• Sequence clustering replaces groups of similar sequences in a database with single representatives. (nih.gov)
  • ModBase currently contains almost 30 million reliable models for domains in 4.7 million unique protein sequences. (nih.gov)
  • When the biologists get an unknown sequence, in general they would compare this unknown sequence (denoted as query sequence) with the known database of sequences (denoted as database sequences) to find the similarity scores and then identify the evolutionary relationships among them. (hindawi.com)
  • However, the exponential increase in the number of known sequences has increased the search time for querying against a database. (hindawi.com)
  • The data may be either a list of database accession numbers, NCBI gi numbers, or sequences in FASTA format. (nih.gov)
  • Predikin now consists of two components: (i) PredikinDB, a database of phosphorylation sites that links substrates to kinase sequences and (ii) a Perl module, which provides methods to classify protein kinases, reliably identify substrate-determining residues, generate scoring matrices and score putative phosphorylation sites in query sequences. (biomedcentral.com)
  • Xpro is a relational database that contains all the eukaryotic protein-encoding DNA sequences contained in GenBank with associated data required for the analysis of eukaryotic gene architecture. (edu.au)
  • Recent spectacular advances by AI programs in 3D structure predictions from protein sequences have revolutionized the field in terms of accuracy and speed. (nsf.gov)
  • 10,000 protein sequences with confirmed. (lu.se)
  • Of these, more than 660 proteins were annotated by WiMT from the resulting ~5800 protein sequences. (lu.se)
  • The highest number of melanoma plasma proteins from undepleted and unfractionated plasma was reported, mapping >1200 proteins from >10,000 protein sequences with confirmed significance scoring. (lu.se)
  • The question of whether proteins originate from random sequences of amino acids is addressed. (lu.se)
  • The results, which are based upon proteins in the SWISS-PROT data base, convincingly show that the amino acid sequences in proteins differ from what is expected from random sequences in a statistical significant way. (lu.se)
  • Performing the same statistical analysis on the sequences that fold well indicates similar deviations from randomness as for the functional proteins. (lu.se)
  • Our results, which differ from previous investigations using other methods, might have impact on how permissive with respect to sequence specificity the protein folding process is - only sequences with non-random hydrophobicity distributions fold well. (lu.se)
  • Secondly, the two statistical applications mainly (A) Amino Acid Dynamics and (B) amino acid composition were added in the database for analysis of sequence of drug target proteins. (scialert.net)
  • The second factor, termed peptide specificity, describes the interaction between amino acid residues in the catalytic domain of the protein kinase and the substrate residues that surround the phosphorylated residue. (biomedcentral.com)
  • Five anti- variants selected serologically are then tested for antibody genic sites in the hemagglutinin protein have been pro- cross-reactivity in human sera to evaluate the potential posed, and 131 amino acid positions have been identified cross-protection against the antigenic variants provided by in the five antigenic sites. (cdc.gov)
  • In addition, 20, 18, and 32 amino acid positions in the hemagglutinin protein have been iden- the current vaccines and to select vaccine strains for the tified as mouse monoclonal antibody-binding sites, posi- next season (2,3). (cdc.gov)
  • For this reason, the American Academy of Pediatrics (AAP) and ESPGHAN recommend the use of extensively hydrolyzed or free amino acid-based formulae in the treatment of cow's milk protein allergy. (medscape.com)
  • Membrane proteins are critical mediators for tumor progression and present enormous therapeutic potentials. (mit.edu)
  • The database can accelerate therapeutic developments and biotechnological applications of cancer-related membrane proteins. (mit.edu)
  • The Smith-Waterman (SW) algorithm has been widely utilized for searching biological sequence databases in bioinformatics. (hindawi.com)
  • The European Bioinformatics Institute, (EBI), and Flanders Interuniversity Institute for Biotechnology (VIB) -Ghent University have launched the PRoteomics IDEntifications database (PRIDE). (technologynetworks.com)
  • A non-redundant set of Xpro database contents is also obtained by cross-referencing to the Swiss-Prot/TrEMBL and Pfam databases. (edu.au)
  • A Drug Target Protein (DTP) Database has been developed having mainly in silico predicted potential drug target proteins and non human homologous genes in bacterial human pathogens. (scialert.net)
  • Protein kinases, the enzymes responsible for protein phosphorylation, make up almost 2% of protein-encoding genes in the human genome [ 1 ] and an estimated 30-50% of human proteins are phosphorylated [ 2 ]. (biomedcentral.com)
  • The database currently contains information for 493 983 genes - 351 918 introncontaining genes and 142 065 intron-less genes. (edu.au)
