Chris Bizon, Andreas Prlic. Calculating All Pairwise Similarities from the RCSB Protein Data Bank: Client/Server Work Distribution on the Open Science Grid,
The average sequence length in UniProtKB/Swiss-Prot is 359 amino acids. The shortest sequence is GWA_SEPOF (P83570): 2 amino acids. The longest sequence is TITIN_MOUSE (A2ASS6): 35213 amino acids. 4. JOURNAL CITATIONS Note: the following citation statistics reflect the number of distinct journal citations. Total number of journals cited in this release of UniProtKB/Swiss-Prot: 2753 4.1 Table of the frequency of journal citations Journals cited 1x: 866 2x: 391 3x: 163 4x: 136 5x: 110 6x: 100 7x: 66 8x: 56 9x: 37 10x: 33 11- 20x: 219 21- 50x: 227 51-100x: 118 ,100x: 231 4.2 List of the most cited journals in UniProtKB/Swiss-Prot Nb Citations Journal name -- --------- ------------------------------------------------------------- 1 24439 Journal of Biological Chemistry 2 11326 Proceedings of the National Academy of Sciences of the U.S.A. 3 6606 Journal of Bacteriology 4 5619 Biochemical and Biophysical Research Communications 5 5312 Biochemistry 6 4984 Nucleic Acids Research 7 4816 FEBS Letters 8 ...
VIEW RECORDING. DOWNLOAD SLIDES. ABSTRACT. I first posed this question in an Editorial in 2005. Well the future is now, so what is the answer to the question? I will give you at least my opinion of an answer and back it up with work that we and others have been doing at this interface. My own experience will be drawn from our database work with the RCSB Protein Data Bank (PDB) and the Immune Epitope Database (IEDB) and as Co-founder and Founding Editor in Chief of the journal PLOS Computational Biology.. SPEAKER BIOGRAPHY. Philip E. Bourne PhD is Associate Vice Chancellor for Innovation and Industry Alliances, a Professor in the Department of Pharmacology and Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California San Diego, Associate Director of the RCSB Protein Data Bank and an Adjunct Professor at the Sanford Burnham Institute. Bournes professional interests focus on relevant biological and educational outcomes derived from computation and scholarly ...
The RCSB Protein Data Bank (http://www.pdb.org) is a publicly accessible information portal for researchers and students interested in structural biology. At its center is the PDB archive -- the sole international repository for the 3-dimensional structure data of biological macromolecules. These structures hold significant promise for the pharmaceutical and biotechnology industries in the search for new drugs and in efforts to understand the mysteries of human disease The primary mission of the RCSB PDB is to provide accurate, well-annotated data in the most timely and efficient way possible to facilitate new discoveries and scientific advances. The RCSB processes, stores, and disseminates these important data, and develops the software tools needed to assist users in depositing and accessing structural information The RCSB Protein Data Bank at Rutgers University in Piscataway, NJ has an opening for a Biochemical Information & Annotation Specialist to curate and standardize macromolecular ...
PDB setzte sich ursprünglich aus Proteinstrukturen aus der Röntgen-Kristallstrukturanalyse und dem 1968 gegründeten Brookhaven RAster Display (BRAD) zusammen. Im Jahr 1969, entstand unter der Förderung durch Walter Hamilton am Brookhaven National Laboratory und der Urheberschaft von Edgar Meyer (Texas A&M University) eine Software zur Speicherung von Atomkoordinaten in einem gemeinsamen Format. Im Jahr 1971 wurde die Suchfunktion SEARCH eingeführt, mit der die Daten heruntergeladen und offline gespeichert werden konnten.[3] Nach Hamiltons Tod 1973 übernahm Tom Koeztle die Leitung für die folgenden 20 Jahre. Im Jahr 1994 ging die Führung an Joel Sussman über. Von Oktober 1998 bis Juni 1999 wurde PDB in das Research Collaboratory for Structural Bioinformatics (RCSB) übertragen.[4][5] Dort wurde Helen M. Berman of Rutgers University neue Direktorin.[6] Im Jahr 2003 wurde PDB mit der Gründung von Worldwide Protein Data Bank (wwPDB) international. Gründungsmitglieder sind PDBe ...
The RCSB web servers returned an unexpected error. It has been logged and will be reviewed by the PDB team. Here are some suggested remedial steps: ...
The RCSB web servers returned an unexpected error. It has been logged and will be reviewed by the PDB team. Here are some suggested remedial steps: ...
The Data Catalogue is a service that allows University of Liverpool Researchers to create records of information about their finalised research data, and save those data in a secure online environment. The Data Catalogue provides a good means of making that data available in a structured way, in a form that can be discovered by both general search engines and academic search tools. There are two types of record that can be created in the Data Catalogue: A discovery-only record - in these cases, the research data may be held somewhere else but a record is provided to help people find it. A record is created that alerts users to the existence of the data, and provides a link to where those data are held. A discovery and data record - in these cases, a record is created to help people discover the data exist, and the data themselves are deposited into the Data Catalogue. This process creates a unique Digital Object identifier (DOI) which can be used in citations to the data ...
2. TAXONOMIC ORIGIN Total number of species represented in this release of UniProtKB/Swiss-Prot: 12922 The first twenty species represent 112553 sequences: 20.9 % of the total number of entries. 2.1 Table of the frequency of occurrence of species Species represented 1x: 5426 2x: 1882 3x: 981 4x: 639 5x: 466 6x: 381 7x: 284 8x: 217 9x: 199 10x: 123 11- 20x: 668 21- 50x: 403 51-100x: 212 ,100x: 1041 2.2 Table of the most represented species ------ --------- -------------------------------------------- Number Frequency Species ------ --------- -------------------------------------------- 1 20233 Homo sapiens (Human) 2 16566 Mus musculus (Mouse) 3 11571 Arabidopsis thaliana (Mouse-ear cress) 4 7815 Rattus norvegicus (Rat) 5 6621 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) 6 5965 Bos taurus (Bovine) 7 5089 Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) 8 4431 Escherichia coli (strain K12) 9 4188 Bacillus subtilis (strain 168) 10 4126 Dictyostelium ...
