Related Research Articles
{{redirect|NCBI} extended size at ro zygote 32GB becaming ro zygote 46GB}
UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from the research literature. It is maintained by the UniProt consortium, which consists of several European bioinformatics organisations and a foundation from Washington, DC, United States.
Protein–protein interactions (PPIs) are physical contacts of high specificity established between two or more protein molecules as a result of biochemical events steered by interactions that include electrostatic forces, hydrogen bonding and the hydrophobic effect. Many are physical contacts with molecular associations between chains that occur in a cell or in a living organism in a specific biomolecular context.
In academia, computational immunology is a field of science that encompasses high-throughput genomic and bioinformatics approaches to immunology. The field's main aim is to convert immunological data into computational problems, solve these problems using mathematical and computational approaches and then convert these results into immunologically meaningful interpretations.
In molecular biology and genetics, transcription coregulators are proteins that interact with transcription factors to either activate or repress the transcription of specific genes. Transcription coregulators that activate gene transcription are referred to as coactivators while those that repress are known as corepressors. The mechanism of action of transcription coregulators is to modify chromatin structure and thereby make the associated DNA more or less accessible to transcription. In humans several dozen to several hundred coregulators are known, depending on the level of confidence with which the characterisation of a protein as a coregulator can be made. One class of transcription coregulators modifies chromatin structure through covalent modification of histones. A second ATP dependent class modifies the conformation of chromatin.
A mimotope is often a peptide, and mimics the structure of an epitope. Because of this property it causes an antibody response similar to the one elicited by the epitope. An antibody for a given epitope antigen will recognize a mimotope which mimics that epitope. Mimotopes are commonly obtained from phage display libraries through biopanning. Vaccines utilizing mimotopes are being developed. Mimotopes are a kind of peptide aptamers.
The Reference Sequence (RefSeq) database is an open access, annotated and curated collection of publicly available nucleotide sequences and their protein products. RefSeq was introduced in 2000. This database is built by National Center for Biotechnology Information (NCBI), and, unlike GenBank, provides only a single record for each natural biological molecule for major organisms ranging from viruses to bacteria to eukaryotes.
Tyrosine-protein kinase-like 7 also known as colon carcinoma kinase 4 (CCK4) is a receptor tyrosine kinase that in humans is encoded by the PTK7 gene.
The Single Nucleotide Polymorphism Database (dbSNP) is a free public archive for genetic variation within and across different species developed and hosted by the National Center for Biotechnology Information (NCBI) in collaboration with the National Human Genome Research Institute (NHGRI). Although the name of the database implies a collection of one class of polymorphisms only, it in fact contains a range of molecular variation: (1) SNPs, (2) short deletion and insertion polymorphisms (indels/DIPs), (3) microsatellite markers or short tandem repeats (STRs), (4) multinucleotide polymorphisms (MNPs), (5) heterozygous sequences, and (6) named variants. The dbSNP accepts apparently neutral polymorphisms, polymorphisms corresponding to known phenotypes, and regions of no variation. It was created in September 1998 to supplement GenBank, NCBI’s collection of publicly available nucleic acid and protein sequences.
The Proteolysis MAP (PMAP) was an integrated web resource focused on proteases. Its domain now links to a scam/spam browser extender.
The ConsensusPathDB is a molecular functional interaction database, integrating information on protein interactions, genetic interactions signaling, metabolism, gene regulation, and drug-target interactions in humans. ConsensusPathDB currently includes such interactions from 32 databases. ConsensusPathDB is freely available for academic use under http://ConsensusPathDB.org.
Richard Michael Durbin is a British computational biologist and Al-Kindi Professor of Genetics at the University of Cambridge. He also serves as an associate faculty member at the Wellcome Sanger Institute where he was previously a senior group leader.
MatrixDB is a biological database focused on molecular interactions between extracellular proteins and polysaccharides. MatrixDB takes into account the multimeric nature of the extracellular proteins. The database was initially released in 2009 and is maintained by the research group of Sylvie Ricard-Blum at UMR5246, Claude Bernard University Lyon 1.
The ChemDB HIV, Opportunistic Infection and Tuberculosis Therapeutics Database is a publicly available tool developed by the National Institute of Allergy and Infectious Diseases to compile preclinical data on small molecules with potential therapeutic action against HIV/AIDS and related opportunistic infections.
The Re-referenced Protein Chemical shift Database (RefDB) is an NMR spectroscopy database of carefully corrected or re-referenced chemical shifts, derived from the BioMagResBank (BMRB). The database was assembled by using a structure-based chemical shift calculation program to calculate expected protein (1)H, (13)C and (15)N chemical shifts from X-ray or NMR coordinate data of previously assigned proteins reported in the BMRB. The comparison is automatically performed by a program called SHIFTCOR. The RefDB database currently provides reference-corrected chemical shift data on more than 2000 assigned peptides and proteins. Data from the database indicates that nearly 25% of BMRB entries with (13)C protein assignments and 27% of BMRB entries with (15)N protein assignments require significant chemical shift reference readjustments. Additionally, nearly 40% of protein entries deposited in the BioMagResBank appear to have at least one assignment error. Users may download, search or browse the database through a number of methods available through the RefDB website. RefDB provides a standard chemical shift resource for biomolecular NMR spectroscopists, wishing to derive or compute chemical shift trends in peptides and proteins.
SHIFTCOR is a freely available web server as well as a stand-alone computer program for protein chemical shift re-referencing. Chemical shift referencing is a particularly widespread problem in biomolecular NMR with up to 25% of existing NMR chemical shift assignments being improperly referenced. Some of these referencing problems can lead to systematic errors of between 1.0 to 2.5 ppm. Errors of this magnitude can play havoc with any attempt to compare assignments between proteins or to structurally interpret chemical shifts. Identifying which proteins are mis-assigned or improperly referenced can be challenging, as can correcting the errors once they are found. The SHIFTCOR program was designed to assist with identifying and fixing these chemical shift referencing problems. Specifically it compares, identifies, corrects and re-references 1H, 13C and 15N backbone chemical shifts of peptides and proteins by comparing the observed chemical shifts with the predicted chemical shifts derived from the 3D structure of the protein(s) of interest [1]. The predicted chemical shifts are calculated using the ShiftX program. The SHIFTCOR program was originally used to construct a database of properly re-referenced protein chemical shift assignments called RefDB. RefDB is a web-accessible database of more than 2000 correctly referenced protein chemical shift assignments. While originally available as a stand-alone program only, SHIFTCOR has since been released for general use as a web server.
The PageRank algorithm has several applications in biochemistry.
CS23D is a web server to generate 3D structural models from NMR chemical shifts. CS23D combines maximal fragment assembly with chemical shift threading, de novo structure generation, chemical shift-based torsion angle prediction, and chemical shift refinement. CS23D makes use of RefDB and ShiftX.
ShiftX is a freely available web server for rapidly calculating protein chemical shifts from protein X-ray coordinates. Protein chemical shift prediction is particularly useful in verifying protein chemical shift assignments, adjusting mis-referenced chemical shifts, refining NMR protein structures and assisting with the NMR assignment of unassigned proteins that have either had their structures determined by X-ray or NMR methods.
References
- ↑ Razick, Sabry; George Magklaras; Ian M Donaldson (2008). "iRefIndex: A consolidated protein interaction database with provenance". BMC Bioinformatics. 9: 405. doi: 10.1186/1471-2105-9-405 . PMC 2573892 . PMID 18823568.