  • This protein has the task of organizing the genetic material in the cell nucleus and facilitates the interaction of other molecules with the DNA, for example to read genes. (mpg.de)
  • The expression of the foreign gene in HRs will result in the production of the foreign protein. (databasefootball.com)
  • This was achieved by fusing the foreign gene with a short DNA sequence encoding a signal peptide that directed the protein towards the secretory pathway of the cells. (databasefootball.com)
  • The fluorescent protein was abundant in the medium of HRs expressing the gene (figure 3) and it was found that adding 2,4-D to the culture medium resulted in the presence of more protein in the culture medium. (databasefootball.com)
  • Although gene profiling can identify their cancer-specific signatures, systematic correlations between protein functions and tumor-related mechanisms are still unclear. (mit.edu)
  • This gene encodes a protein containing an N-terminal Kruppel-associated box-containing (KRAB) domain and 13 Kruppel-type C2H2 zinc finger domains. (nih.gov)
  • To track down the cause, he and his colleagues decoded the genome of five affected individuals and found that the gene for the protein HMGB1 was altered in all patients. (mpg.de)
  • He adds, "It then becomes trivial to analyse protein identifications from many different sources, or compare the proteins produced by a particular tissue under different conditions. (technologynetworks.com)
  • The new features significantly enhance the ability of Predikin to analyse protein kinases and their substrates. (biomedcentral.com)
  • PROTEIN STRUCTURES: DATA, VALIDATION AND DATABASES * * * * OPEN MEETING * * * * Organised by Professor Janet Thornton for the UK CCP11 group * * * * Windeyer Building, University College, London * * * * Wednesday 25th March 1992 * * * ********************************************************************** The UK Collaborative Computing Project ( CCP11 ) are organising a one day open database meeting, to be held in London on Wednesday 25th March A provisional program is attached. (bio.net)
  • PROVISIONAL TIMETABLE * * * * PROTEIN STRUCTURES: DATA, VAIDATION AND DATABASES * * * ************************************************************************** One day meeting to be held on the Wednesday 25th March in the Windeyer Building, University of London. (bio.net)
  • Kurz M, Brachvogel V, Matter H, Stengelin S, Thuring H, Kramer W: Insights into the bile acid transportation system: the human ileal lipid-binding protein-cholyltaurine complex and its comparison with homologous structures. (hmdb.ca)
  • Native and redesigned proteins exhibited highly similar characteristics, predicted structures and binding pockets, and slightly different docking poses against known ligands, although task-specific designs are still required for proteins more susceptible to internal hydrogen bond formations. (mit.edu)
  • Especially the applications to protein structure prediction, e.g. prediction of secondary structures, prediction of surface structure, fold class recognition and prediction of the 3-dimensional structure of protein backbones, is being discussed here. (dtu.dk)
  • Crystal structures of protein kinases with bound substrate peptides show that substrate residues at positions -3 to +3 relative to the phosphorylated serine, threonine or tyrosine residue adopt an extended conformation and bind to a pocket in the catalytic domain of the protein kinase [ 8 ]. (biomedcentral.com)
  • Overall, this implementation of the US-SOMO-AF database should already aid in rapidly evaluating the consistency in solution of a relevant portion of AlphaFold predicted protein structures. (nsf.gov)
  • New features in Predikin include the use of SQL queries to PredikinDB to generate predictions, scoring of predictions, more reliable identification of substrate-determining residues and putative phosphorylation sites, extended options to handle protein kinase and substrate data and an improved web interface. (biomedcentral.com)
  • The post-translational modification of proteins by phosphorylation of serine, threonine or tyrosine residues is a ubiquitous process in cellular regulation. (biomedcentral.com)
  • However, it is recognised that for many protein kinase families, particularly those that phosphorylate Ser/Thr residues, peptide specificity is the major factor that determines substrate specificity. (biomedcentral.com)
  • These mutations affect critical residues in the cytoplasmic BTK protein and are highly variable and uniformly dispersed throughout the molecule. (medscape.com)
  • Proteomics labs were publishing their protein identifications," explains Henning Hermjakob, leader of the EBI's Proteomics Services Team. (technologynetworks.com)
  • This entails a multi-level dynamic protein database with different immunodepletion strategies by applying single-shot proteomics. (lu.se)
  • There are two types of biological databases. (iucr.org)
  • I'm happy to have identified a new one in ProNIT, whose thermodynamic data for protein-DNA interactions is "very useful for understanding the principles of molecular recognition. (genengnews.com)
