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Proteins
Proteins
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"Hot spots are energetically important residues at protein interfaces and they are not randomly distributed across the interface but rather clustered. These clustered hot spots form hot regions. Hot regions are important for the stability of protein complexes, as well as providing specificity to binding sites. We propose a database called HotRegion, which provides the hot region information of the interfaces by using predicted hot spot residues, and structural properties of these interface residues ... [Miscellaneous as indicated]
Factual databases
http://prism.ccbb.ku.edu.tr/hotregion
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32.
IDEAL Database
IDEAL provides a collection of knowledge on experimentally verified intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs). IDEAL contains manually curated annotations on IDPs in locations, structures, and functional sites such as protein binding regions and posttranslational modification sites together with references and structural domain assignments.
One of the unique phenomena seen in IDPs is so-called the coupled folding and binding, where a short flexible segment ... [Information of the supplier]
Factual databases
http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/
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Indel Flanking Region Database is an online resource for indels and the flanking regions of proteins in SCOP superfamilies. It aims at providing a comprehensive dataset for analyzing the qualities of amino acid insertion/deletions(indels), substitutions and the relationship between them.
SCOP Tree provides information grouped by the classification of SCOP(Structural Classification of Proteins). Match records have been gathered from PDBeFold and can be retrieved from Match label. All of the Indel ... [Information of the supplier]
Factual databases
http://indel.bioinfo.sdu.edu.cn/
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From a Keyword or the PDB entry of a complex, you can browse: Chain homologs for every chain in other complexes; Structural interologs for every interface; Retrieve interface structures, superimposed interologs structures, and pre-computed sequence alignments in diverse species.
If you don't know what is InterEvol or how to use it, please visit the FAQ and the help page.
[Information of the supplier]
Factual databases
http://biodev.cea.fr/interevol
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35.
JASPAR database
JASPAR is a collection of transcription factor DNA-binding preferences, modeled as matrices. These can be converted into Position Weight Matrices (PWMs or PSSMs), used for scanning genomic sequences.
JASPAR is the only database with this scope where the data can be used with no restrictions (open-source). For a comprehensive review of models and how they can be used, please see the following reviews: DNA binding sites: representation and discovery. In: Bioinformatics. 2000 Jan;16(1):16-23; Applied ... [Information of the supplier]
Factual databases
http://jaspar.genereg.net/
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The membrane organization and subcellular location of a protein can provide information about its functional role. Historically, these data have been difficult to produce on a large scale for higher eukaryotic organisms. However, recent advances in membrane organization prediction methods and high-throughput subcellular localization assays have made it possible to generate these datasets. LOCATE is a curated, web-accessible database that houses data describing the membrane organization and subcellular ... [Information of the supplier]
Factual databases
http://locate.imb.uq.edu.au/
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Mass spectrometry (MS)-based proteomics has become a powerful technology to map the protein composition of organelles, cell types and tissues. In our department, a large-scale effort to map these proteomes is complemented by the Max-Planck Unified (MAPU) proteome database. MAPU contains several body fluid proteomes; including plasma, urine, and cerebrospinal fluid. Cell lines have been mapped to a depth of several thousand proteins and the red blood cell proteome has also been analyzed in depth. ... [Information of the supplier]
Factual databases
http://www.mapuproteome.com/
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The Membrane Protein Data Bank (MPDB) is an online, searchable, relational database of structural and functional information on integral, anchored and peripheral membrane proteins and peptides. Data originates from the Protein Data Bank and other databases, and from the literature. Structures are based on X-ray and electron diffraction, nuclear magnetic resonance and cryoelectron microscopy. The MPDB is searchable online by protein characteristic, structure determination method, crystallization technique, ... [Information of the supplier]
Factual databases
http://www.mpdb.tcd.ie/
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This website provides a current list of membrane protein structures determined by x-ray and electron diffraction with links to the Protein Data Bank and other useful sites. Although this database emphasizes structures determined by diffraction methods, some NMR structures are included as well. [Information of the supplier, modified]
Factual databases
http://blanco.biomol.uci.edu/mpstruc/
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MfunGD provides a resource for annotated mouse proteins and their occurence in protein networks. Protein function annotation is performed using the Functional Catalogue (FunCat) annotation scheme, which is a hierarchically structured classification system (Ruepp et al., NAR, 2004). To provide up-to-date similarity search results and InterPro domain analyses, the protein entries are interconnected with the SIMAP database (Rattei et al., NAR, 2006). The gene models are based on the RefSeq mouse cDNAs ... [Information of the supplier]
Factual databases
http://mips.helmholtz-muenchen.de/genre/proj/mfungd/
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