane glycoproteins (MEMBRANE GLYCOPROTEINS) consisting of noncovalent heterodimers. They interact with a wide variety of ligands including EXTRACELLULAR MATRIX PROTEINS; COMPLEMENT, and other cells, while their intracellular domains interact with the CYTOSKELETON. The integrins consist of at least three identified families: the cytoadhesin receptors(RECEPTORS, CYTOADHESIN), the leukocyte adhesion receptors (RECEPTORS, LEUKOCYTE ADHESION), and the VERY LATE ANTIGEN RECEPTORS. Each family contains a common beta-subunit (INTEGRIN BETA CHAINS) combined with one or more distinct alpha-subunits (INTEGRIN ALPHA CHAINS). These receptors participate in cell-matrix and cell-cell adhesion in many physiologically important processes, including embryological development; HEMOSTASIS; THROMBOSIS; WOUND HEALING; immune and nonimmune defense mechanisms; and oncogenic transformation.Encyclopedias as Topic: Works containing information articles on subjects in every field of knowledge, usually arranged in alphabetical order, or a similar work limited to a special field or subject. (From The ALA Glossary of Library and Information Science, 1983)Metabolic Networks and Pathways: Complex sets of enzymatic reactions connected to each other via their product and substrate metabolites.Metabolomics: The systematic identification and quantitation of all the metabolic products of a cell, tissue, organ, or organism under varying conditions. The METABOLOME of a cell or organism is a dynamic collection of metabolites which represent its net response to current conditions.Molecular Biology: A discipline concerned with studying biological phenomena in terms of the chemical and physical interactions of molecules.Ethanolaminephosphotransferase: An enzyme that catalyzes reversibly the transfer of phosphoethanolamine from CDP-ethanolamine to diacylglycerol to yield phosphatidylethanolamine (cephalin) and CMP. The enzyme is found in the endoplasmic reticulum. EC 2.7.8.1.Shigella flexneri: A bacterium which is one of the etiologic agents of bacillary dysentery (DYSENTERY, BACILLARY) and sometimes of infantile gastroenteritis.Dysentery, Bacillary: DYSENTERY caused by gram-negative rod-shaped enteric bacteria (ENTEROBACTERIACEAE), most often by the genus SHIGELLA. Shigella dysentery, Shigellosis, is classified into subgroups according to syndrome severity and the infectious species. Group A: SHIGELLA DYSENTERIAE (severest); Group B: SHIGELLA FLEXNERI; Group C: SHIGELLA BOYDII; and Group D: SHIGELLA SONNEI (mildest).Rhamnose: A methylpentose whose L- isomer is found naturally in many plant glycosides and some gram-negative bacterial lipopolysaccharides.Sporosarcina: A genus of endospore-forming bacteria in the family Planococcaceae. The species are strict or facultative anerobes.O Antigens: The lipopolysaccharide-protein somatic antigens, usually from gram-negative bacteria, important in the serological classification of enteric bacilli. The O-specific chains determine the specificity of the O antigens of a given serotype. O antigens are the immunodominant part of the lipopolysaccharide molecule in the intact bacterial cell. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)Dysentery: Acute inflammation of the intestine associated with infectious DIARRHEA of various etiologies, generally acquired by eating contaminated food containing TOXINS, BIOLOGICAL derived from BACTERIA or other microorganisms. Dysentery is characterized initially by watery FECES then by bloody mucoid stools. It is often associated with ABDOMINAL PAIN; FEVER; and DEHYDRATION.Torture: The intentional infliction of physical or mental suffering upon an individual or individuals, including the torture of animals.PubMed: A bibliographic database that includes MEDLINE as its primary subset. It is produced by the National Center for Biotechnology Information (NCBI), part of the NATIONAL LIBRARY OF MEDICINE. PubMed, which is searchable through NLM's Web site, also includes access to additional citations to selected life sciences journals not in MEDLINE, and links to other resources such as the full-text of articles at participating publishers' Web sites, NCBI's molecular biology databases, and PubMed Central.Newspapers: Publications printed and distributed daily, weekly, or at some other regular and usually short interval, containing news, articles of opinion (as editorials and letters), features, advertising, and announcements of current interest. (Webster's 3d ed)User-Computer Interface: The portion of an interactive computer program that issues messages to and receives commands from a user.Abbreviations as Topic: Shortened forms of written words or phrases used for brevity.Posters as Topic: Single or multi-sheet notices made to attract attention to events, activities, causes, goods, or services. They are for display, usually in a public place and are chiefly pictorial.Abstracting and Indexing as Topic: Activities performed to identify concepts and aspects of published information and research reports.Periodicals as Topic: A publication issued at stated, more or less regular, intervals.Dictionaries as Topic: Lists of words, usually in alphabetical order, giving information about form, pronunciation, etymology, grammar, and meaning.Abbreviations: Works consisting of lists of shortened forms of written words or phrases used for brevity. Acronyms are included here.Economics, Pharmaceutical: Economic aspects of the fields of pharmacy and pharmacology as they apply to the development and study of medical economics in rational drug therapy and the impact of pharmaceuticals on the cost of medical care. Pharmaceutical economics also includes the economic considerations of the pharmaceutical care delivery system and in drug prescribing, particularly of cost-benefit values. (From J Res Pharm Econ 1989;1(1); PharmacoEcon 1992;1(1))Drug Industry: That segment of commercial enterprise devoted to the design, development, and manufacture of chemical products for use in the diagnosis and treatment of disease, disability, or other dysfunction, or to improve function.High-Throughput Nucleotide Sequencing: Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.Gene Expression Profiling: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.Antigen-Antibody Complex: The complex formed by the binding of antigen and antibody molecules. The deposition of large antigen-antibody complexes leading to tissue damage causes IMMUNE COMPLEX DISEASES.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Pharmaceutical Preparations: Drugs intended for human or veterinary use, presented in their finished dosage form. Included here are materials used in the preparation and/or formulation of the finished dosage form.LondonDatabase Management Systems: Software designed to store, manipulate, manage, and control data for specific uses.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Eagles: Large members of the FALCONIFORMES order of birds, family Accipitridae, most especially the genera Aquila, Haliaeetus, Harpia, and Circaetus. They are characterized by their powerful talons, which carry long, curved, pointed claws and by their opposable hindtoe.
MetaCycThe data in the database is manually curated from the scientific literature, and covers all domains of life. MetaCyc has ... MetaCyc data on metabolites includes chemical structures, predicted Standard energy of formation, and links to external ... MetaCyc is used as a reference data set for computationally predicting the metabolic network of organisms from their sequenced ... The MetaCyc database is one of the largest metabolic pathways and enzymes databases currently available. ...
... sequence database (GenBank) Protein: sequence database Genome: whole genome sequences and mapping Structure: three-dimensional ... high-throughput sequencing data Cancer Chromosomes: cytogenetic databases PubChem BioAssay: bioactivity screens of chemical ... Entrez searches the following databases: PubMed: biomedical literature citations and abstracts, including Medline - articles ... unique small molecule chemical structures PubChem Substance: deposited chemical substance records Genome Project: genome ...
Chemical literature databases correlate structures or other chemical information to relevant references such as academic papers ... Large molecules such as proteins are however more compactly represented using the sequences of their amino acid building blocks ... A chemical database is a database specifically designed to store chemical information. This information is about chemical and ... Chemical databases are particularly different from other general purpose databases in their support for sub-structure search. ...
The HMDB supports a wide variety of online queries including text searches, chemical structure searches, sequence similarity ... The Yeast Metabolome Database is a freely accessible, online database of >2000 small molecule metabolites found in or produced ... as well as extensive literature mining. According to their data, the human serum metabolome contains at least 4200 different ... The YMDB supports a wide variety of queries including text searches, chemical structure searches, sequence similarity searches ...
T3DB is fully searchable and supports extensive text, sequence, chemical structure, relational query and spectral searches. It ... and scientific literature. The primary focus of the T3DB is on providing mechanisms of toxicity and identifying target proteins ... The Toxin and Toxin-Target Database (T3DB), also known as the Toxic Exposome Database, is a freely accessible online database ... While a number of other toxic compound databases do exist, their emphasis is on covering large numbers of chemical compounds ...
Furthermore, cross-references to external information resources such as sequence and 3D-structure databases, as well as ... Links to the literature are established with PubMed. BRENDA links to some further databases and repositories such as: BRENDA ... synonyms or via the chemical structure. The term "ligand" is used in this context to all low molecular weight compounds which ... These text-mining results were derived from the titles and abstracts of all articles in the literature database PubMed. Data ...
Databases. *Sequence databases: GenBank, European Nucleotide Archive and DNA Data Bank of Japan. ... What began as a modest task of abstracting information from literature soon became a major database activity with direct ... Chemical Entities of Biological Interest (ChEBI) - database and ontology of molecular entities ... organisation and dissemination of data on biological macromolecular structures ...
It also provides enzyme mini-reviews and literature references. MetaCyc data on metabolites includes chemical structures, ... "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases". Nucleic Acids ... include use as a reference data set for computationally predicting the metabolic pathways of organisms from their sequenced ... The MetaCyc database contains extensive information on metabolic pathways and enzymes from many organisms. MetaCyc data cover ...
Protein: sequence database. *Genome: whole genome sequences and mapping. *Structure: three-dimensional macromolecular ... Databases[edit]. Entrez searches the following databases: *PubMed: biomedical literature citations and abstracts, including ... Cancer Chromosomes: cytogenetic databases. *PubChem BioAssay: bioactivity screens of chemical substances. *Probe: sequence- ... Entrez can efficiently retrieve related sequences, structures, and references. The Entrez system can provide views of gene and ...
Chemical Substances Academic publishing Beilstein Registry Number Chemical database Chemical file format Dictionary of chemical ... Frequently these are arcane and constructed according to regional naming conventions relating to chemical formulae, structures ... to every chemical substance described in the open scientific literature (currently including all substances described from 1957 ... It currently identifies more than 129 million organic and inorganic substances and 67 million protein and DNA sequences, plus ...
... structure and functional databases. Nucleic acid and protein sequences are stored in sequence databases and structure databases ... a database of biological databases) NCBI PubMed (a database of biomedical literature) Death Domain database Szklarczyk D; ... Model Organism Databases Gene Disease Database Biobank Biological data Chemical database European Bioinformatics Institute ... Primary Databases and Secondary Databases. These two differ in their archive structure. Primary databases often hold only one ...
Metathesaurus concepts can also link to resources outside of the database, for instance gene sequence databases. Each concept ... The major semantic types are organisms, anatomical structures, biologic function, chemicals, events, physical objects, and ... Often this is a problem due to the large volume of documents retrieved when the medical literature is searched. The purpose of ... UMLS consists of Knowledge Sources (databases) and a set of software tools. The UMLS was designed and is maintained by the US ...