2. TAXONOMIC ORIGIN Total number of species represented in this release of UniProtKB/Swiss-Prot: 12726 The first twenty species represent 111314 sequences: 20.8 % of the total number of entries. 2.1 Table of the frequency of occurrence of species Species represented 1x: 5365 2x: 1849 3x: 955 4x: 628 5x: 463 6x: 374 7x: 272 8x: 218 9x: 198 10x: 110 11- 20x: 655 21- 50x: 392 51-100x: 209 ,100x: 1038 2.2 Table of the most represented species ------ --------- -------------------------------------------- Number Frequency Species ------ --------- -------------------------------------------- 1 20246 Homo sapiens (Human) 2 16473 Mus musculus (Mouse) 3 11018 Arabidopsis thaliana (Mouse-ear cress) 4 7690 Rattus norvegicus (Rat) 5 6619 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) 6 5885 Bos taurus (Bovine) 7 4976 Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) 8 4431 Escherichia coli (strain K12) 9 4244 Bacillus subtilis 10 4122 Dictyostelium discoideum (Slime ...
Thus, for the same protein, different sets of binding-site residues might be obtained depending on the PDB structure that is considered, and a residue of a protein may be defined as binding-site residue in one PDB structure but as non-binding-site residue in another. This inconsistency can cause serious problems in research. Thus, for a given protein, researchers need to identify all PDB structures that contain the protein, and calculate binding-site residues on the protein using all of them.. After users have found all the PDB structures that contain a given protein, the protein sequences shown in different PDB structures must be aligned properly to combine the binding-site information obtained from different structures. This step is not as simple as it may first appear. It cannot be done by matching the sequence indexes of residues in the PDB structures, because the same protein chain may have different sequence indexing in different PDB structures. For example, 1qqi_A and 1gxp_A are the same ...
Summary of the gene family classification of four related species, Cyclina sinensis, Crassostrea gigas, Lottia gigantea and Capitella teleta.Only putative pepti
An improved multistage intelligent database search method includes (1) a prefilter that uses a precomputed index to compute a list of most
The table below provides information about proteins whose structures have been determined by solid-state NMR, to a resolution sufficient to have resulted in a file deposited with the worldwide Protein Data Bank (wwPDB). Here is the NMR page of the wwPDB ...
Accession numbers must be cited immediately following the Materials and Methods section. Accession numbers are unique identifiers in bioinformatics allocated to nucleotide and protein sequences to allow tracking of different versions of that sequence record and the associated sequence in a data repository [e.g., databases at the National Center for Biotechnical Information (NCBI) at the National Library of Medicine (GenBank) and the Worldwide Protein Data Bank]. There are different types of accession numbers in use based on the type of sequence cited, each of which uses a different coding. Authors should explicitly mention the type of accession number together with the actual number, bearing in mind that an error in a letter or number can result in a dead link in the online version of the article. Please use the following format: accession number type ID: xxxx (e.g., MMDB ID: 12345; PDB ID: 1TUP). Note that in the final version of the electronic copy, accession numbers will be linked to the ...
Are you a structural biologist looking for an exciting career change in 2016?. We are looking to recruit an expert structural biologist (with experience in structure determination) to join the Protein Data Bank in Europe curation team (PDBe: pdbe.org) at the European Bioinformatics Institute (EMBL-EBI, Cambridge, UK: ebi.ac.uk) as a Scientific Data Curator. The work involves annotating preliminary PDB and Electron Microscopy Data Bank (EMDB) submissions and extracting relevant biological information. In addition, curators contribute to training, outreach and user-support activities of PDBe and the EMBL-EBI.. For more information, please go to:. https://ig14.i-grasp.com/fe/tpl_embl01.asp?newms=jj&id=54423&aid=15470. ...
The Protein Identifier Mapping Service provides a free interface to resolve protein identifiers across multiple databases that correspond to the same logical protein.
Protein structure mining using a structural alphabet.: Protein structure mining using a structural alphabet. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
Biomedical applications drive all aspects of our methods development efforts. We do this through collaborations with biomedical scientists, and through primary biomedical research within the CCSB. We also have a strong commitment to biomedical education and outreach, using CCSB tools to disseminate the results of biomedical research to diverse audiences.. As part of the HIVE Center, we are studying HIV and its interaction with host cells throughout the viral life cycle.. In collaboration with Barry Sharpless, we are designing specific covalent inhibitors and applying them to multiple biomedical targets.. Working with PDB-101, the outreach/education portal of the RCSB Protein Data Bank, we produce many materials and resources for use in education and outreach.. ...
Figure 1. Above is a Jmol image of the consensus V3 loop of gp120. The partially-hidden nature of the conserved region of gp120 makes it difficult for our bodies to develope effective neutralizing antibodies. The image is from the RCSB Protein Data Bank. PDB 1CE4. Antibodies specific to gp120 and the gp41 envelope proteins (Janeway et al, 2005) can be found in plasma of infected patients within weeks of initial infection (Paul, 2003), and may play a role in minimizing viral impact during the asymptomatic period, but are unable to clear an infection. Despite the early presence of HIV-specific antibodies, the high levels of antibodies with the ability to neutralize viruses are generally only found in long-term nonprogressors (Paul, 2003). Two trimers of gp120 and gp41 create the envelope protein gp160, which is heavily glycosylated. CD4 T cells bind gp120 on a depression in the protein (Paul, 2003). The virus also binds chemokine receptors on another depressed site on gp120 as co-receptors. Both ...