  • Machine learning was used to extract key functional descriptions for protein visualization in the 3D-space, where spatial distributions provide function-based predictive connections between proteins and cancer types. (mit.edu)
  • Theoretical expectations of these variables from random distributions of hydrophobicities are compared with those obtained from functional proteins. (lu.se)
  • Here, an overview of the publicly available knowledge about IDRs is reported, including manually curated resources, deposition databases and prediction repositories. (iucr.org)
  • Pfam, available via servers in the UK (http//pfam.sanger.ac.uk/) and the USA (http//pfam.janelia.org/), is a widely used database of protein families , containing 14 831 manually curated entries in the current release, version 27.0. (bvsalud.org)
  • The HR system was first assessed using a jellyfish green fluorescent protein as a model. (databasefootball.com)
  • PSLSSmKate is a photoswitchable long stokes shift fluorescent protein published in 2014, derived from Entacmaea quadricolor. (fpbase.org)
  • sREACh is a basic (constitutively fluorescent) yellow fluorescent protein published in 2008, derived from Aequorea victoria. (fpbase.org)
  • Protein kinases and their substrates regulate essentially all cellular processes through complex regulatory networks, in which phosphorylated proteins act as switches that tune the response of the cell to environmental stimuli. (biomedcentral.com)
  • Repositories, archives or deposition databases collect primary ( i.e. experimental) data. (iucr.org)
  • Sometimes resources are of both types, and the majority of deposition databases also process data to facilitate visualization. (iucr.org)
  • The Nuclear Magnetic Resonance Spectral Measurement Database (NMR-SMDB) was developed for the purpose of organizing and searching NMR spectral data of protein therapeutics, linking spectra to corresponding sample information and enabling quick access to full datasets and entire studies. (nist.gov)
  • 1. Steinegger, M., Söding, J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. (nih.gov)
  • PRIDE is an open source: the PRIDE database, source code, data, and support tools are freely available for web access or download and local installation. (technologynetworks.com)
  • As a part of the Korean Personal Genome Project (KPGP), we constructed the KoVariome database using 5.5 terabases of whole genome sequence data from 50 healthy Korean individuals in order to characterize the benign ethnicity-relevant genetic variation present in the Korean population. (nature.com)
  • Reaxys enables you to search by structure, substructure, reaction, text, and property data.Being based on the CrossFire Beilstein, CrossFire Gmelin and Patent Chemistry databases Reaxys has a long history beginning with chemical data from 1771. (lu.se)
  • The methods described in this study could be applied to of the HA protein of A/Aichi/2/68 (H3N2) has been deter- predict vaccine-induced cross-reactive antibody responses in humans, which may further improve the selection of vac- mined, and five antigenic sites on the HA1 polypeptide cine strains. (cdc.gov)
  • Current inactivated vaccines provide essential protection described in this study could be used to predict vaccine- when the vaccine antigens and the circulating viruses share induced cross-reactive antibody responses in humans, high degree of similarity in the HA protein. (cdc.gov)
  • However, other soy proteins can act as allergens in humans. (medscape.com)
  • Gir2 is a highly acidic cytoplasmic protein of Saccharomyces cerevisiae. (disprot.org)
  • Antigenic high degree of similarity in hemagglutinin protein. (cdc.gov)
  • Since the last update article 2 years ago, we have generated 1182 new families and maintained sequence coverage of the UniProt Knowledgebase (UniProtKB) at nearly 80%, despite a 50% increase in the size of the underlying sequence database. (bvsalud.org)
  • We have previously described an approach to predicting the substrate specificity of serine-threonine protein kinases. (biomedcentral.com)
  • The relative contribution of substrate recruitment and peptide specificity to protein kinase substrate specificity varies between protein kinases. (biomedcentral.com)
  • The prediction of peptide specificity is therefore the basis for most of the available computational methods aimed at predicting substrates of protein kinases. (biomedcentral.com)
  • Bohr, H 1998, Neural Networks for protein Structure Prediction . (dtu.dk)
  • However, these works mainly focused on the protein database search by using the intertask parallelization technique, and only using the GPU capability to do the SW computations one by one. (hindawi.com)
  • Hence, in this paper, we will propose an efficient SW alignment method, called CUDA-SWfr, for the protein database search by using the intratask parallelization technique based on a CPU-GPU collaborative system. (hindawi.com)
  • In 2008, Manavski and Valle [ 16 ] presented the first SW algorithm by CUDA for the protein database search on GPU. (hindawi.com)
  • Ligowski and Rudnicki [ 18 ] also presented another SW algorithm for the protein database search on GPU in 2009. (hindawi.com)
  • proposed CUDASW++1.0 [ 19 ] and CUDASW++2.0 [ 20 ] for protein database search in 2009 and 2010, respectively. (hindawi.com)