Its collection of domain models utilizes 3D structure to provide insights into sequence/structure/function relationships. ... ENZYME has direct links to other gene/enzyme/literature databases such as KEGG, BRENDA, and PUBMED. BRENDA: A comprehensive ... Information about the chemical reactions of metabolism and the genetic background of various metabolic properties (sequence to ... Several inconsistencies exist between gene, enzyme, reaction databases, and published literature sources regarding the ...
cDNA sequence and structure/function relationships". European Journal of Biochemistry / FEBS. 224 (2): 549-57. doi:10.1111/j. ... to a Medline literature search about the enzyme, and to entries in other databases. Molecular and Cellular Biology portal. ... as revealed in crystallographic structures, which has been studied computationally with quantum chemical as well as with ... ADH was also one of the first oligomeric enzymes that had its amino acid sequence and three-dimensional structure determined. ...
A huge data base is present in literature regarding its sedimentary evolution, in studies by French and Swiss research groups. ... The structure and technical details which define the Project(van Dijk 2011) were described in a Work Plan which was written in ... A new sequence stratigraphic scheme was built based on the field work, 25 sections were logged in detail (see e.g. (Cippolari ... The chemical characteristics of this oil was previously and extensively studies by Eni experts, and compared with source rocks ...
Database of kinase structure-activity and chemical synthesis data. Kinase.Com: Genomics, evolution and large-scale analysis of ... "Protein kinase catalytic domain sequence database: identification of conserved features of primary structure and classification ... The Protein Kinase Ontology (ProKinO): A unified protein kinase resource The literature-curated human signaling network, the ... Curated database of protein kinase structures and related data Human and mouse protein kinases: classification and index The ...
Many databases exist, covering various information types: for example, DNA and protein sequences, molecular structures, ... the study of chemical processes in biological systems). Computers became essential in molecular biology when protein sequences ... Literature analysis aims to employ computational and statistical linguistics to mine this growing library of text resources. ... The amino acid sequence of a protein, the so-called primary structure, can be easily determined from the sequence on the gene ...
In AntigenDB, a database entry contains information regarding the sequence, structure, origin, etc. of an antigen with ... It is a compilation of sequence data after extensive manual literature search and from publicly available databases. HMRbase ... OSDDchem: OSDDChem chemical database is an open repository of information on synthesised, semi-synthesized, natural and ... It is a manually curated database where most of data has been collected from PubMed and PubMed Central literature databases. ...
FIZ Karlsruhe PubChem ChemSpider Chemical database Beilstein database Inorganic Crystal Structure Database "CAS Printed ... The database is updated quarterly. Beyond CASSI lists abbreviated journal titles from early chemical literature and other ... The sequence information comes from CAS and GenBank, produced by the National Institutes of Health. The chemical information is ... and graphic representation of its chemical structure. The assignment of chemical names is done according to the chemical ...
Human Protein Reference Database, MINT - Molecular Interaction database, MIPS - Munich Information center for Protein Sequences ... With RNA interference, it is possible to distill the inferences contained in the experimental literature and primary databases ... and to the assembly of structured knowledge repositories. Data repositories, which contain information regarding sequence data ... A biochemical cascade, also known as a signaling cascade or signaling pathway, is a series of chemical reactions which are ...
Molander, Gary A.; Harris, Christina R. (1 January 1996). "Sequencing Reactions with Samarium(II) Iodide". Chemical Reviews. 96 ... all have the same UB4 structure. The structure has a boron sub-lattice consists of chains of octahedral B6 clusters linked by ... In the older literature, the name "lanthanon" was often used. Gray, Theodore (2009). The Elements: A Visual Exploration of ... ISBN 978-3-540-00494-3. Pettit, L. and Powell, K. SC-database. Acadsoft.co.uk. Retrieved on 2012-01-15. ...
Bender, A (2010). "Databases: Compound bioactivities go public". Nature Chemical Biology. 6: 309. doi:10.1038/nchembio.354. ... The system incorporates and links sequence, structure, compounds and screening data. GPCR SARfari is a similar workbench ... 2011). "Collation and data-mining of literature bioactivity data for drug discovery". Biochemical Society Transactions. 39: ... ChEMBL or ChEMBLdb is a manually curated chemical database of bioactive molecules with drug-like properties. It is maintained ...
Each gene in PHI-base is presented with its nucleotide and deduced amino acid sequence as well as a detailed structured ... Since 2015 the web-site includes an online literature curation tool called PHI-Canto for community literature curation of ... which may be potential targets for chemical intervention › Comparative genome analyses › Annotation of newly sequenced pathogen ... additions to the pathogen host interactions database" (PDF). Nucleic Acids Research. 36 (Database Issue): D572-576. doi:10.1093 ...
Scores and Ranks the Literature for Improving Chemical-Gene-Disease Curation at the Comparative Toxicogenomics Database". PLoS ... It is a comprehensive, first-class and freely accessible database of protein sequence and functional information, that has many ... In Bioinformatics, a Gene Disease Database is a systematized collection of data, typically structured to model aspects of ... Essentially, there are four types of databases: curated databases, predictive databases, literature databases and integrative ...
A chemical exchange takes place between the alkoxy groups of an ester compound by an alcohol. Usually, methanol and ethanol are ... "Sequence Analysis of the Genome of an Oil-Bearing Tree, Jatropha curcas L". Oxford Journals, DNA Research, Kazusa DNA Research ... a literature review) Biomass and Bioenergy 32(12), 1063-1084.[2] doi:10.1016/j.biombioe.2008.03.003The Jatropha Archives ... Goel, Gunjan; Makkar, Harinder P. S.; Francis, George; Becker, Klaus (30 November 2016). "Phorbol Esters: Structure, Biological ...
T. Kottke, D. Stalke (September 1993). "Structures of Classical Reagents in Chemical Synthesis: (nBuLi)6, (tBuLi)4, and the ... 8).[66] Upon heating of KC8, the elimination of potassium atoms results in the conversion in sequence to KC24, KC36, KC48 and ... hence any data that may be found in the literature are certainly speculative extrapolations.[65] ... "The Internet Database of Periodic Tables". meta-synthesis.com. Retrieved 6 April 2012 ...
People - School of Chemistry - University of St AndrewsStructures, gene sequences, mechanisms, metabolic pathways and kinetic data are currently spread between many different ... We have created MACiE, the worlds first comprehensive electronic database of the chemical mechanisms of enzymatic reactions. ... databases and throughout the literature. ... melting point and hydrophobicity from chemical structure, using ... Lecturer CH5714 Chemical Applications of Electronic Structure Calculations; Lecturer CH4431 Scientific Writing; Lecturer CH3717 ...
Search Resource Resources | NCBO BioPortal... makes it unique from existing databases. It is also fully searchable and supports extensive text, sequence, chemical structure ... Many of the datasets come from published literature, but publication is not a prerequisite for inclusion in the CCDB. Any ... A public database that enhances understanding about the effects of environmental chemicals on h ... [more]A public database ... A public database that enhances understanding about the effects of environmental chemicals on h ... [more]A public database ...
Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure ...... sequences and a set of 14 sequences with known secondary structure and chemical modification data taken from the literature, ... The average accuracy of secondary structure prediction is 73% ± 9% of known canonical base pairs for a database (8) of ≈150,000 ... On average for sequences with ,6% of nucleotides in pseudoknots, the structures predicted with constraints from chemical ... For C. albicans 5S rRNA, chemical mapping in vivo is consistent with the structure determined by comparative sequence analysis ...
Chemical literature databases correlate structures or other chemical information to relevant references such as academic papers ... Large molecules such as proteins are however more compactly represented using the sequences of their amino acid building blocks ... A chemical database is a database specifically designed to store chemical information. This information is about chemical and ... Chemical databases are particularly different from other general purpose databases in their support for sub-structure search. ...
Cell Adhesion Assays > Reference Materials/Research Services Laboratory Product Directory and Equipment Reviews on...STN - Online Scientific Database Literature and Patent Search. Chemical Abstracts Service (CAS). STN is an online database ... service that provides global access to published research, journal literature, patents, structures, sequences, properties, and ... SciFinder - Online Scientific Literature Search (1). Chemical Abstracts Service (CAS). CAS SciFinder - The First Choice With ... Chemical Abstracts SciFinder search allows you to get results fast withou... Read more... ...
T3DB is fully searchable and supports extensive text, sequence, chemical structure, relational query and spectral searches. It ... and scientific literature. The primary focus of the T3DB is on providing mechanisms of toxicity and identifying target proteins ... The Toxin and Toxin-Target Database (T3DB), also known as the Toxic Exposome Database, is a freely accessible online database ... While a number of other toxic compound databases do exist, their emphasis is on covering large numbers of chemical compounds ...
ChemMine. A Compound Mining Database for Chemical Genomics | Plant PhysiologyVia this linkage, ChemMine users can retrieve the target protein sequences, three-dimensional structures, and literature for ... tools for structure similarity comparisons, database searching, structure-activity comparisons, evaluations of the chemical ... Finally, the chemicals can be used to inactivate a family of proteins with related sequences or structures in a single step. In ... Comparison of the NCI open database with seven large chemical structural databases. J Chem Inf Comput Sci 41: 702-712. ...
RNA methylation and diseases: experimental results, databases, Web servers and computational models, Briefings in...... databases, Web servers and computational models, Briefings in Bioinformatics" on DeepDyve, the largest online rental service ... Chemical property of nucleotide in RNA sequence Chemical property Class Nucleotides Ring structure Purine A, G Pyrimidine C, U ... MODOMICS also provides literature information, and links to other databases, including the available protein sequence and ... Chemical property of nucleotide in RNA sequence Chemical property Class Nucleotides Ring structure Purine A, G Pyrimidine C, U ...
UniChemA database that combines drug (i.e. chemical, pharmacological and pharmaceutical) data with drug target (i.e. sequence, ... It maps curated physicochemical property data associated with chemical substances to their corresponding chemical structures ... A database of bioactive drug-like small molecules and bioactivities abstracted from the scientific literature. name: chembl ... The foundation of chemical safety testing relies on chemistry information such as high-quality chemical structures and ...
A database that combines drug (i.e. chemical, pharmacological and pharmaceutical) data with drug target (i.e. sequence, ... It maps curated physicochemical property data associated with chemical substances to their corresponding chemical structures ... A database of bioactive drug-like small molecules and bioactivities abstracted from the scientific literature. name: chembl ... An NMR database (web database) for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for ...
The data in the database is manually curated from the scientific literature, and covers all domains of life. MetaCyc has ... MetaCyc data on metabolites includes chemical structures, predicted Standard energy of formation, and links to external ... MetaCyc is used as a reference data set for computationally predicting the metabolic network of organisms from their sequenced ... The MetaCyc database is one of the largest metabolic pathways and enzymes databases currently available. ...
Discovery-2: an interactive resource for the rational selection and comparison of putative drug target proteins in malaria |...Searching by chemical structure is also available. The updated functionality of the Discovery-2 resource is presented, together ... A short example of a chemical search with pyrimethamine is also illustrated. The updated Discovery-2 resource allows ... Newly added features include drugability measures from ChEMBL, automated literature relations and links to clinical trial ... and literature links. The resource also contains chemical compounds from the ChEMBL database with chemical search functionality ...