Mitochondrial tRNAs have been the subject of study for structural biologists interested in their secondary structure characteristics, evolutionary biologists have researched patterns of compensatory and structural evolution and medical studies have been directed towards understanding the basis of human disease. However, an up to date, manually curated database of mitochondrially encoded tRNAs from higher animals is currently not available. We obtained the complete mitochondrial sequence for 277 tetrapod species from GenBank and re-annotated all of the tRNAs based on a multiple alignment of each tRNA gene and secondary structure prediction made independently for each tRNA. The mitochondrial (mt) tRNA sequences and the secondary structure based multiple alignments are freely available as Supplemental Information online. We compiled a manually curated database of mitochondrially encoded tRNAs from tetrapods with completely sequenced genomes. In the course of our work, we reannotated more than 10% of all
Although domain-centric annotations hold great promise in describing phenotypic nature of independent domains, most domains themselves may not just work alone. In multi-domain proteins, they may be combined together to form distinct domain architectures. The recombination of the existing domains is considered as one of major driving forces for phenotypic diversificaation. As an extension, we have also generated supra-domain phenotype ontology and its annotations. Compared to domain-centric phenotype ontology and annotations (SCOP domains at the Superfamily level and Family level), this version focuses on supra-domains and individual SCOP domains ONLY at the Superfamily level. Besides, in terms of individual superfamilies, their annotations from the domain-centric version may be different from those from supra-domains version. Depending on your focus, the former should be used for the consideration of both the Superfamily level and Family level, otherwise the latter should be used if you are ...
There are 330 cases currently listed in Australia. Results are displayed 25 per page. Login or create an account for additional advocacy tools, including e-mail notifications when updates are posted to selected cases.. Pages: 1 2 3 4 5 6 7 8 9 10 Next» ...
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InterPro is an integrated resource for protein families, domains, and active sites. The resource provides an invaluable means for automatic classification of protein sequences into families or domains with a view to providing functional annotation for the proteins. It constitutes an amalgamation of the major protein signature databases: PROSITE, PRINTS, Pfam, ProDom, SMART, TIGRFAMs, PIR SuperFamily, and SUPERFAMILY into a unified database where similarities and differences between the signatures from each of these databases are rationalized for ease of use. All signatures representing the same family or domain are collated into unique InterPro entries, with annotation and a list of the proteins in UniProt that these signatures match. New sequences not available in UniProt can be run through all signatures in InterPro using the InterProScan software. InterPro is useful for large-scale classification of whole genomes, as well as for functional annotation of individual protein sequences. ...
... builds a database of protein sequences that are linked to scientific articles. These links come from automated text searches against the articles in EuropePMC and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot, BRENDA, CAZy (as made available by dbCAN), CharProtDB, MetaCyc, EcoCyc, REBASE, and the Fitness Browser. Given this database and a protein sequence query, PaperBLAST uses protein-protein BLAST to find similar sequences with E , 0.001. To build the database, we query EuropePMC with locus tags, with RefSeq protein identifiers, and with UniProt accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use queries of the form "locus_tag AND genus_name" to try to ensure that the paper is actually discussing that gene. Because EuropePMC indexes most recent biomedical papers, even if they are not open access, some of the links may be to papers that you cannot read or that our computers cannot read. We query each of these identifiers that appears ...
Tutor: Micaela Lewinson. Bioinformatics is an interdisciplinary area of study linking computational tools and databases to biology. Topics such as DNA sequence analysis, genome sequencing, expression of genes, 3D-structures of proteins are all considered parts of bioinformatics. In my Bioinformatics course (BIO 260) students are introduced to this exciting new interdisciplinary area spanning computational science and biology. This is a non-traditional biology course - it does not have a "wet lab", but students spend a significant time in the computer lab using various databases (such as DNA sequence databases, protein structure databases) and software packages to solve problems in biology. One of the class projects is analysis and annotation of a previously unpublished, newly sequenced genome. Through this project students have an opportunity to use digital research to make a novel contribution to science! This exciting project is made possible through my participation in a multi-institution ...
ARLINGTON Va.- The assets of the Protein Data Bank (PDB) justkeep ...The PDB holds the three-dimensional structures of nearly 24000p...This month with a doubling in the number of the federal agencies...Mary Clutter assistant director for NSFs Directorate forBiolog... Biological processes involve small molecular machines shesaid...,Protein,data,bank,opens,new,era,with,broader,support,biological,biology news articles,biology news today,latest biology news,current biology news,biology newsletters
Technical Library Search Help provides information on wildcards, boolean operators, Google searches, and other tips to improve your search results.
08h30 Protein sequence databases: theory. 10h30 COFFEE BREAK. 11h00 Controlled vocabularies and standardization resources: theory. 12h15 LUNCH. 13h30 Protein sequence databases and Gene Ontology: practicals. 15h00 COFFEE BREAK. 15h30 Analysis tools using ontologies : theory. 16h00 Protein sequence databases and Gene Ontology: practicals. 17h00 Evaluation / Exam. 18h00 END ...
Current Protein & Peptide Science covers a field by discussing research from the leading laboratories in a field and should pose questions for futu...
Current Protein & Peptide Science covers a field by discussing research from the leading laboratories in a field and should pose questions for futu...
Genomic locations of UniProt/SwissProt variants are labeled with the amino acid change at a given position and, if known, the abbreviated disease name. A ? is used if there is no disease annotated at this location, but the protein is described as being linked to only a single disease in UniProt. Mouse over a mutation to see the UniProt comments. Artificially-introduced mutations are colored green and naturally-occurring variants are colored red. For full information about a particular variant, click the UniProt variant linkout. The UniProt record linkout lists all variants of a particular protein sequence. The Source articles linkout lists the articles in PubMed that originally described the variant(s) and were used as evidence by the UniProt curators. ...
Genomic locations of UniProt/SwissProt variants are labeled with the amino acid change at a given position and, if known, the abbreviated disease name. A ? is used if there is no disease annotated at this location, but the protein is described as being linked to only a single disease in UniProt. Mouse over a mutation to see the UniProt comments. Artificially-introduced mutations are colored green and naturally-occurring variants are colored red. For full information about a particular variant, click the UniProt variant linkout. The UniProt record linkout lists all variants of a particular protein sequence. The Source articles linkout lists the articles in PubMed that originally described the variant(s) and were used as evidence by the UniProt curators. ...
