Binding Pocket and Binding Site Prediction
IBIS is the NCBI Inferred Biomolecular Interactions Server. For a given protein sequence or structure query, IBIS reports physical interactions observed in experimentally-determined structures for this protein. IBIS also infers/predicts interacting partners and binding sites by homology, by inspecting the protein complexes formed by close homologs of a given query.
http://www.ncbi.nlm.nih.gov/Structure/ibis/ibis.cgi
Pocket-Finder is a pocket detection algorithm based on Ligsite written by Hendlich et al (1997). Pocket-Finder works by scanning a probe radius 1.6 angstoms along all gridlines of a grid resolution 0.9 angstroms surrounding the protein.
http://www.modelling.leeds.ac.uk/pocketfinder/
FINDSITE is a threading-based binding site prediction/protein functional inference/ligand screening algorithm that detects common ligand binding sites in a set of evolutionarily related proteins. Crystal structures as well as protein models can be used as the target structures.
http://cssb.biology.gatech.edu/findsite
LIGSITE is a web server for the automatic identification of pockets on protein surface using the Connolly surface and the degree of conservation!
http://projects.biotec.tu-dresden.de/pocket/
PocketPicker - Binding Site Prediction
http://gecco.org.chemie.uni-frankfurt.de/pocketpicker/index.html
metaPocket is a meta server to identify pockets on protein surface to predict ligand-binding sites!
http://metapocket.eml.org/
castP server uses the weighted Delaunay triangulation and the alpha complex for shape measurements. It provides identification and measurements of surface accessible pockets as well as interior inaccessible cavities, for proteins and other molecules.
http://sts.bioengr.uic.edu/castp/
3DLigandSite is an automated method for the prediction of ligand binding sites.
http://www.sbg.bio.ic.ac.uk/~3dligandsite/
Fast Prediction and Visualization of Protein Binding Pockets.
http://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py?form=PASS
The MEDock (Maximum-Entropy based Docking) web server is aimed at providing an efficient utility for prediction of ligand binding site.
http://medock.ee.ncku.edu.tw/
Q-SiteFinder is a new method of ligand binding site prediction. It works by binding hydrophobic (CH3) probes to the protein, and finding clusters of probes with the most favourable binding energy. These clusters are placed in rank order of the likelihood of being a binding site according to the sum total binding energies for each cluster.
http://www.modelling.leeds.ac.uk/qsitefinder/
Protein binding site prediction with an empirical scoring function.
http://sparks.informatics.iupui.edu/PINUP/
Metal ion binding sites, affinities, and specificities from structure
http://protinfo.compbio.washington.edu/soak/
The aim of this server is to predict MHC Class-II binding regions in an antigen sequence, using quantitative matrices.
http://www.imtech.res.in/raghava/propred/
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