STN International: CAplus and CAS Registry... journal literature, patents, structures, sequences, properties, and other data. With STN, find precisely the patent and sci- ... STN is an online database service that provides global access to published research, ... Chemical Abstracts Plus (CAplusSM) is the most current and comprehensive bibliographic database of chemical information ... The CAS databases CAplus and CAS REGISTRY offer intellectually analyzed content obtained from journal and patent literature. ...
Document Description (sorted by Category)... and for database searches, the search logic or chemical structure sequence used as a query, the name of the file or files ... Document code is used for indicating Non Patent Literature (NPL) submitted by applicant or cited by the examiner.. ... Sequence Listing (Text File). Application Part. In a patent application,a sequence listing filed as a .txt file is either the " ... Sequence Listing (Text File). PCT - Application Part. In a PCT application, the sequence listing is filed as a .txt file either ...
Exploring Chemical and Biological Knowledge Spaces with PubChem... sequences) Drugs * 3. Connecting the Spaces Database cross-links Assays (PubChem)Literature(PubMed) Active MeSH Inactive ... Search fields and defaults vary by database Chemical structure search, and other specialized algorithms, must be done outside ... More Space to Explore Genes Literature Assays (PubMed) (PubChem) Chemicals (PubChem) Targets Patents (sequences) Drugs Diseases ... PDB structures (with VAST neighbors) Text and numeric search fields Cross-links Between databases Within databases ( ...
DiVA - Sökresultat... coli O-antigen structures, polymerase and flippase amino acid sequences, NMR chemical shift data of O-antigens as well as ... The database content has been compiled from scientific literature. Furthermore, the system has evolved from being a repository ... The structure was determined using chemical methods, and one- and two-dimensional NMR spectroscopy. The results showed a ... The underlying database was also expanded and the improved capabilities were demonstrated by determining O-antigenic structures ...
GLIDA is a public GPCR-related Chemical Genomics database that is primarily focused on the integration of information betw ... Hattori M,Okuno Y,Goto S,Kanehisa M. Development of a Chemical Structure Comparison Method for Integrated Analysis of Chemical ... In particular, the ordering along the x- and y-axes allows users to evaluate the sequence similarities among GPCRs and the ... The references are hyperlinked with the corresponding PubMed literature. The activity types include agonist, antagonist and ...
Databases. *Sequence databases: GenBank, European Nucleotide Archive and DNA Data Bank of Japan. ... What began as a modest task of abstracting information from literature soon became a major database activity with direct ... Chemical Entities of Biological Interest (ChEBI) - database and ontology of molecular entities ... organisation and dissemination of data on biological macromolecular structures ...
Chemical Information Sources/Chemical Patent Searches - Wikibooks, open books for an open worldSearching by chemical structure, formula or registry number is not available. The USPTO website also hosts a trademark database ... Several specialized commercial databases exist for the chemical patent literature, some with Markush searching capabilities ... structural databases, biological sequences, and their uses, which may result from the genomics field. Other types of patents ... For chemical patents, generic inventions usually take the form of a MARKUSH STRUCTURE, a structure that contains one or more ...
Mining metabolites: extracting the yeast metabolome from the literature | SpringerLinkText mining methods have added considerably to our capacity to extract biological knowledge from the literature. Recently the ... a major chemical database, to identify appropriate structures. We have identified structures for 55% of unique names (2,415/ ... and carries a tripeptide sequence, alanine-lysine-phenylalanineCOOH, that closely resembles the consensus sequence for type-1 ... a major chemical database, we have identified structures for much of the reported metabolome and, where structure ...
Protein: sequence database. *Genome: whole genome sequences and mapping. *Structure: three-dimensional macromolecular ... Databases[edit]. Entrez searches the following databases: *PubMed: biomedical literature citations and abstracts, including ... Cancer Chromosomes: cytogenetic databases. *PubChem BioAssay: bioactivity screens of chemical substances. *Probe: sequence- ... Entrez can efficiently retrieve related sequences, structures, and references. The Entrez system can provide views of gene and ...
... nonribosomal peptides are usually represented by atomic structures and stored in chemical compounds databases. Classical chemo- ... The database contains more than 1,100 nonribosomal peptides extracted from scientific literature with manually curated ... structure prediction from the sequence of its non-ribosomal peptide synthetase. FEMS Microbiol Lett 187:111-114. doi: 10.1111/j ... Finally, chemical structures are determined. Those structures can, finally, be mimicked leading to artificial compounds. To ...
WO2007126631A1 - Causal analysis in complex biological systems
- Google Patents... literature references, underlying structural information, e.g., amino acid sequence, physico-chemical descriptors, anatomical ... 0030] Figure 1 is a flow chart illustrating the structure of a data base in accordance with one embodiment of the invention; ... for automated inference of physico-chemical interaction knowledge via co-occurrence analysis of indexed literature databases ... Method and system for automated inference creation of physico-chemical interaction knowledge from databases of co-occurrence ...
CSB2008 - Call for PostersBiological Databases. • Microbial Community Analysis. • Biological Literature Mining. • MicroRNA. • Biomedical Applications. • ... Sequence Analysis. • Gene Function Inference. • SNPs and Haplotyping Analysis. • Gene Prediction. • Synthetic Biological ... Protein Structures and Complexes. • Evolution, Phylogenetics, and. Phylogenomics. • RNAi Analysis. • Executable Biology. • ... Chemical Genetics. • Pathways, Networks, Systems. Biology. • Comparative Genomics. • Promoter Analysis and Discovery. ...
Frontiers | Applications of Deep-Learning in Exploiting Large-Scale and Heterogeneous Compound Data in Industrial...... or imaging have also been established as routine profiling experiments thanks to the advancement of Next Generation Sequencing ... Besides the structure activity data from traditional bioassays, more complex assays such as transcriptomics profiling or ... Besides the structure activity data from traditional bioassays, more complex assays such as transcriptomics profiling ... imaging have also been established as routine profiling experiments thanks to the advancement of Next Generation Sequencing or ...
ProteinsMolecularGenomesGenesSimilarityCompoundsAnnotationPatentsBibliographicPeptideGenBankGenomicsPathwaysManually curatedAnnotationsAmino acidDataOrganismWorld'sMultiple sequence alignmentsMoleculesStructuralOrganismsCompoundInteractionsHazardous chemicalsDatasetPredictionEnzymeGenome DatabasesBiological databasesExperimentalFunctionalInorganicNucleicChemSpiderSubstancesBiomedicalProteomicsNucleotidesReactionsProtein StructuresBiochemicalMillion sequencesPeptidesMutationsToxicologyBioinformaticsMacromoleculesSearchHigh-throughputBiologyChemistryEntities of Biological InterestExperimentally determinedAlignmentDescriptors
- Large molecules such as proteins are however more compactly represented using the sequences of their amino acid building blocks. (wikipedia.org)
- Subsequently, the isolated bioactive chemicals are used to study the molecular and biological functions of poorly characterized proteins in vivo. (plantphysiol.org)
- By contrast, chemicals can be targeted with spatiotemporal precision against a selected spectrum of proteins. (plantphysiol.org)
- Finally, the chemicals can be used to inactivate a family of proteins with related sequences or structures in a single step. (plantphysiol.org)
- The Discovery resource attempts to use a similar approach in associating chemical compounds with malaria proteins using sequence homology, and also selective chemical similarity searches. (biomedcentral.com)
- Structure and function of major classes of biomolecules, including proteins, carbohydrates and lipids. (stanford.edu)
- The Protein Data Bank (PDB) archive is the single worldwide repository of information about the 3D structures of large biological molecules, including proteins and nucleic acids. (stanford.edu)
- Remodeling is often mediated through chemical modifications of the DNA template, DNA-associated proteins, and RNA-mediated processes. (embl-heidelberg.de)
- AH-DB (Apo and Holo structures DataBase) collects the apo and holo structure pairs of proteins. (fairsharing.org)
- These amino acids are creating proteins through chemical bonds. (mpg.de)
- Using the Biomolecular Interaction Network Database (BIND - http://www.bind.ca ) [ 15 ] as an integration platform, we have collected 15,143 yeast protein-protein interactions among 4,825 proteins (about 75% of the yeast proteome). (springer.com)
- This review, from a pharmaceutical perspective, highlights some of the most relevant and interesting protein structures for the pharmaceutical industry and shows examples of how ligand-binding sites, membrane proteins, both big and small, pseudo symmetry and complexes are being addressed by this technique. (portlandpress.com)
- The study of structure-function relationships of membrane proteins (MPs) has been one of the major goals in the field of structural biology. (portlandpress.com)
- Some classes of proteins show considerable variety in the sequences of amino acids, and do not differ too greatly from other families of proteins. (creation.com)
- A collection of reference sequences for genomes, gene transcripts, and proteins. (nih.gov)
- The database collects and organizes the following types of information: (i) DNA damage linked to environmental mutagenic and cytotoxic agents, (ii) pathways comprising individual processes and enzymatic reactions involved in the removal of damage, (iii) proteins participating in DNA repair and (iv) diseases correlated with mutations in genes encoding DNA repair proteins. (genesilico.pl)
- The DNA repair and tolerance pathways are represented as graphs and in tabular form with descriptions of each repair step and corresponding proteins, and individual entries are cross-referenced to supporting literature and primary databases. (genesilico.pl)
- SpliProt3D is an online database of representative experimentally determined and computationally predicted structures of proteins of the human spliceosome. (genesilico.pl)
- RNA Bricks is a database of RNA 3D structure motifs and their contacts, both with themselves and with proteins. (genesilico.pl)
- In addition, we have made predictions on all 6.3 million proteins in the Yeast Resource Center (YRC) database. (psu.edu)
- In this series of projects of sequencing human cDNA clones which correspond to relatively long transcripts, we newly determined the entire sequences of 100 cDNA clones which were screened on the basis of the potentiality of coding for large proteins in vitro. (psu.edu)
- Proteins are biological macromolecules synthesized with genetically determined sequences of amino acids by the formation of peptide bonds through the removal of water molecules. (schoolbag.info)
- The formation of stable secondary structures and a unique tertiary structure of proteins are dictated by the interactions between constituent amino acid residues along the polypeptide chain and by their interactions with the surrounding medium. (schoolbag.info)
- Hence, many methods have been developed to determine the three-dimensional structures of proteins experimentally. (schoolbag.info)
- X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and electron microscopy are widely used to determine the structures of proteins and their complexes. (schoolbag.info)
- Currently, the PDB has nearly 50,000 structures, and the wealth of data provide valuable information on relating the structures of proteins with their functions, interactions, and evolution. (schoolbag.info)
- The article is divided into five main sections that include the biological insights on protein structures, chemical applications including protein functions, thermodynamics of proteins, protein interactions, and computational protein design. (schoolbag.info)
- For pairs of proteins sharing a common ligand, we use protein and chemical superimpositions combined with fast structural compatibility screens to predict whether additional compounds bound by one protein would bind the other. (plos.org)
- The basic premise is that two proteins sharing a common bound chemical will likely share others. (plos.org)
- We show for a benchmark that known protein-chemical structures are reconstructed with good accuracy and sometimes via very different proteins and chemicals. (plos.org)
- We exploited the basic premise that if two proteins in the network share one bound chemical they are likely to share others. (plos.org)
- A single prediction candidate ( Figure 1 ) involves combining three protein-chemical complex structures, two of which involve two distinct proteins (P 1 and P 2 ) binding a common ligand (L a ) and a third where one protein (P 1 ) binds another ligand (L b ). (plos.org)