2008 yılında Ege Üniversitesi İstatistik bölümünden lisans derecesiyle mezun oldu. 2011 yılında Ege Üniversitesi Tıp Fakültesi Biyoistatistik Anabilim Dalından yüksek lisans derecesini aldı. Yüksek lisans tez çalışmasında, biyoeşdeğerlik çalışmaları üzerine çalıştı. 2016 yılında Hacettepe Üniversitesi Tıp Fakültesi Biyoistatistik Anabilim Dalından doktora derecesini aldı. Doktora çalışması kapsamında 2015-2016 yılları arasında University of California San Diego üniversitesinde bulunan San Diego Supercomputer Centera bağlı RCSB Protein Data Bankta doktora tez çalışmasını yürüttü. Doktora tez çalışması kapsamında Protein Data Bankta bulunan protein yapılarının kestirimi üzerine yeni yöntemler geliştirdi. 2017 yılından itibaren Trakya Üniversitesi Tıp Fakültesi Biyoistatistik ve Tıbbi Bilişim Anabilim Dalıında öğretim üyesi olarak görev yapmaktadır. İlgi alanları makine öğrenimi, proteomik, genetik ve ...
AE006468.YBAD Location/Qualifiers FT CDS 469392..469841 FT /codon_start=1 FT /transl_table=11 FT /gene="ybaD" FT /locus_tag="STM0415" FT /product="putative transcriptional regulator" FT /note="similar to E. coli orf, hypothetical protein FT (AAC73516.1); Blastp hit to AAC73516.1 (149 aa), 95% FT identity in aa 1 - 149" FT /db_xref="EnsemblGenomes-Gn:STM0415" FT /db_xref="EnsemblGenomes-Tr:AAL19369" FT /db_xref="GOA:P0A2M1" FT /db_xref="InterPro:IPR003796" FT /db_xref="InterPro:IPR005144" FT /db_xref="UniProtKB/Swiss-Prot:P0A2M1" FT /protein_id="AAL19369.1" FT /translation="MHCPFCFAVDTKVIDSRLVGEGSSVRRRRQCLVCNERFTTFEVAE FT LVMPRVIKSNDVREPFNEDKLRSGMLRALEKRPVSADDVEMALNHIKSQLRATGEREVP FT SKMIGNLVMEQLKKLDKVAYIRFASVYRSFEDIKDFGEEIARLQD" MHCPFCFAVD TKVIDSRLVG EGSSVRRRRQ CLVCNERFTT FEVAELVMPR VIKSNDVREP 60 FNEDKLRSGM LRALEKRPVS ADDVEMALNH IKSQLRATGE REVPSKMIGN LVMEQLKKLD 120 KVAYIRFASV YRSFEDIKDF GEEIARLQD 149 ...
75% of the Pfam model length. long_domain=1 sequences are found in library_long_domains.fa.gz and in library_all_domains.fa.gz non_redundant Useful to calculate family size "0" flags a redundant domain that overlaps with another with longer sequence homology annotation "1" flags the non-redundant domain with the longer sequence homology annotation ======================= 3. Supplementary Annotation files ================================== pfam_to_clan.txt - Lists the pfam family to clan superfamily correspondence. Note: The annotations on this database are at the superfamily level, which we recommend for homology evaluation. See the FAQ.txt and (Gonzalez and Pearson, NAR, 2010) for more details of why coalescing superfamilies is the preferred choice when evaluating homology. refprotdom_domain_bound_ext.txt - Lists the domains that in pfam v.21 were annotated as partial homologies whose coordinates we extended. Current uniprot accessions and sequence ids are provided, as well as the corresponding ...
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. The complete paper is available on-line by following links from the PubMed website ...
1zlm: Function and biology annotation of Crystal structure of the SH3 domain of human osteoclast stimulating factor. Includes SCOP, CATH, InterPro, GO and Intenz annotation.
CP000247.PE653 Location/Qualifiers FT CDS complement(696239..696502) FT /codon_start=1 FT /transl_table=11 FT /locus_tag="ECP_0661" FT /product="hypothetical protein" FT /db_xref="EnsemblGenomes-Gn:ECP_0661" FT /db_xref="EnsemblGenomes-Tr:ABG68689" FT /db_xref="InterPro:IPR007454" FT /db_xref="InterPro:IPR027471" FT /db_xref="UniProtKB/Swiss-Prot:Q0TK42" FT /protein_id="ABG68689.1" FT /translation="MKTKLNELLEFPTPFTYKVMGQALPELVDQVVEVVQRHAPGDYTP FT TVKPSSKGNYHSVSITINATHIEQVETLYEELGKIDIVRMVL" MKTKLNELLE FPTPFTYKVM GQALPELVDQ VVEVVQRHAP GDYTPTVKPS SKGNYHSVSI 60 TINATHIEQV ETLYEELGKI DIVRMVL 87 ...
Biochemistry is a rich source of important computational problems that should be of interest to mathematicians, computer scientists and engineers. The dramatic drop in the cost of sequencing DNA as well as progress in several structural genomics initiatives have created many new and exciting opportunities. ...
Using X-ray crystallography, researchers at the University of Pittsburgh School of Medicine led by structural biologist Joanne I. Yeh, Ph.D., have become the first to decipher the three-dimensional st...
MedeA 2.19 provides a range of enhancements and new capabilities in the MedeA® environment.. MedeA® database search results can now be directly linked to MedeA-Flowchart calculations for efficient computational screening studies. You can search InfoMaticA databases (InfoMaticA provides access to hundreds of thousands of crystallographic structures), generate targeted selections of structures, optionally modify stoichiometry, and submit these structures for efficient first-principles property evaluation using MedeA-Flowcharts. A range of capabilities are combined in MedeA-HighThroughput to facilitate such calculations, these enhancements include the efficient generation of structure lists and analysis tools.. MedeA-Morphology allows you to analyze the macroscopic consequences of interatomic forces and crystal symmetry in terms of crystal shape. Taking as input a defined unit cell and symmetry, MedeA-Morphology computes the equilibrium crystal shape, based on BFDH rules, and allows users to ...
