Footprinting protein functional surfaces by comparative spatial patterns. fPOP provides the spatial patterns of protein binding sites including both holo and apo forms from more than 40,000 structures. This database provides an easily accessible resource for studying functional surfaces, assessing conformational changes between bound and unbound forms and analyzing functional divergence.
Allows users to visualize the ion distributions and provides a summary on quantitative analysis of distributions. IDPM contains several web pages that show different information: (1) the main page, where the distributions of ions are shown in two formats; (2) the introduction page, that supplies the background of the study; (3) the method page, that describes how the datasets are obtained and analyzed; or (4) the amino acid page, that summarizes ion distributions and key observations.
Provides an ultimate resource for functional site classifications in intrinsically disordered proteins (IDPs). DisBind is a database dedicated to residue-level classification of functional binding sites in disordered and structured regions of intrinsically disordered proteins. This resource compiles information from the structural database (protein databank), the database of experimentally validated disordered proteins (DisProt), and the comprehensive protein sequence and functional database (UniProt).
A database of predicted multiple, possibly overlapping, protein-protein interaction (PPI). JET2 Viewer reports putative protein binding sites for all three-dimensional (3D) structures available in the Protein Data Bank (PDB). This knowledge base was generated by applying the computational method JET2 at large-scale on more than 20,000 chains. JET2 strategy yields very precise predictions of interacting surfaces and unravels their evolutionary process and complexity. JET2 Viewer provides an online intelligent display, including interactive 3D visualization of the binding sites mapped onto PDB structures and suitable files recording JET2 analyses. Predictions were evaluated on more than 15,000 experimentally characterized protein interfaces. The data can be used to foster new strategies for PPI modulation and interaction surface redesign.
Facilitates the exploration of the Protein Data Bank (PDB). PDBeMotif is a search tools allowing users to combining protein sequence, chemical structure and 3D data in a single search. This resource can serve for studying characteristics of the binding sites of single proteins or classes of proteins, such as kinases and the conserved structural features of their immediate environments, either within the same specie or across different species. It can be used online or downloaded and installed locally.
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