- Recent methodological advances in the field of molecular and structural biology allow us to use evidence of strong co-evolution as a reliable marker of important evolutionary relationships at molecular level to better understand and predict fundamental aspects of the structure and function of proteins. (bsc.es)
- Implementation of the syntax in the relational database enables the application of many different analysis protocols of minimotif data and is an important tool that will help to better understand specificity of minimotif-driven molecular interactions with proteins. (biomedcentral.com)
- The winners of the contest developed a tool (Reflect) that addresses the routine need of life scientists to be able both to jump from gene or protein names to their molecular sequences, and to understand more about particular genes, proteins or small molecules encountered in the literature . (nih.gov)
- 1.5 million proteins from 373 organisms) that links names and synonyms to source databases. (nih.gov)
- It is important to note that finding three-dimensional structures of the proteins is by it self is a costly and time-consuming task which is done using experimental methods such as NMR and X-ray Crystallography. (nature.com)
- Moreover, three dimensional structures are very difficult to predict for ion channel proteins and G-protein coupled receptors (GPCRs). (nature.com)
- A worldwide repository on the 3D structures of large biological molecules (proteins, nucleic acids, etc. (campusguides.com)
- Proteins constitute the next level of the gene expression program, and here diversity comes in two forms: variants affecting the primary sequence of amino acids, and post-translational modifications (PTMs). (mcponline.org)
- The Protein Data Bank (PDB) is one such database, handling structure and sequence data for proteins with a determined crystal structure. (wikibooks.org)
- The most significant reason for this is that proteomics techniques revolve around separation methods (some of which are explored in detail later) which use the unique characteristics of the proteins, such as structure and molecular weight, to identify and purify them. (wikibooks.org)
- These vesicles are complex structures made of proteins encoded by at least 14 genes. (wikipedia.org)
- This work spans quantum chemistry, molecular simulation, QSAR and chemical informatics. (st-andrews.ac.uk)
- Chemical genomics has several outstanding advantages over classical genetics and molecular techniques for studying gene functions. (plantphysiol.org)
- Each toxic compound record (ToxCard) in T3DB contains nearly 100 data fields and holds information such as chemical properties and descriptors, mechanisms of action, toxicity or lethal dose values, molecular and cellular interactions, medical (symptom and treatment) information (Fig. 1-3), NMR an MS spectra, and up- and down-regulated genes. (wikipedia.org)
- http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI%3A base_id_url_available: 1 description: ChEBI is a freely available dictionary of molecular entities focused on 'small' chemical compounds name: chebi name_label: ChEBI name_long: ChEBI (Chemical Entities of Biological Interest). (ebi.ac.uk)
- This is a a non-proprietary, free, unique, unambiguous, nonsemantic, alphanumeric identifier based on a substances molecular structure and/or descriptive information. (ebi.ac.uk)
- Modern molecular biology is a science dominated by very large quantities of data, yet most useful knowledge remains locked in the scientific literature. (springer.com)
- For the civil engineering programs chemical engineering, molecular biotechnology, and bioinformatics required are at least 120 credits, of which 30 within bioscience. (uu.se)
- GenBank is part of the International Nucleotide Sequence Database Collaboration, which comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at NCBI. (fairsharing.org)
- Each toxin record (ToxCard) contains over 90 data fields and holds information such as chemical properties and descriptors, toxicity values, molecular and cellular interactions, and medical information. (feish.online)
- Structure prediction and computational analysis of the mutants have proven to be a valuable aid in understanding the molecular aspects of clinical thrombophilia. (biomedcentral.com)
- These tools can also be used to teach basic prin- ciples of chemical biology, molecular evolution, and enzyme structure and function in silico. (atlas-publishing.org)
- how to tell if you have pink eye or allergies The Gene resource at NCBI is a central hub for accessing nearly all molecular and literature resources for a particular gene. (rocksurfers.org)
- Understanding of cellular processes and underlying molecular events requires knowledge about different aspects of molecular interactions, networks of molecules and pathways in addition to the sequence, structure and function of individual molecules involved. (nus.edu.sg)
- We introduce a new database of Kinetic Data of Bio-molecular Interactions (KDBI) aimed at providing experimentally determined kinetic data of protein-protein, protein-RNA, protein-DNA, protein-ligand, RNA-ligand, DNA-ligand binding or reaction events described in the literature. (nus.edu.sg)
- ICSD enables scientists to search for text in titles in combination with chemical compound information, e.g., compound classes which cannot be described through specific compound information such as the molecular formula. (fiz-karlsruhe.de)
- In addition to the published data, many items are added through expert evaluation or are generated by computer programs such as the Wyckoff sequence, molecular formula and weight, ANX formula, mineral group, etc. (fiz-karlsruhe.de)
- One of the most important developments in bioinformatics over the past few decades has been the observation that short linear peptide sequences (minimotifs) mediate many classes of cellular functions such as protein-protein interactions, molecular trafficking and post-translational modifications. (biomedcentral.com)
- PubMed also provides access to molecular biology databases in the National Center for Biotechnology Information s (NCBI) Entrez retrieval system with components for searching DNA and protein sequences, 3-D protein structure data, population study data sets, and assemblies of complete genomes. (wfu.edu)
- We have successfully performed exhaustive searches on the various databases covering the wide range of biological and chemical areas such as Nucleotide sequences, Protein sequences, Genomes, Macromolecular structures, Molecular interactions, Protein families, Enzymes, etc. (promaxlegal.com)
- These data are integrated with chemicals, genes and diseases in CTD to provide insights into molecular networks that may be affected by chemicals, and possible mechanisms underlying environmental diseases. (mdibl.org)
- This tree allowed us to identify and correct incongruences in the molecular identification of apicomplexan sequences. (medworm.com)
- Several branches of the original MeSH vocabulary were excluded from CTD's chemical vocabulary because they are not molecular reagents, environmental chemicals or clinical drugs (e.g. (ctdbase.org)
- A dictionary of molecular entities focused on small chemical compounds. (ctdbase.org)
- THE sequencing of whole genomes of species from all kingdoms of life progresses at an ever increasing pace. (genetics.org)
- The genomes of several bacterial strains have been sequenced and annotated and have been used in combination with biochemical and physiological data to reconstruct metabolic networks at a genome-scale [ 9 ]. (hindawi.com)
- In the future, these "chemical family knock-downs" may be the method of choice for the functional characterization of paralogous genes with redundant functions. (plantphysiol.org)
- Uses a combination of literature curation and gene ontology development for heart-specific genes to aid the analysis of genes responsible for the spread of the cardiac action potential through the heart. (jax.org)
- These results may assist in the functional annotation of CAR coding genes in genomic databases. (frontiersin.org)
- A comprehensive database of genes and associated information. (nih.gov)
- Prediction of the coding sequences of unidentified human genes. (psu.edu)
- OMIM data and disease terms are integrated into CTD to provide disease information associated with chemicals and genes. (mdibl.org)
- This chart provides a view of the ten genes with the most curated interactions for this chemical. (ctdbase.org)
- The critical software and database resources for bioactive chemical discovery projects are: tools for structure similarity comparisons, database searching, structure-activity comparisons, evaluations of the chemical descriptor (property) space, design of customized libraries (subsetting), lead optimization steps, and compound and screening databases. (plantphysiol.org)
- The ability to explore not only chemical similarity but relationships between diseases and disease targets has crucial value in repurposing. (slideshare.net)
- This article provides a summary of the GLIDA database and user facilities, and describes recent improvements to database design, data contents, ligand classification programs, similarity search options and graphical interfaces. (biomedsearch.com)
- Compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. (fairsharing.org)
- A tool that finds regions of similarity between biological sequences. (nih.gov)
- The OR's sequence similarity searches can be carried out in the database using a server-side version of the program Ssearch and the ligand similarity searches can be performed by using a server-side version of OpenBabel (http://openbabel.sf.net). (sapub.org)
- The overlap of the residue contact maps of two structures can be easily calculated, providing a sensitive measure of protein structure similarity. (genesilico.pl)
- We look for exact, sub-sequence, motif, uncommon sequence in our Identity and Similarity Search for comparing DNA or protein sequences against the sequences that are in patents or known patent literature. (promaxlegal.com)
- About 60% OTUs were not assigned at a class or order level and at least 45% OTUs shared a sequence similarity no more than 97% with the described species, indicating a great potential for ciliate species discovery in the offshore sediments. (springer.com)
- The database currently houses nearly 3,700 toxic compounds or poisons described by nearly 42,000 synonyms. (wikipedia.org)
- While a number of other toxic compound databases do exist, their emphasis is on covering large numbers of chemical compounds that are almost never seen outside a chemical laboratory. (wikipedia.org)
- http://zinc15.docking.org/substances/ base_id_url_available: 1 description: A free database of commercially-available compounds for virtual screening, provided by the Shoichet Laboratory in the Department of Pharmaceutical Chemistry at the University of California, San Francisco (UCSF). (ebi.ac.uk)
- Compounds are derived from either chemical names found in text or in chemical depictions. (ebi.ac.uk)
- http://pubchem.ncbi.nlm.nih.gov/compound/ base_id_url_available: 1 description: A database of normalized PubChem compounds (CIDs) from the PubChem Database. (ebi.ac.uk)
- MetaCyc has extensive information about chemical compounds, reactions, metabolic pathways and enzymes. (wikipedia.org)
- While in-depth studies are ongoing on a relatively small number of selected putative targets for future exploitation, not many resources are available that focus on performing data mining and target identification on the complete malaria genome, in concert with relations to chemical compounds. (biomedcentral.com)
- The resource also contains chemical compounds from the ChEMBL database with chemical search functionality and putative ligand-protein prediction information. (biomedcentral.com)
- CAS REGISTRY is the world's largest substance database covering substance information on all types of organic and inorganic substances, including polymers, alloys, coordination compounds, and mixtures. (stn-international.de)
- Most patents of interest to chemists cover compositions of matter (new chemical compounds, mixtures, pharmaceuticals) or processes (e.g., synthesis of a drug). (wikibooks.org)
- Those structures can, finally, be mimicked leading to artificial compounds. (springer.com)
- To reduce the time and cost of the specific steps, the optimal process is to predict the compounds produced by an organism directly from its genome sequence. (springer.com)
- Typically, databases in pharma companies contain around 1-4 million compounds with biological data for several thousands of biological end-points such as targets or activities in cellular assays. (frontiersin.org)
- BitterDB is a free and searchable database of bitter compounds. (fairsharing.org)
- The database also contains information on mutations in bitter taste re- ceptors that were shown to influence receptor activation by bitter compounds. (fairsharing.org)
- Multiple databases with physical, chemical, environmental fate, and degradation properties of chemical and compounds. (mblwhoilibrary.org)
- It covers 4825 chemical classes of organic and inorganic compounds. (wishartlab.com)
- ClassyFire automatically provides a hierarchical chemical classification for all known chemical compounds (including small molecules, peptides and peptide sequences), as well as a structure-based textual description. (wishartlab.com)