[email protected]: Protease cleavage sites predicted with PeptideCutter from the Expert Protein Analysis System (ExPASy) proteomics server of the Swiss Institute of Bioinformatics (SIB ...
[email protected]: Protease cleavage sites predicted with PeptideCutter from the Expert Protein Analysis System (ExPASy) proteomics server of the Swiss Institute of Bioinformatics (SIB ...
Protein structures are stabilized using noncovalent interactions. In addition to the traditional noncovalent interactions, newer types of interactions are thought to be present in proteins. One such interaction, an anion-p pair, in which the positively charged edge of an aromatic ring interacts with an anion, forming a favorable anion-quadrupole interaction, has been previously proposed [Jackson, M. R., et al. (2007) J. Phys. Chem. B111, 8242?8249]. To study the role of anion-? interactions in stabilizing
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Results from your Search are visible below. You may further refine your search using the Refine Your Results links below, right. Clicking on one of the refinement items will return a subset of your original search. To return to your original results, simply choose the Any [term] link at the top of each section. You may also sort your results, either by Relevance/Ranking (default result), Title, or Date Modified. ...
Results from your Search are visible below. You may further refine your search using the Refine Your Results links below, right. Clicking on one of the refinement items will return a subset of your original search. To return to your original results, simply choose the Any [term] link at the top of each section. You may also sort your results, either by Relevance/Ranking (default result), Title, or Date Modified. ...
The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies. As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards. The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. These molecules are visualized, downloaded, and analyzed by users who range from students to specialized scientists.
The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies. As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards. The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. These molecules are visualized, downloaded, and analyzed by users who range from students to specialized scientists.
The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies. As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards. The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. These molecules are visualized, downloaded, and analyzed by users who range from students to specialized scientists.
The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies. As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards. The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. These molecules are visualized, downloaded, and analyzed by users who range from students to specialized scientists.
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SCOPe: Structural Classification of Proteins - extended database, and ASTRAL compendium for protein structure and sequence analysis
SCOPe: Structural Classification of Proteins - extended database, and ASTRAL compendium for protein structure and sequence analysis
APSnet Feature. July, 2002... Jan E. LeachDepartment of Plant PathologyKansas State UniversityManhattan, KS [email protected] Scott GoldDepartment of Plant PathologyUniversity of GeorgiaAthens, GA [email protected] Sue A. TolinDept of Plant Path, Physiology, & Weed SciVirginia Pol...
Professor Sean Grimmond (formally of The University of Queenslands Institute for Molecular Bioscience) leads an international team of researchers has analysed the genetics of pancreatic cancer, revealing it is actually four separate diseases, each with different genetic triggers and survival ...
Clear Search​. Search for all ICES publications. Use the refinement panel on the left to narrow down your search. Having trouble finding what you are looking for? Go to Search FAQs for more detailed instructions or contact our librarian at [email protected] ...
ATOM 1 N ALA 1 46.457 12.189 21.556 0.1414 1.8240 ATOM 2 CA ALA 1 47.614 11.997 22.448 0.0962 1.9080 ATOM 3 C ALA 1 47.538 12.947 23.645 0.6163 1.9080 ATOM 4 O ALA 1 46.441 13.476 23.962 -0.5722 1.6612 ATOM 5 CB ALA 1 48.911 12.134 21.650 -0.0597 1.9080 ATOM 6 H2 ALA 1 45.672 11.684 21.917 0.1997 0.6000 ATOM 7 H3 ALA 1 46.235 13.163 21.506 0.1997 0.6000 ATOM 8 H ALA 1 46.683 11.849 20.642 0.1997 0.6000 ATOM 9 HA ALA 1 47.603 11.052 22.786 0.0889 1.1000 ATOM 10 HB1 ALA 1 49.041 11.319 21.087 0.0300 1.4870 ATOM 11 HB3 ALA 1 48.855 12.941 21.064 0.0300 1.4870 ATOM 12 HB2 ALA 1 49.679 12.231 22.281 0.0300 1.4870 ATOM 13 N ASP 2 48.702 13.128 24.279 -0.5163 1.8240 ATOM 14 CA ASP 2 48.826 13.956 25.493 0.0381 1.9080 ATOM 15 C ASP 2 48.614 15.471 25.323 0.5366 1.9080 ATOM 16 O ASP 2 49.292 16.362 24.807 -0.5819 1.6612 ATOM 17 CB ASP 2 50.156 13.635 26.226 -0.0303 1.9080 ATOM 18 CG ASP 2 49.984 12.419 27.136 0.7994 1.9080 ATOM 19 OD1 ASP 2 50.595 12.308 28.221 -0.8014 1.6612 ATOM 20 OD2 ASP 2 49.198 ...
Cebula, Anna, Michal Seweryn, Grzegorz A. Rempala, Simarjot Singh Pabla, Richard A. McIndoe, Timothy L. Denning, Lynn Bry, Piotr Kraj, Pawel Kisielow, and Leszek Ignatowicz. 2013. "Thymus-derived regulatory T cells control tolerance to commensal microbiota." Nature 497 (7448): 258-262. doi:10.1038/nature12079. http://dx.doi.org/10.1038/nature12079. [Peer Reviewed Journal]. ...
Lango Allen, H; Estrada, K; Lettre, G; Berndt, SI; Weedon, MN; Rivadeneira, F; Willer, CJ; Jackson, AU; Vedantam, S; Raychaudhuri, S; +283 more... (2010) Hundreds of variants clustered in genomic loci and biological pathways affect human height. Nature, 467 (7317). pp. 832-8 [Peer Reviewed Journal]. ...
