Pocket identification software tools | Protein interaction data analysis
The prediction of functional sites including ligand binding sites or catalytic sites can guide the design of small molecules that could interact with a protein and modulate its function or drive the selection of targeted mutations for protein engineering. It largely relies on the identification and characterization of clefts and cavities in protein structures.
An online tool that locates and measures pockets and voids on 3D protein structures. CASTp includes annotated functional information of specific residues on the protein structure. The annotations are derived from the Protein Data Bank (PDB), Swiss-Prot, as well as Online Mendelian Inheritance in Man (OMIM), the latter contains information on the variant single nucleotide polymorphisms (SNPs) that are known to cause disease.
Allows users to access and preprocess structural data for all kinds of life science research, and gives an immediate visual impression of the overall protein structure and contained ligand molecules. ProteinPlus contains a server for special interest to life scientists with an occasional need to work with protein structures thanks to six services addressing the most important tasks at the beginning of structure analysis (Protoss; PoseView; EDIA; SIENA; DoGSiteScorer; HyPPI). Users can choose an application service of interest, set additional tool configurations and start the calculation.
Generates molecular surfaces and gaps between surfaces from 3D coordinates supplied in a PDB-format file. The gap regions can correspond to the voids between two or more molecules, or to the internal cavities and surface grooves within a single molecule. The program is particularly useful in clearly delineating the regions of the active site of a protein. It can also generate 3D contour surfaces of the density distributions of any set of 3D data points.
Recognizes ligand binding sites for virtual screening and allows de novo drug design. Q-SiteFinder can realize prediction of ligand binding sites by investigating clusters of energetically favorable methyl binding site. It employs the interaction energy between the protein and a simple van der Waals probe to proceed. This tool classifies clustered energetically favorable probe sites according to the sum of interaction energies for sites within each cluster.
Identifies pockets on protein surface using the Connolly surface and the degree of conservation. LIGSITEcsc is a web server that extends the LIGSITE algorithm by defining surface-solvent-surface events and ranking them by the degree of conservation. Four key parameters influence the results: grid size, minimal number of surface-solvent-surface events (MINSSS), the radius of the sphere to calculate the conservation score and the distance threshold for defining hits.
Identifies ligand binding sites on protein surface. metaPocket is a consensus method in which the predicted pocket sites from eight methods (LIGSITECS, PASS, Q-SiteFinder, SURFNET, Fpocket, GHECOM, ConCavity and POCASA) are combined together to improve the prediction success rate. Each of eight single methods is treated as a plug-in in metaPocket. This plug-in pattern makes the server automatically detect the failed methods and the algorithm is only applied to those results from successful methods.