- Compounds of interest are isolated by semi- and preparative chromatographic methods and their structure is determined by mass spectrometry and NMR-spectroscopy. (uibk.ac.at)
- Information on chemical properties and structural formulas of chemical compounds. (smu.edu)
- Offers text and structure searching to find compounds of interest. (smu.edu)
- Marvin Live (for 2D design), Schrodinger's Maestro Elements (for 3D design), and an ideation and collaboration tool are integrated with each other, and provide the front end for registering virtual compounds into the eDesign database. (chemaxon.com)
- Favoriteideas can be submitted into a specific database for virtual BI compounds. (chemaxon.com)
- The database web interface allows static and dynamic queries and provides integrated analysis tools including sequence annotation. (fairsharing.org)
- Describes the content and structure of GO annotation extensions and how they provide additional contextual information. (jax.org)
- 2013. Gene Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a large-scale curation effort. (jax.org)
- Such enterprise requires a coordinated effort to obtain, process and integrate very heterogeneous sources of information ranging from the sequencing and annotation of genomic variants to the mining of medical literature, as well as the construction of context-specific in-silico models. (bsc.es)
- Herein, we present a structured syntax of minimotifs and their functional annotation. (biomedcentral.com)
- Each of these databases model functional minimotifs in some capacity, often using individualized annotation schemes useful for the subset of minimotif data being managed. (biomedcentral.com)
- A standardized syntax will also allow refinement of minimotif sequence definitions, reduce redundant data, and normalize future annotation efforts. (biomedcentral.com)
- All data sets are made available as supplementary material as well as web-accessible databases and within the functional context via the Chlamydomonas-adapted MapMan annotation platform. (genetics.org)
- The need to develop automatic or at least semiautomatic methods to reconstruct metabolic networks from genome annotation is increasing because the number of complete genome sequences available is growing fast. (hindawi.com)
- There has been a tendency to enrich annotation records of many of the existing expert-curated databases with previously missing but biologically relevant aspects by incorporating new fields or extending the inventory of terms used to describe these aspects. (biomedcentral.com)
- Even if general annotation databases such as UniProt - which stores a set of annotations linked to over 134,000 literature citations (February 2008) - are of great practical value, such databases are generally only capable of covering a small fraction of the biological context information that can be encountered in the literature. (biomedcentral.com)
- Chemical literature databases correlate structures or other chemical information to relevant references such as academic papers or patents. (wikipedia.org)
- It is designed to radically reduce the time spent acquiring patents and pinpointing the relevant chemical substance information within. (stn-international.de)
- We are actively developing new infrastructure to support such analyses, and pursuing new methods of exploring inter- and intra-database relationships between chemicals, targets, diseases, and patents. (slideshare.net)
- At Promax, our team specializes in searching bio-sequences based patents, having expertise both in free and paid databases, and skilled with tools required for conducting a comprehensive sequence search. (promaxlegal.com)
- Our search methodology involves various algorithms searches, broad class-based searches, assignee/inventor- based searches, etc., to provide thorough coverage of all biological sequence information from patents as well as non-patent literature. (promaxlegal.com)
- Find reactions, predicted property values, experimental properties, patents, and sequences from CAS and Genbank databases, which are linked to the scientific journal literature. (smu.edu)
- Chemical Abstracts Plus (CAplus SM ) is the most current and comprehensive bibliographic database of chemical information available from Chemical Abstracts Service (CAS). (stn-international.de)
- The database contains more than 1,100 nonribosomal peptides extracted from scientific literature with manually curated annotations such as biological activity, producing organisms or bibliographic references and, most importantly, their monomeric structure. (springer.com)
- The archives contain atomic coordinates, bibliographic citations, primary and secondary structure information, as well as crystallographic structure factors and NMR experimental data. (paulbourke.net)
- MathSciNet provides access to Mathematical Reviews (reference journal of the world's current mathematical literature) and Current Mathematical Publications (subject index of bibliographic data for recent and forthcoming publications). (wfu.edu)
- A bibliographic database covering the biochemical, pharmacological, physiological, and toxicological effects of drugs and other chemicals. (ctdbase.org)
- FASTA format is a text-based format for representing either nucleotide sequences or peptide sequences, in which nucleotides or amino acids are represented using single-letter codes. (fairsharing.org)
- ClassyFire is a web-based application for automated rule-based structural classification of chemical entities (including peptide and nucleotide sequences). (wishartlab.com)
- GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences. (fairsharing.org)
- Much of our data has been extracted from Genbank and augmented with the consent of the original sequencing groups. (fairsharing.org)
- We go beyond to bring you all sequences - even "hard-to-find" sequences in figures and tables to have the complete picture by performing the searches on various platforms like STN, Questel Orbit, Derwent GENESEQ, USGENE, GenomeQuest, and GENBANK. (promaxlegal.com)
- Chemical genomics is a promising new technology for studying gene functions in the context of living organisms or cell systems. (plantphysiol.org)
- In chemical genomics experiments the libraries are used to identify in high-throughput screens interesting agonistic or antagonistic candidates that interfere with a biological process of interest. (plantphysiol.org)
- Forward chemical genomics screens probe modulations of complex biological processes rather than isolated targets. (plantphysiol.org)
- In contrast to this forward strategy, reverse chemical genomics screens resemble, in their initial stage, drug discovery approaches by screening known targets ( Drews, 2000 ). (plantphysiol.org)
- In spite of the broad spectrum of new opportunities, chemical genomics has not yet evolved into a widely used strategy for biological systems analysis in academic research. (plantphysiol.org)
- This Update will provide a short outline of the existing open-access informatics resources that are relevant for chemical genomics-based research, and how ChemMine fills some of the missing links. (plantphysiol.org)
- GLIDA: GPCR--ligand database for chemical genomics drug discovery--database and tools update. (biomedsearch.com)
- GLIDA is a public GPCR-related Chemical Genomics database that is primarily focused on the integration of information between GPCRs and their ligands. (biomedsearch.com)
- These data are connected with each other in a relational database, allowing users in the field of Chemical Genomics research to easily retrieve such information from either biological or chemical starting points. (biomedsearch.com)
- We hope that it will prove very useful for Chemical Genomics research and GPCR-related drug discovery. (biomedsearch.com)
- Under the patent laws of some countries it is even possible to patent things such as 3D atomic structures, structural databases, biological sequences, and their uses, which may result from the genomics field. (wikibooks.org)
- A database of genomics datasets related to health effects of Bisphenol A exposure. (mdibl.org)
- Genomics is by no means an obsolete science, but in the cases of protein analysis, structure prediction, and function prediction, it can be outdone by proteomics. (wikibooks.org)
- Structures, gene sequences, mechanisms, metabolic pathways and kinetic data are currently spread between many different databases and throughout the literature. (st-andrews.ac.uk)
- Chemical modification can also be used to deduce possible tertiary contacts within an RNA ( 29 ), to probe RNA bound to protein ( 25 , 26 , 30 - 35 ), or to follow RNA folding pathways ( 36 - 38 ). (pnas.org)
- The MetaCyc database is one of the largest metabolic pathways and enzymes databases currently available. (wikipedia.org)
- MetaCyc includes mini reviews for pathways and enzymes that provide background information as well as relevant literature references. (wikipedia.org)
- Databases of interacting molecules, pathways and related chemical reaction equations have been developed. (nus.edu.sg)
- It integrates information about the chemical structure of modified nucleosides, their localization in RNA sequences, pathways of their biosynthesis and enzymes that carry out the respective reactions (including the available protein sequence and structure data). (genesilico.pl)
- Options for data presentation include graphs of pathways involving the query nucleoside, multiple sequence alignments of RNA sequences and tabular forms with enzyme and literatiure data. (genesilico.pl)
- The data in the database is manually curated from the scientific literature, and covers all domains of life. (wikipedia.org)
- OlfactionDB, a manually curated database providing comprehensive information for nearly 400 odorant-receptor interactions at the current state, has been developed for managing information about odorants and their receptors. (sapub.org)
- The database provides structure-quality score annotations and tools for the RNA 3D structure search and comparison. (genesilico.pl)
- In compiling and managing this large dataset, we have had a lengthy and detailed exposure to the functional annotations currently reported in the scientific literature. (biomedcentral.com)
- Recent studies [ 13 , 14 ] have highlighted the problems associated with genome annotations and databases, which perform automatic reconstructions and, thus, require manual assessment. (hindawi.com)
- Crucial details of experimental conditions can still only be found in the underlying articles, making direct pointers to evidence passages from the literature especially important for interpreting existing annotations. (biomedcentral.com)
- Little is known about the structure of CARs and their catalytically important amino acid residues. (frontiersin.org)
- However, the narrow range of amino acid sequence variability found throughout nature seems inconsistent with the notion of an ancient origin and very little change through mutations. (creation.com)
- Given the large amount of data available in public databases, I decided to see how much variety in amino acid sequence exists and how the data might be interpreted from a creationist or evolutionist framework. (creation.com)
- Filtrest3D is a program for discrimination of a large number of alternative models of protein structure or protein-ligand structure against a set of restraints derived from low-resolution experimental analyses (such as cross-linking, mutagenesis, circular dichrosm etc.) as well as from computational predictions (e.g. solvent accessibility, amino acid contact maps). (genesilico.pl)
- We perform searching for both amino acid and nucleotide sequences to ensure a comprehensive search to get maximum hits in the dataset. (promaxlegal.com)
- Within the field of proteomics, bioinformatics is often used in protein structure prediction , and the "holy grail" of proteomics/bioinformatics is to create a bioinformatics application that can predict the final structure of a protein by its amino acid sequence alone. (wikibooks.org)
- Previous studies demonstrated that nuclease cleavage data can be used to refine structure prediction and improve accuracy ( 8 , 11 ). (pnas.org)
- This information is about chemical and crystal structures, spectra, reactions and syntheses, and thermophysical data. (wikipedia.org)
- Crystallographic databases store X-ray crystal structure data. (wikipedia.org)
- Common examples include Protein Data Bank and Cambridge Structural Database. (wikipedia.org)
- NMR spectra databases correlate chemical structure with NMR data. (wikipedia.org)
- These databases often include other characterization data such as FTIR and mass spectrometry. (wikipedia.org)
- The research of RNA methylation is based on sequencing data processing, and effective bioinformatics techniques can benefit better understanding of RNA methylation. (deepdyve.com)
- http://www.drugbank.ca/drugs/ base_id_url_available: 1 description: A database that combines drug (i.e. chemical, pharmacological and pharmaceutical) data with drug target (i.e. sequence, structure, and pathway) information. (ebi.ac.uk)
- MetaCyc data on metabolites includes chemical structures, predicted Standard energy of formation, and links to external databases. (wikipedia.org)
- It provides interaction data between GPCRs and their ligands, along with chemical information on the ligands, as well as biological information regarding GPCRs. (biomedsearch.com)