Option 2 - Submit MOTIFS to scan them against a PROTEIN sequence database. Submit a PROSITE motif, a custom pattern or a combination of any of the latter and scan them against a protein database. The choice of protein database includes UniProtKB, PDB, a custom database or randomized database of the UniProtKB reviewed section. Doing so you can tune a number of parameters regarding the motif being scanned, such as the number of hits it must have in a sequence for a match to be reported or some criteria that the matched sequences must fulfill to be reported like for instance having a minimal size. ...
This information is based on mapping of SMART genomic protein database to KEGG orthologous groups. Percentage points are related to the number of proteins with EGF_like domain which could be assigned to a KEGG orthologous group, and not all proteins containing EGF_like domain. Please note that proteins can be included in multiple pathways, ie. the numbers above will not always add up to 100%. ...
This information is based on mapping of SMART genomic protein database to KEGG orthologous groups. Percentage points are related to the number of proteins with FU domain which could be assigned to a KEGG orthologous group, and not all proteins containing FU domain. Please note that proteins can be included in multiple pathways, ie. the numbers above will not always add up to 100%. ...
Protein Data Bank Japan maintains the database for experimentally determined protein structures: the PDB. PDBj annotates deposited structures, provides additional annotations and offers various services to search for and analyze deposited structures.
This activity demonstrates the concept of how genes encode proteins. You use a codon wheel to translate DNA sequences into amino acid chains. Using this information, you then search for the proteins that contain those sequences using the UNIPROT database and find out what the proteins do.. DNA sequence is converted into a string of amino acids that form the functional protein. There are 20 different amino acids and the order and combinations of amino acids that make up a protein determine the proteins unique function in the body. The human genome contains over 20,000 protein-coding genes.. A PowerPoint presentation is provided for teachers who may wish to do this activity with a class. This presentation provides an outline of how to run the activity and details of each of the proteins featured in the activity. Files are also provided so you can view the 3D structure of the proteins using the protein modelling software Rasmol.. ...
Membrane proteins are very difficult to work on . . . so when you have two independent groups actually coming up with seemingly identical or very similar structures, its very gratifying," said structural biologist Chris Tate of the Medical Research Councils Laboratory of Molecular Biology in Cambridge, UK, who was not involved in the studies ...
The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies. As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards. The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. These molecules are visualized, downloaded, and analyzed by users who range from students to specialized scientists.
Yes still in Italy. Looking back at this post, it looks like most of the small biologists (excluding structural biologists) who practiced the molecule-centric approach have been weeded out by the stagnation in NIH funding, but I still beleive that the temptation to perform such research is still there for many young scientists … so…. ...
New structural images help explain how young neurons make the right connections, showing how a signal, Netrin-1, interacts with specific receptors that tell neurons in which direction to reach. "Our work provides the first high-resolution view of the molecular complexes that form on the surface of a developing axon and tell it to move in one direction or another," says a structural biologist involved in the study. "This detailed understanding of these assemblies helps us better understand neural wiring, and may one day be useful in the development of drugs to treat spinal cord or brain injuries ...
Used in a context in which domain name services, or domain name like services, are managed in a fashion that is integrated with the management of other computer and network related information. Used in the same context as the collection of information domain sense ...
Subfamily: Where superfamilies are presumed to be complete, subfamilies represent an incomplete set of homologous proteins which yet encompass proteins of diverse function. Since superfamilies, however, are often impractical to construct, subfamilies are far more common in TIGRFAMs. Subfamilies fulfill a number of useful roles in tha annotation process. The construction of equivalogs is a process which results in models which may not identify all homologous sequences of conserved function due to the limits of current experimental characterization - a subfamily may encompass all of the sequences included within one (or more) equivalog(s) as well as related sequences which fall outside of an equivalogs scope. Subfamilies, then, are often a hierarchical level above equivalogs and may provide information through their associated comment fields which may assist in the naming of genes which are not members of any current equivalog. In certain situations equivalogs may not be constructed because of ...
Ata were parsed from the set of PDB files available as of November 2012. Chains were counted rather than PDB entries as expression information is recorded by
Hi. For all those who took the time to complete my online survey on protein database use, many thanks. If you missed the first post and would like to add your perspective regarding the use of these databases the survey is still open for a little while longer. The link is below and the survey should only take 10-15 minutes to fill out. I would appreciate your input. KBA http://www.surveymonkey.com/s.aspx?sm=tNKIQHxUhEven_2fQ4DqiiHA_3d_3d ...
NOTE : If one of the query terms is found within another word (e.g. protein in flavoprotein in search item 6 in above table), it is still considered as a hit. The above table does not show the results obtained in the AND mode search. In the case of real searches this would not happen ...
Workflow of SELPHI. SELPHI first identifies the UniprotKB IDs and sequence location of the input phosphosites. The data are then filtered according to the input
PTS system trehalose-specific IIB component, Glc family (TC 4.A.1.2.4)/PTS system trehalose-specific IIC component, Glc family (TC 4.A.1.2.4)/PTS system trehalose-specific IIA component, Glc family (T ...
赾壮昫梻柧乸腸痀痀皈释覀影僐孧於泚,佋盬削固冂夐具亏PDB赾壮衪玫皈砘穻载導》末砘穻刞歫观寗PDB皈髜颏赾壮衪玫,仧期揓髜丶庈诌斦凅硱玉,凐導漑诌叏诮诌》
filtered_set; other; UniRef90: No significant hits (1e-5); maizesequence.org: GO:0007186; G-protein coupled receptor protein signaling pathway , GO:0016021; integral to ...
core: 3 layers, a/b/a ; mixed sheet of 5 strands: order 21354; strand 4 is antiparallel to the rest; contains crossover loops ...