  • The course also discusses the advantages and disadvantages of different search strategies, tools, and databases. (lu.se)
  • The course consists of a series of lectures that cover available databases relevant to chemistry, search strategies, and relevant search terms within chemistry. (lu.se)
  • Search across multiple databases and the library catalog simultaneously. (lu.se)
  • The high-throughput identification of proteins is gathering momentum, until recently there was no straightforward means of sharing or comparing the results. (technologynetworks.com)
  • We created a methodology for protein identification known as Wise MS Transfer (WiMT). (lu.se)
  • This HR system has been used to produce a number of proteins, some of them of human origin. (databasefootball.com)
  • Please upgrade your browser to a newer version to get the best experience on Human Metabolome Database. (hmdb.ca)
  • Oelkers P, Dawson PA: Cloning and chromosomal localization of the human ileal lipid-binding protein. (hmdb.ca)
  • The resulting "folding frenzy" has already produced predicted protein structure databases for the entire human and other organisms' proteomes. (nsf.gov)
  • Close-ups of cell nuclei in a human cell culture: HMGB1 protein (green) is usually found throughout the nucleus (dotted line). (mpg.de)
  • At least 9 proteins with MW ranging from 14,875-54,500 were found to react with human IgE in patients with asthma. (medscape.com)
  • All soybean proteins and foods currently available for human consumption contain significant amounts of the isoflavones daidzein and genistein, either in the unconjugate form or as different types of glycoside conjugates. (medscape.com)
  • Two heat-stable globulins constitute 90% of the pulp-derived proteins: beta-conglycinin, which has a molecular weight (MW) of 180,000, and glycinin, which has an MW of 320,000. (medscape.com)
  • Defects in these networks result in a variety of disease states making protein kinases important targets for drug design [ 3 ]. (biomedcentral.com)
  • Intrinsically disordered regions (IDRs) lacking a fixed three-dimensional protein structure are widespread and play a central role in cell regulation. (iucr.org)
  • In addition to the information found in the GenBank records, which includes properties such as sequence, position, length and description about introns, exons and protein-coding regions, Xpro provides annotations on the splice sites and intron phases. (edu.au)
  • KoVariome health records were used to identify novel disease-causing variants in the Korean population, demonstrating the value of high-quality ethnic variation databases for the accurate interpretation of individual genomes and the precise characterization of genetic variations. (nature.com)
  • Protein database may refer to: Any protein structure database Any protein sequence database Exact names "Protein" database of the National Institute of Health Protein Database of Bio-Synthesis, Inc. This disambiguation page lists articles associated with the title Protein database. (wikipedia.org)
  • ModBase (http://salilab.org/modbase) is a database of annotated comparative protein structure models. (nih.gov)
  • Such proteins contain sequence features that function as address labels, telling the protein which condensate to move into. (mpg.de)
  • For many years after the first description by Duke in 1934, soy was considered a weak sensitizing protein based on animal study findings. (medscape.com)
  • Expert biocurators play a crucial role in IDP databases by providing a direct interpretation of disorder derived from structural experiments and manually curating these ID annotations. (iucr.org)
  • CrMP-Sol also presents QTY-enabled water-soluble designs to facilitate native membrane protein studies despite natural hydrophobicity. (mit.edu)
  • PRIDE is designed to allow scientists to exploit the growing mass of information on how the body's complement of proteins is altered in many disease states, paving the way towards predictive and diagnostic methods in medicine. (technologynetworks.com)
  • Clustering large protein databases like the NCBI Non-Redundant database (NR) using even the best currently available clustering algorithms is very time-consuming and only practical at relatively high sequence identity thresholds. (nih.gov)
  • Clustered nr is the standard NCBI nr database clustered with each sequence within 90% identity and 90% length to other members of the cluster. (nih.gov)
  • Currently 10 bacterial pathogens are considered as initials of the database with their general information (disease caused, common symptoms, available drugs etc). (scialert.net)
  • influenza virus antigenic variants emerge frequently from accumulation of point mutations in the HA protein (i.e. (cdc.gov)
  • If you'd like to fund a research project, work on any of these solutions, share information about related efforts that are already underway, or elevate new ideas for advancing the alternative protein industry, we'd love to hear from you! (gfi.org)
  • Nucleic Acids Research , 32 (Database issue), D59-D63. (edu.au)
  • Returned records include extensive basic protein information as well as thermodynamic information regarding binding and other parameters. (genengnews.com)