- The roots of the EMBL-EBI lie in the EMBL Nucleotide Sequence Data Library (now known as EMBL-Bank), which was established in 1980 at the EMBL laboratories in Heidelberg, Germany and was the world's first nucleotide sequence database. (wikipedia.org)
- What began as a modest task of abstracting information from literature soon became a major database activity with direct electronic submissions of data and the need for highly skilled informatics staff. (wikipedia.org)
- It soon became apparent that the EMBL Nucleotide Sequence Data Library needed better financial security to ensure its long-term viability and to cope with the sheer scale of the task. (wikipedia.org)
- When the EMBL-EBI moved to Hinxton it hosted two databases, one for nucleotide sequences (the EMBL Data Library, which was renamed EMBL-Bank and eventually became part of the European Nucleotide Archive ) and one for protein sequences (Swiss-Prot-TrEMBL, now known as UniProt ). (wikipedia.org)
- Patent offices also sell patent data (at nominal prices) to commercial patent information companies, most notably Thomson Reuters , IFI CLAIMS , LexisNexis , and Questel , that incorporate it into their database products. (wikibooks.org)
- Besides the structure activity data from traditional bioassays, more complex assays such as transcriptomics profiling or imaging have also been established as routine profiling experiments thanks to the advancement of Next Generation Sequencing or automated microscopy technologies. (frontiersin.org)
- suggestions and costings for project-based methods for organising, searching and sharing complex project-based data internally, or later externally - e.g. a project database (if required). (imperial.ac.uk)
- Students will also learn to critically analyze data from the primary biochemical literature. (stanford.edu)
- Protein data bank of Europe : bringing structure to biology. (stanford.edu)
- CSD-Enterprise includes everything in the CSD-System, CSD-Discovery and CSD-Materials, software and application data for the Cambridge Structural Database (CSD), the world's only comprehensive, up-to-date, and fully-curated knowledge base of small molecule crystal structures. (stanford.edu)
- The Aspergillus Genome Database is a resource for genomic sequence data as well as gene and protein information for Aspergilli. (fairsharing.org)
- The Toxin and Toxin Target Database (T3DB), or, soon to be referred as, the Toxic Exposome Database, is a unique bioinformatics resource that combines detailed toxin data with comprehensive toxin target information. (feish.online)
- Protein structure [ 8 ] and gene expression data [ 9 ] is also accumulating at a rapid rate. (springer.com)
- ProCMD is an up-to-date interactive mutant database that integrates phenotypical descriptions with functional and structural data obtained by computational approaches. (biomedcentral.com)
- apid search of these vast sets of data, the integration of their results, and the linking of information regarding en- zyme families, function, chemical mechanism, and structures of homologous enzymes. (atlas-publishing.org)
- The second part of the exercise consists of search- ing the literature database to provide a plausible chemical mechanism based on the available data from homologous enzymes. (atlas-publishing.org)
- Secondly, we have tied several tools together to serve the purpose of seamless data how to use php myadmin to create a database Once such variations are identified and cataloged in the database, additional laboratories can use the sequence information around the polymorphism and the specific experimental conditions for further research applications. (rocksurfers.org)
- NCBI is the US National Institutes of Health archive for nucleotide and protein sequence data. (rocksurfers.org)
- Sequence data from numerous genomic projects are pouring out of the sequence centers and into public databases at an unprecedented rate. (rocksurfers.org)
- The exact amount has not yet been reported in the literature, using all data now available. (creation.com)
- For example, when identical sequences for the same organism was found, reported from different laboratories, the first one in the data file was kept. (creation.com)
- New data added to the public databases 1 later may require future datasets to be generated, and such scripts can save much effort. (creation.com)
- You can also find kinetic data in this free online database. (concordia.ca)
- The kinetic data for these interactions, which is important for mechanistic investigation, quantitative study and simulation of cellular processes and events, is not provided in the existing databases. (nus.edu.sg)
- The Protein Data Bank (PDB) is an archive of experimentally determined three-dimensional structures of biological macromolecules, serving a global community of researchers, educators, and students. (paulbourke.net)
- Here we present a free, publicly available, database, OlfactionDB, that contains affinity data of human/mouse olfactory receptors (OR) and ligands, manually compiled and extracted from the literature, containing experimental values for almost 400 OR-odorant interacting pairs. (sapub.org)
- These structures have been deposited in Protein Data Bank (PDB) and are available at http://www.rcsb.org/ (1). (schoolbag.info)
- Analysis of SH3 binding minimotif data spanning many different studies within our database reveals unique attributes and frequencies which can be used to classify different types of binding minimotifs. (biomedcentral.com)
- A standardized syntax will facilitate exchange of data with different minimotif databases. (biomedcentral.com)
- Likewise, a standardized syntax will allow integration with other non-motif databases enabling researchers to examine the connection of minimotifs with new types of data (e.g. disease mutations, protein structures, cellular activities, etc.), providing new opportunities for data mining. (biomedcentral.com)
- Calling International Rescue: knowledge lost in literature and data landslide! (nih.gov)
- Portents of impending catastrophe pervade the literature, calling us to action in the face of unmanageable volumes of scientific data. (nih.gov)
- Methods and system for automated inference of physico-chemical interaction knowledge from databases of term co-occurrence data. (google.com)
- The co-occurrence data includes co-occurrences between chemical or biological molecules or co-occurrences between chemical or biological molecules and biological processes. (google.com)
- Likelihood statistics are determined and applied to decide if co-occurrence data reflecting physico-chemical interactions is non-trivial. (google.com)
- Recently, genomic models were reconstructed for some bacterial species aiming to increase the amount and quality of data that has been annotated in either the literature or databases [ 10 - 12 ]. (hindawi.com)
- Life science research is characterized by the production of large and heterogeneous collections of biological data, including protein and genomic sequence data, expression profiles, and protein structure coordinates [ 1 ]. (biomedcentral.com)
- Structured database entries are designed to enable efficient data retrieval, exchange, and analysis. (biomedcentral.com)
- Low-overhead customizable databases for quick and flexible organization of data. (openwetware.org)
- Primary databases are populated with experimentally derived data such as nucleotide sequence, protein sequence or macromolecular structure. (lickerish.com.au)
- It contains evaluated data and information derived from both short- and long-term bioassays on over 8,000 chemicals. (mdibl.org)
- A semantic framework for linking and data mining chemogenomic and systems chemical biology data. (mdibl.org)
- A resource that combines detailed drug (i.e., chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e., sequence, structure, and pathway) information. (mdibl.org)
- In the field of genetic toxicology, selected mutagenicity assay systems and the source literature are reviewed by work panels of scientific experts for each of the test systems under evaluation, and the GENE-TOX data bank is the product of these data review activities. (mdibl.org)
- Using publicly available small subunit (SSU) rRNA gene databases, high-throughput environmental sequencing (HTES) surveys, and our own generated HTES data, we developed an apicomplexan reference database, which includes the largest apicomplexan SSU rRNA tree available to date and encompasses comprehensive sampling of this group and their closest relatives. (medworm.com)
- Searching RGD data specifically for cancer phenotypes provides access to data and literature that may offer utility, and for a focus specifically on mammary cancer the Disease portal may be searched. (nih.gov)
- BRENDA contains enzyme-specific data manually extracted from primary scientific literature and additional data derived from automatic information retrieval methods such as text mining . (wikivisually.com)
- The database contains more than 40 data fields with enzyme-specific information on more than 7000 EC numbers that are classified according to the IUBMB . (wikivisually.com)
- The different data fields cover information on the enzyme's nomenclature, reaction and specificity, enzyme structure , isolation and preparation, enzyme stability, kinetic parameters such as Km value and turnover number , occurrence and localization, mutants and engineered enzymes, application of enzymes and ligand-related data. (wikivisually.com)
- Since 2006, the data in BRENDA is supplemented with information extracted from the scientific literature by a co-occurrence based text mining approach. (wikivisually.com)
- For this purpose, four text-mining repositories FRENDA (Full Reference ENzyme DAta), AMENDA (Automatic Mining of ENzyme DAta), DRENDA (Disease-Related ENzyme information DAtabase) and KENDA (Kinetic ENzyme DAta) were introduced. (wikivisually.com)
- Find commonly needed chemical data, basic constants, units and conversion factors. (smu.edu)
- Medivir had 30 years' worth of unstructured data, and a compound database in an unsupported and out of date RS3 system. (chemaxon.com)
- and some of the data were of very poor data quality in RS3 because of bad database integrity, and lack of validation on registration. (chemaxon.com)
- Huge volumes of primary data are archived in numerous open-access databases, and with new generation technologies becoming more common in laboratories, large datasets will become even more prevalent. (oup.com)
- Database development and biocuration are at the forefront of the endeavor to make sense of this mounting deluge of data. (oup.com)
- Previous attempts to achieve this through the prior fields were based on expanding off their data using chemical knowledge. (wikibooks.org)
- The metabolite recognition tool has been applied to the literature covering an important model organism, the yeast Saccharomyces cerevisiae , to define its reported metabolome. (springer.com)
- Thus,P. agglomeranscorrectly characterized appears to be a more infrequent clinical organism than literature indicates. (anti-cancers.com)
- Sequences for which the organism was not annotated in the source database. (creation.com)
- Each enzyme entry is clearly linked to at least one literature reference, to its source organism , and, where available, to the protein sequence of the enzyme. (wikivisually.com)
- We have created MACiE, the world's first comprehensive electronic database of the chemical mechanisms of enzymatic reactions. (st-andrews.ac.uk)
- PubChem is world's largest collection of freely accessible chemical information. (rocksurfers.org)
- We studied the function of conserved residues by multiple sequence alignments and mutational replacements of these residues. (frontiersin.org)
- A predicted secondary structure can guide further experiments or comparative sequence analysis ( 19 ) and also aid in the design of RNA molecules ( 20 , 21 ). (pnas.org)
- Large chemical databases for structures are expected to handle the storage and searching of information on millions of molecules taking terabytes of physical memory. (wikipedia.org)
- Most chemical databases store information on stable molecules but in databases for reactions also intermediates and temporarily created unstable molecules are stored. (wikipedia.org)
- By looking at the fragments present in a search structure it is possible to eliminate the need for ABAS comparison with target molecules that do not possess the fragments that are present in the search structure. (wikipedia.org)
- The performance of such keys depends on the choice of the fragments used for constructing the keys and the probability of their presence in the database molecules. (wikipedia.org)
- https://www.ebi.ac.uk/chembldb/compound/inspect/ base_id_url_available: 1 description: A database of bioactive drug-like small molecules and bioactivities abstracted from the scientific literature. (ebi.ac.uk)
- With ten-fold cross validation on a manually annotated corpus, our recognition tool generates an f -score of 78.49 (precision of 83.02) and demonstrates greater suitability in identifying metabolite names than other existing recognition tools for general chemical molecules. (springer.com)
- The molecules of life : physical and chemical principles / John Kuriyan, Boyana Konforti, David Wemmer. (stanford.edu)
- Odorants are volatile molecules that efficiently carry chemical information, providing one of the main ways for communicating with the environment in all kingdoms of life. (sapub.org)