Data from different size: Consider the implications of data volumes in terms of storage, backup and access. Estimate the volume of data in MB/GB/TB and how this will grow to make sure any additional storage and technical support required can be provided. Type of variables Physical format and structure Data is often found as a digital file containing numbers and text, but you
An understanding protein structure is vital for the elucidation of its function. Information gleaned from the three dimensional structures of proteins is used to understand the biochemical and functional roles of such molecules in life and for the design and discovery of drug molecules for a variety of diseases and illnesses such as cancer, influenza and tuberculosis. The Protein Data Bank (PDB) is the central publicly accessible repository of all experimentally derived macromolecular structures. Containing over 80,000 structures of proteins and nucleic acids the PDB is an essential scientific resource. The PDB is managed by a consortium of international organizations collectively known as the worldwide Protein Data Bank (wwPDB). The Protein Data Bank in Europe (PDBe) is one of the founding members of the wwPDB along with the RCSB Protein Data Bank in the USA and Protein Data Bank Japan(PDBj) in Japan. In addition to serving as a deposition site for data deposited to the PDB, the PDBe also ...
An understanding protein structure is vital for the elucidation of its function. Information gleaned from the three dimensional structures of proteins is used to understand the biochemical and functional roles of such molecules in life and for the design and discovery of drug molecules for a variety of diseases and illnesses such as cancer, influenza and tuberculosis. The Protein Data Bank (PDB) is the central publicly accessible repository of all experimentally derived macromolecular structures. Containing over 80,000 structures of proteins and nucleic acids the PDB is an essential scientific resource. The PDB is managed by a consortium of international organizations collectively known as the worldwide Protein Data Bank (wwPDB). The Protein Data Bank in Europe (PDBe) is one of the founding members of the wwPDB along with the RCSB Protein Data Bank in the USA and Protein Data Bank Japan(PDBj) in Japan. In addition to serving as a deposition site for data deposited to the PDB, the PDBe also ...
An understanding protein structure is vital for the elucidation of its function. Information gleaned from the three dimensional structures of proteins is used to understand the biochemical and functional roles of such molecules in life and for the design and discovery of drug molecules for a variety of diseases and illnesses such as cancer, influenza and tuberculosis. The Protein Data Bank (PDB) is the central publicly accessible repository of all experimentally derived macromolecular structures. Containing over 80,000 structures of proteins and nucleic acids the PDB is an essential scientific resource. The PDB is managed by a consortium of international organizations collectively known as the worldwide Protein Data Bank (wwPDB). The Protein Data Bank in Europe (PDBe) is one of the founding members of the wwPDB along with the RCSB Protein Data Bank in the USA and Protein Data Bank Japan(PDBj) in Japan. In addition to serving as a deposition site for data deposited to the PDB, the PDBe also ...
An understanding protein structure is vital for the elucidation of its function. Information gleaned from the three dimensional structures of proteins is used to understand the biochemical and functional roles of such molecules in life and for the design and discovery of drug molecules for a variety of diseases and illnesses such as cancer, influenza and tuberculosis. The Protein Data Bank (PDB) is the central publicly accessible repository of all experimentally derived macromolecular structures. Containing over 80,000 structures of proteins and nucleic acids the PDB is an essential scientific resource. The PDB is managed by a consortium of international organizations collectively known as the worldwide Protein Data Bank (wwPDB). The Protein Data Bank in Europe (PDBe) is one of the founding members of the wwPDB along with the RCSB Protein Data Bank in the USA and Protein Data Bank Japan(PDBj) in Japan. In addition to serving as a deposition site for data deposited to the PDB, the PDBe also ...
MODBASE (http://guitar.rockefeller.edu/modbase) is a relational database of annotated comparative protein structure models for all available protein sequences matched to at least one known protein structure. The models are calculated by MODPIPE, an automated modeling pipeline that relies on PSI-BLAS …
The problem: There are far too many proteins for which the sequence is known, but the function is not. The gap between what we know and what we do not know is growing. A major challenge in the field of bioinformatics is to predict the function of a protein from its sequence (and all other data one can find). At the same time, how can we judge how well these function prediction algorithms are performing and whether we are making progress over time?. The solution: The Critical Assessment of protein Function Annotation algorithms (CAFA) is an experiment designed to provide a large-scale assessment of computational methods dedicated to predicting protein function. We will evaluate methods in predicting the Gene Ontology (GO) terms in the categories of Molecular Function, Biological Process, and Cellular Component. In addition, predictors may use the Human Phenotype Ontology (HPO) for the human dataset. A set of protein sequences is provided by the organizers, and participants are expected to submit ...
The Protein Data Bank archive (PDB) is a worldwide archival repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies, managed by the Worldwide PDB (wwPDB). The PDB Exchange Dictionary (PDBx) is used by the wwPDB to define data content for deposition, annotation and archiving of PDB entries. PDBx incorporates the community standard metadata representation, the Macromolecular Crystallographic Information Framework (mmCIF), orginally developed under the auspices of the International Union of Crystallography (IUCr). PDBx has been extended by the wwPDB to include descriptions of other experimental methods that produce 3D macromolecular structure models such as Nuclear Magnetic Resonance Spectroscopy, 3D Electron Microscopy and Tomography. ...
The Cambridge Structural Database (CSD) is a highly curated and comprehensive resource.. Established in 1965, the CSD is the worlds repository for small-molecule organic and metal-organic crystal structures. Containing over 900,000 entries from x-ray and neutron diffraction analyses, this unique database of accurate 3D structures has become an essential resource to scientists around the world.. With comprehensive and fully retrospective coverage of the published literature you can have full confidence that your CSD searches are returning all crystal structure matches. The CSD also contains data published directly through the CSD as CSD Communications that are not available anywhere else.. ...
Many journals impose guidelines for the reporting of database search results, designed to ensure that the data are reliable. This was initiated by the Editors of Molecular and Cellular Proteomics, who organised a workshop in 2005 to discuss the issues, culminating in the Paris Guidelines. The current guidelines require For large scale experiments, the results of any additional statistical analyses that estimate a measure of identification certainty for the dataset, or allow a determination of the false discovery rate, e.g., the results of decoy searches or other computational approaches.. This is a recommendation to repeat the search, using identical search parameters, against a database in which the sequences have been reversed or randomised. You do not expect to get any true matches from the decoy database. So, the number of matches that are found is an excellent estimate of the number of false positives that are present in the results from the real or target database. This approach ...