- The three dimensional structures of the odorant molecules can be visualized with Jmol and the multiple sequence alignment of the ORs included in the database can be analyzed by a Jalview applet. (sapub.org)
- Though not always considered as such, the database of protein three-dimensional (3D) structures is also a large network, where links are physical associations between molecules within structurally determined complexes. (plos.org)
- Using this approach, promising potentially biologically active molecules can be identified from large structure databases by performing in silico (virtual) screening experiments. (uibk.ac.at)
- A next node or an unknown target representing chemical or biological molecules in a biological pathway is selected based on co-occurrence values. (google.com)
- The method of claim 1 wherein the chemical or biological molecules and biological processes co-occur in a cell. (google.com)
- 4. The method of claim 1 wherein the step generating automatically one or more biological inferences includes generating a collection of a plurality of chemical or biological molecules logically associated with a plurality of biological processes, or a collection of a plurality of biological processes logically associated with a chemical or biological molecule. (google.com)
- 5. The method of claim 1 wherein the step of generating automatically one or more biological inferences between chemical or biological molecules and a biological process using results from the Likelihood statistic analysis methods includes generating automatically one or more biological inferences between chemical or biological molecules and a biological process in a cell using results from the Likelihood statistic analysis methods. (google.com)
- Includes information on the chemical properties and biological activities of small molecules. (smu.edu)
- Chemical structures are traditionally represented using lines indicating chemical bonds between atoms and drawn on paper (2D structural formulae). (wikipedia.org)
- It contributes to epigenetic alterations as structural modification that does not affect gene sequence but regulates its expression. (deepdyve.com)
- In the last two decades, many have been the technical advances and breakthroughs in the field of MP structural biology that have contributed to an exponential growth in the number of unique MP structures in the Protein. (portlandpress.com)
- Similarly, the development of free- ly available threading programs, which provide a 3-dimen- sional (3D) structural model of an enzyme of interest, have facilitated structural and functional studies that contribute to the understanding of the chemical mechanism of a target enzyme. (atlas-publishing.org)
- RNArchitecture is a database that provides a comprehensive description of relationships between known families of structured non-coding RNAs, with a focus on structural similarities. (genesilico.pl)
- The highest level, Class, organizes Families into very broad structural categories, such as simple or complex structured RNAs. (genesilico.pl)
- RNArchitecture also presents theoretical models of RNA 3D structure and is open for submission of structural models by users. (genesilico.pl)
- It requires a pairwise sequence alignment and a structural template to generate a 3D structural model of the target RNA sequence via either a fully automated or script-based approaches. (genesilico.pl)
- These perspectives include 1) comparison of protein structures, 2) structural analysis, and 3) protein structure prediction. (schoolbag.info)
- The invention of new chemical reactions provides new bond construction strategies for improved access to diverse regions of structural space. (sciencemag.org)
- Both forward and reverse approaches utilize the identified chemicals as "research tools" for determining the functions, interactions, and architecture of cellular networks in living organisms. (plantphysiol.org)
- Since chemical switches can act in a similar manner across a range of model or nonmodel organisms, their identification is of great interest for researchers working with different model systems. (plantphysiol.org)
- it has been used to perform pathway predictions for thousands of organisms, including those in the BioCyc Database Collection . (wikipedia.org)
- Ubiquitin is an interesting candidate to examine, since the standard university textbooks claim there is very little variability in sequence across many kinds of organisms. (creation.com)
- Duplicate sequences from the same organisms. (creation.com)
- A database of taxonomic names of lineages of organisms represented in NCBI's sequence databases. (nih.gov)
- The study conducted by the UZH researchers reveals that, through their unique network structure, rivers collect and transport DNA containing information on the organisms in the water and on land. (eawag.ch)
- Also covers patent literature, compound, and reaction information. (wfu.edu)
- In addition, the tremendous growth in the Biomedical literature has increased the redundancy problem of the compound names or the gene names and has been the main obstacle for literature based systematic text mining methods. (nature.com)
- Links together compound information across the web, providing free text and structure search access of millions of chemical structures. (mdibl.org)
- Two-dimensional maps of contacts summarize interactions between amino acids in the structure. (genesilico.pl)
- They reveal characteristic patterns of interactions between secondary and super-secondary structures and are very attractive for visual analysis. (genesilico.pl)
- Here we use this principle to suggest new protein-chemical interactions via the network derived from three-dimensional structures. (plos.org)
- We take a novel approach using protein-chemical interactions derived from 3D structures. (plos.org)
- We use protein and chemical superimpositions and physical tests of chemical-protein compatibility to identify the most likely candidates among the nearly one million potential interactions. (plos.org)
- We make thousands of confident predictions, including structures for known protein-drug interactions lacking a structure (e.g. topoisomerase-2/radicicol) and many new interactions. (plos.org)
- The network contains many thousands of protein-protein and protein-chemical interactions, of which several hundred involve drugs. (plos.org)
- In this paper we explored this large network systematically to predict new potential protein-chemical interactions. (plos.org)
- Considering protein-chemical interactions alone would lead to many thousands of predictions including mostly false positives. (plos.org)
- From 10,842 complexes forming the network of known structures, we identified 907,827 potential interactions, of which 20,067 (including 19,578 novel structures and 489 complexes with a previously determined structure) were significant (p≤0.05). (plos.org)
- Annotated and predicted chemical-protein interactions. (mdibl.org)
- Some chemicals do not yet have curated gene interactions and/or disease associations. (ctdbase.org)
- Specific chemical-gene and protein interactions in vertebrates and invertebrates are being curated from the published literature. (ctdbase.org)
- The colored bars are linked to corresponding interactions within the interaction report for this chemical (see the Interactions tab). (ctdbase.org)
- A dataset based on all known functional sequences of ubiquitin (UB) has been prepared. (creation.com)
- From a previous 18S rRNA gene pyrosequencing dataset of the benthic microeukaryotes, we retrieved the sequences affiliated with phylum Ciliophora and analyzed alpha and beta diversities of ciliate communities. (springer.com)
- Nevertheless, structurally, the dominant class appeared to be Spirotrichea in the sequencing dataset, which differs from previous morphology-based results (dominance of classes Prostomatea and Karyorelictea in biomass). (springer.com)
- His group have worked extensively on prediction of bioactivity, solubility, melting point and hydrophobicity from chemical structure, using both informatics and theoretical chemistry methodologies. (st-andrews.ac.uk)
- A dynamic programming algorithm for prediction of RNA secondary structure has been revised to accommodate folding constraints determined by chemical modification and to include free energy increments for coaxial stacking of helices when they are either adjacent or separated by a single mismatch. (pnas.org)
- In this study, a dynamic programming algorithm for prediction of RNA secondary structure has been revised to use experimentally determined chemical modification constraints. (pnas.org)
- It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties. (ebi.ac.uk)
- From this study it appears that our fingerprint, built from monomer composition, allows an effective screening and prediction of biological activities of NRPs database. (springer.com)
- The biological insights obtained from the analysis of known protein structures and their applications to protein structure prediction and folding rates are outlined. (schoolbag.info)
- While predictions of this sort would need to be verified like any other prediction from bioinformatics tools, these predictions, if possible, could speed up analysis of protein structure and function, which is in itself the focus of proteomics. (wikibooks.org)
- However, only a few enzyme sequences have been identified and characterized to date (Table 1 ). (frontiersin.org)
- You can usually find EC numbers by searching for your enzyme in BRENDA (an enzyme database). (concordia.ca)
- Its name was originally an acronym for the Braunschweig Enzyme Database . (wikivisually.com)
- An important part of BRENDA represent the more than 110,000 enzyme ligands, which are available on their names, synonyms or via the chemical structure. (wikivisually.com)
- BRENDA provides links to several other databases with a different focus on the enzyme , e.g., metabolic function or enzyme structure . (wikivisually.com)
- Free Online Tutorials Teach Anyone How to Use Genome Databases. (rocksurfers.org)
- When clicked on, the tagged items invoke pop-ups (see Figure 8) displaying brief summaries of key features (domain structures, small-molecule structures, interaction partners, etc.), and allow navigation to core biological databases like UniProtKB. (nih.gov)
- Even if curators of biological databases were able to keep up with the ever increasing volume of literature, biologists would still need text mining to link the database entries to the evidence and the argumentation contained in the literature. (biomedcentral.com)
- Database: The Journal of Biological Databases and Curation provides an open access platform for the presentation of novel ideas in database research and biocuration, and aims to help strengthen the bridge between database developers, curators, and users. (oup.com)
- 8 ). Hairpin loop parameters (Tables 1 and 2 ) are revised on the basis of recent experimental results ( 47 , 48 ) and the previous database of RNA hairpin stabilities ( 49 - 55 ). (pnas.org)
- RNA methylation and diseases: experimental results, databases, Web servers and computational models Chen, Xing;Sun, Ya-Zhou;Liu, Hui;Zhang, Lin;Li, Jian-Qiang;Meng, Jia 2017-11-18 00:00:00 Abstract Ribonucleic acid (RNA) methylation is a type of posttranscriptional modifications occurring in all kingdoms of life. (deepdyve.com)
- Most metabolites are known and reported through the scientific literature, rather than through large-scale experimental surveys. (springer.com)
- The Isolation and Sequence of a Novel Gene From a Human Functional T Cell Line", J. Exp. (patentgenius.com)
- As both the creators and curators of a database which catalogues minimotifs, Minimotif Miner, the authors have a unique perspective on the commonalities of the many functional roles of minimotifs. (biomedcentral.com)
- Our derived minimotif syntax is currently being used to normalize minimotif covalent chemistry and functional definitions within the MnM database. (biomedcentral.com)
- lemons suffer the best download handbook of inorganic chemicals for suggesting ll. (mbca-lasvegas.org)
- It takes an below Public download handbook of inorganic chemicals for clicking the mobility of the older page of Black products and topics, the Octal clones editor who However was me only in the 2007-2008 incidence TB. (mbca-lasvegas.org)
- The ICSD contains an almost exhaustive list of known inorganic crystal structures published since 1913, including their atomic coordinates. (fiz-karlsruhe.de)
- Also disclosed are methods for utilizing such polypeptides in diagnostic assays for identifying mutations in nucleic acid sequences encoding the polypeptides of the present invention, for detecting altered levels of the polypeptide of the present invention as a means of detecting diseases and methods of screening potential modulators, especially inhibitors, of the novel PDE4D7s disclosed herein. (freepatentsonline.com)
- By coupling to ChemSpider, a major chemical database, we have identified structures for much of the reported metabolome and, where structure identification fails, been able to suggest extensions to ChemSpider. (springer.com)
- The Toxin and Toxin-Target Database (T3DB), also known as the Toxic Exposome Database, is a freely accessible online database of common substances that are toxic to humans, along with their protein, DNA or organ targets. (wikipedia.org)
- Coverage includes substances reported in the literature back to the early 1800s. (stn-international.de)
- Chemical substances Acetylcholine chloride, sodium nitroprusside dihydrate, and thromboxane A2 analog had been bought from Sigma-Aldrich Co. (Saint Louis, USA). (healthandwellnesssource.org)
- A resource providing access to structure and nomenclature information for the identification of chemical substances cited in NLM ® databases. (mdibl.org)
- The EMBL-EBI hosts a number of publicly open, free to use life science resources, including biomedical databases, analysis tools and bio-ontologies. (wikipedia.org)
- biomedical literature citations and abstracts, including Medline - articles from (mainly medical ) journals , often including abstracts. (wikipedia.org)
- Web version of SciFinder Scholar, Chemical Abstracts Service's database of literature from many scientific disciplines including chemistry, biomedical sciences, materials science, environmental science, and more. (wfu.edu)
- Furthermore, cross-references to external information resources such as sequence and 3D-structure databases, as well as biomedical ontologies , are provided. (wikivisually.com)
- Like EST sequencing, proteomics methods provide actual evidence for the presence of gene products and thus can serve as validation of gene models. (genetics.org)
- 1 Today primary sequence variation is mainly studied indirectly by means of deep RNA sequencing, although top-down and shotgun proteomics could provide more direct and quantitative results in the future ( 2 ). (mcponline.org)
- It contains both curated literature and links to many databases and resources for proteomics and biology in general. (wikibooks.org)
- Chemical modification is a technique that reveals solvent accessible nucleotides ( 22 ). (pnas.org)
- Reactions in MetaCyc are presented in a visual display that includes the structures of all components. (wikipedia.org)
- While increasingly identified by high-throughput experiments, most knowledge of metabolites and their reactions is primarily reported in the scientific literature. (springer.com)
- Voet and Pratt's 4th edition of "Principles of Biochemistry, " challenges readers to better understand the chemistry behind the biological structure and reactions occurring in living systems. (stanford.edu)
- Generally, enzymatic carboxylate reduction provides several advantages compared to chemical reductions: The reactions are carried out in one step under mild conditions in aqueous solutions. (frontiersin.org)
- 7 million single and multiple step reactions: reactions diagrams, structures for reactants, reagents, products, and reference information. (carroll.edu)
- Complex networks describe a wide range of systems in nature and society, much quoted examples including the cell, a network of chemicals linked by chemical reactions, or the Internet, a network of routers and computers connected by physical links. (psu.edu)
- With the advent of several technological improvements, including direct electron detectors, automation, better microscope vacuums and lenses, phase plates and improvements in computing power enabled by GPUs, it is now possible to record and analyse images of protein structures containing high-resolution information. (portlandpress.com)
- The classification is hierarchical and similar to the system used in the SCOP and CATH databases of protein structures. (genesilico.pl)
- The chemical nature of amino acids is important for the folding and stability of protein structures. (schoolbag.info)
- The availability of many protein structures has enabled researchers to perform various computational analysis from different perspectives such as structure, function, and stability. (schoolbag.info)
- The computational studies on protein structures have been carried out from different perspectives in biology. (schoolbag.info)
- Thanks to the flexibility and simplicity of its structure as well as its chemo-taxonomic definition, ClassyFire is meant to easily evolve to cover the increasing number of newly discovered scaffolds of natural and synthetic chemical entities, facilitating biochemical research. (wishartlab.com)
- 32 million sequences. (carroll.edu)
- http://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId= base_id_url_available: 1 description: The IUPHAR (International Union of Basic and Clinical Pharmacology)/BPS (British Pharmacological Society) Guide to PHARMACOLOGY database contains structures of small molecule ligands, peptides and antibodies, with their affinities at protein targets. (ebi.ac.uk)
- Information of identified peptides is also available directly via the JGI-Chlamydomonas genomic resource database ( http://genome.jgi-psf.org/Chlre3/Chlre3.home.html ). (genetics.org)
- We have built a specialized relational database and a search tool for natural mutants of protein C. It contains 195 entries that include 182 missense and 13 stop mutations. (biomedcentral.com)
- An occupational toxicology database designed to link jobs to hazardous job tasks. (nih.gov)
- A database created by the US Environmental Protection Agency with genetic toxicology test results on thousands of chemicals. (mdibl.org)
- To this end, in 1992, the EMBL Council voted to establish the European Bioinformatics Institute and to locate it at the Wellcome Trust Genome Campus in the United Kingdom where it would be in close proximity to the major sequencing efforts at the Wellcome Sanger Institute . (wikipedia.org)
- The exercise includes the use of bioinformatics programs to identify a target protein from a partial gene sequence, identify its family, and obtain a 3D model. (atlas-publishing.org)
- Simple and advanced searching for macromolecules and ligands, tabular reports, specialized visualization tools, sequence-structure comparisons, RCSB PDB Mobile, Molecule of the Month and other educational resources at PDB-101, and more. (stanford.edu)
- Broad signals underlying in vivo 1H MRS spectra are referred to in literature as macromolecules, and have been assigned to amino acids by Behar et al. (mpg.de)
- Chemists can search databases using parts of structures, parts of their IUPAC names as well as based on constraints on properties. (wikipedia.org)
- Chemical databases are particularly different from other general purpose databases in their support for sub-structure search. (wikipedia.org)
- CAS SciFinder - The First Choice With SciFinder from CAS, you can increase your productivity and achieve faster breakthroughs Advancing the pace of research, Chemical Abstracts SciFinder search allows you to get results fast withou. (selectscience.net)
- https://www.emolecules.com/cgi-bin/more?vid= base_id_url_available: 1 description: A free chemical structure search engine containing millions of public domain structures. (ebi.ac.uk)
- A short example of a chemical search with pyrimethamine is also illustrated. (biomedcentral.com)
- 10. Limitations of Entrez Only text or numeric search Search fields hard to discover Search fields and defaults vary by database Chemical structure search, and other specialized algorithms, must be done outside Entrez The kicker: links are incomplete Only 500-10,000 ids! (slideshare.net)
- The Entrez (pronounced ɒnˈtreɪ ) Global Query Cross-Database Search System is a federated search engine, or web portal that allows users to search many discrete health sciences databases at the National Center for Biotechnology Information (NCBI) website. (wikipedia.org)
- Entrez Global Query is an integrated search and retrieval system that provides access to all databases simultaneously with a single query string and user interface. (wikipedia.org)
- All databases indexed by Entrez can be searched via a single query string, supporting boolean operators and search term tags to limit parts of the search statement to particular fields. (wikipedia.org)
- This returns a unified results page, that shows the number of hits for the search in each of the databases, which are also links to actual search results for that particular database. (wikipedia.org)
- Entrez also provides a similar interface for searching each particular database and for refining search results. (wikipedia.org)
- Users with a MyNCBI account can save queries indefinitely and also choose to have updates with new search results e-mailed for saved queries of most databases. (wikipedia.org)
- Rich information about all PDB entries, multiple search and browse facilities, advanced services including PDBePISA, PDBeFold and PDBeMotif, advanced visualisation and validation of NMR and EM structures, tools for bioinformaticians. (stanford.edu)
- Getting to Yes: What Patent Attorneys Want to Learn from a Sequence Search , Joan Switzer, Merck & Co. Inc. (piug.org)
- Ensuring a Thorough Sequence Patent Search , Dr. Kamalakar Gulukota, GenomeQuest Inc. (piug.org)
- 2. Materials and methods 2.1 Publication search We searched for studies in the PubMed, Embase, Web of Science, and CNKI (China National Knowledge Infrastructure) electronic databases to include in this meta-analysis, using the terms ""CYP1A1,"" ""Cytochrome P450 1A1,"" ""polymorphism,"" and ""lung cancer. (anti-cancers.com)
- Retrieve information from this American Chemical Society database, and simultaneously search Medline. (carroll.edu)
- For your search query How To Use NCBI Database MP3 we have found 1000000 songs matching your query but showing only top 10 results. (rocksurfers.org)
- Limit your search results to NCBI-Curated domains, which include 3-dimensional structures and conserved core motifs, by adding the following criterion to your query at the top of the search results page: AND cdd[Database], and press the "Go" button. (rocksurfers.org)
- A blast-p 1 search based on a known ubiquitin sequence identified about 860 similar sequences, which were downloaded to a PC. (creation.com)
- A resource that provides pre-formulated PubMed search strategies to find published literature to support achieving Healthy People 2020 objectives. (nih.gov)
- Entrez, the life sciences search engine, searches across multiple health sciences databases at the National Center for Biotechnology Information. (mblwhoilibrary.org)
- Portal for PubChem, Structure Search, Protein, PubMed, and numerous other databases from the National Center for Biotechnology Information. (campusguides.com)
- Search by chemical name or CAS number. (campusguides.com)
- Includes ChemIDplus: search by name or registry number for information on structure, properties, and toxicity. (campusguides.com)
- Biological Sequence Search relates to finding a specific arrangement of DNA / RNA / Amino Acids in a given patent or non-patent document. (promaxlegal.com)
- We carefully tackle sequences with low complexity regions with a progressive search strategy to address the objective in a structured manner. (promaxlegal.com)
- maplit.hopto.org mapLit] is a new way to visualize literature search results that uses nested tree views for displaying related articles in context. (openwetware.org)
- Owing to the development of high-throughput sequencing technology, plenty of achievement had been obtained in RNA methylation research recently. (deepdyve.com)
- Wilson and Nicholls, 2015 ) thanks to the rapid development of high-throughput screening (HTS) and gene sequencing technologies. (frontiersin.org)
- A centralized page providing access and links to resources developed by the Structure Group of the NCBI Computational Biology Branch (CBB). (stanford.edu)
- 2013. Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology. (jax.org)
- REPAIRtoire is an online database for systems biology of DNA damage and repair. (genesilico.pl)
- MODOMICS is the first comprehesive database system for systems biology of RNA modification. (genesilico.pl)
- In this article, we give an overview of the computational analysis of protein structure and function from the viewpoint of chemical biology. (schoolbag.info)
- Physical Chemistry Chemical Physics. (st-andrews.ac.uk)
- RNA methylation, biological function, disease, database, Web server and software, computational model RNA methylation Methylation is a form of alkylation in chemistry, which adds a methyl group on a substrate or substitutes the original atom or group. (deepdyve.com)
- https://www.surechembl.org/chemical/ base_id_url_available: 1 description: SureChEMBL automatically extracts chemistry from the full text of all major patent authorities. (ebi.ac.uk)
- The applications of the chemistry of amino acids to the biological problem, protein structure and function, and folding and stability are the main focus of this article. (schoolbag.info)
- Our trained professionals include doctorates and graduates from biochemistry, biotechnology, microbiology, and chemistry andhave profound knowledge of their field coupled with years of hands-on experience of working with multiple databases. (promaxlegal.com)
- Describes a collaboration between the GO and the Chemical Entities of Biological Interest (ChEBI) ontology developers to ensure the representation of chemicals in the GO is consistent with expertise captured in ChEBI. (jax.org)
- For each Family with an experimentally determined 3D structure(s), a representative one is provided. (genesilico.pl)
- A multiple sequence alignment of CARs with confirmed activity recently identified in our lab and from the literature revealed a fingerprint of conserved amino acids. (frontiersin.org)
- We not only provide the sequence mapping but also the percentage of alignment of sequence bases. (promaxlegal.com)
- When available, it also provides descriptors from some external databases such as ChEBI and LIPID MAPS. (wishartlab.com)