ID NIRB_ECOLI Reviewed; 847 AA. AC P08201; Q2M731; DT 01-AUG-1988, integrated into UniProtKB/Swiss-Prot. DT 01-NOV-1995, sequence version 4. DT 25-OCT-2017, entry version 161. DE RecName: Full=Nitrite reductase (NADH) large subunit; DE EC=1.7.1.15; GN Name=nirB; OrderedLocusNames=b3365, JW3328; OS Escherichia coli (strain K12). OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; OC Enterobacteriaceae; Escherichia. OX NCBI_TaxID=83333; RN [1] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RC STRAIN=K12; RX PubMed=2543955; DOI=10.1093/nar/17.10.3865; RA Bell A.I., Gaston K.L., Cole J.A., Busby S.J.W.; RT "Cloning of binding sequences for the Escherichia coli transcription RT activators, FNR and CRP: location of bases involved in discrimination RT between FNR and CRP."; RL Nucleic Acids Res. 17:3865-3874(1989). RN [2] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RC STRAIN=K12; RX PubMed=2200672; DOI=10.1111/j.1432-1033.1990.tb19125.x; RA Peakman T., Crouzet J., Mayaux J.F., Busby S.J.W., Mohan S., ...
Protein 3D structures are currently determined experimentally via X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. The process is slow (it can take weeks or even months to figure out how to crystallize a protein for the first time) and costly (around US$100,000 per protein).[15] Unfortunately, the rate at which new sequences are discovered far exceeds the rate of structure determination - out of more than 7,400,000 protein sequences available in the National Center for Biotechnology Information (NCBI) nonredundant (nr) protein database, fewer than 52,000 proteins 3D structures have been solved and deposited in the Protein Data Bank, the main repository for structural information on proteins.[16] One of the main goals of [email protected] is to predict protein structures with the same accuracy as existing methods, but in a way that requires significantly less time and money. [email protected] also develops methods to determine the structure and docking of membrane proteins (e.g., G ...
The signal peptide plays an important role in protein targeting and protein translocation in both prokaryotic and eukaryotic cells. This transient, short peptide sequence functions like a postal address on an envelope by targeting proteins for secretion or for transfer to specific organelles for further processing. Understanding how signal peptides function is crucial in predicting where proteins are translocated. To support this understanding, we present SPdb signal peptide database http://proline.bic.nus.edu.sg/spdb , a repository of experimentally determined and computationally predicted signal peptides. SPdb integrates information from two sources (a) Swiss-Prot protein sequence database which is now part of UniProt and (b) EMBL nucleotide sequence database. The database update is semi-automated with human checking and verification of the data to ensure the correctness of the data stored. The latest release SPdb release 3.2 contains 18,146
ESPRIT: Screening of tens of thousands of constructs of a single gene to identify well-behaving soluble constructs. Academic structural biologists often work on proteins that lack accurate domain annotations. When the full-length protein cannot be expressed and a domain-focused approach is necessary, problems arise since it is unclear how to design high yielding, soluble expression constructs. Some proteins have little or no sequence similarity to others and this prevents domain identification using multiple sequence alignments. More often, some functional annotation exists e.g. from mutagenesis or deletion studies, but these regions do not define well the structural boundaries. Even when a soluble construct is obtained, disordered extensions may confound crystallisation attempts. We are all familiar with these situations; in many cases they are what keep our proteins "hot" and out of the PDB.. The ESPRIT technology was developed in the Hart lab at EMBL to express proteins whose domain ...
The SCOP classification for the S13-like H2TH domain superfamily including the families contained in it. Additional information provided includes InterPro annotation (if available), Functional annotation, and SUPERFAMILY links to genome assignments, alignments, domain combinations, taxonomic visualisation and hidden Markov model information.
The SCOP classification for the XPC-binding domain superfamily including the families contained in it. Additional information provided includes InterPro annotation (if available), Functional annotation, and SUPERFAMILY links to genome assignments, alignments, domain combinations, taxonomic visualisation and hidden Markov model information.
The SCOP classification for the Nucleoporin domain superfamily including the families contained in it. Additional information provided includes InterPro annotation (if available), Functional annotation, and SUPERFAMILY links to genome assignments, alignments, domain combinations, taxonomic visualisation and hidden Markov model information.
The SCOP classification for the ISP domain superfamily including the families contained in it. Additional information provided includes InterPro annotation (if available), Functional annotation, and SUPERFAMILY links to genome assignments, alignments, domain combinations, taxonomic visualisation and hidden Markov model information.
File: ID Symbol Taxon Taxon Name Evidence GO ID GO Name + Aspect Reference With Source H1SXX9 Symbol1 12345 Homo Sapiens IEA GO:0015031 pro +tein transport Process GO_REF:0000002 InterPro:IPR027282 +InterPro H1SXZ5 Symbol2 12345 Homo Sapiens IEA GO:0003824 cat +alytic activity Function GO_REF:0000002 InterPro:IPR003607 + InterPro H1SXZ5 Symbol2 12345 Homo Sapiens IEA GO:0008152 met +abolic process Process GO_REF:0000002 InterPro:IPR002912 +InterPro H1SXZ5 Symbol2 12345 Homo Sapiens IEA GO:0008728 GTP + diphosphokinase activity Function GO_REF:0000003 EC:2.7.6.5 + UniProt H1SXZ5 Symbol2 12345 Homo Sapiens IEA GO:0015969 gua +nosine tetraphosphate metabolic process Process GO_REF:0000002 + InterPro:IPR004811,InterPro:IPR007685 InterPro H1SXZ5 Symbol2 12345 Homo Sapiens IEA GO:0016301 kin +ase activity Function GO_REF:0000038 UniProtKB-KW:KW-0418 + UniProt H1SXZ5 Symbol2 12345 Homo Sapiens IEA GO:0016310 pho +sphorylation Process GO_REF:0000038 UniProtKB-KW:KW-0418 +UniProt H1SXZ5 Symbol2 12345 ...