Identi fication of Pockets on Protein Surface to Predict Protein–Ligand Binding Sites - Identification of Ligand Binding Site and Protein-Protein Interaction Area - page 37

binding site prediction success rate. Please note that some of these 8 methods might
fail to return any prediction results due to some reasons. This plug-in pattern makes
metaPocket automatically detect the failed methods and the metaPocket algorithm
is only applied to those results from successful methods. The users can provide a
PDB ID and a chain ID or upload their own structures. The metaPocket server will
output the prediction results from eight single methods and the meta-pocket sites of
metaPocket based on those results. The predicted pocket sites and those surround-
ing residues can be downloaded as standard PDB files to be investigated locally by
the users in PyMOL (Delano 2002 ) or directly be visualized on the server based
on JMOL ( http://www.jmol.org ) plug-in. Normally it only takes about 10 seconds
to a few minutes for metaPocket to finish pocket identification depending on the size
of protein. We envisage that our metaPocket web-server will become an all-in-one
tool for protein ligand binding site prediction to the community and provide useful
guide to structure-based functional annotation, site-directed mutagenesis experiments,
protein-ligand docking and large scale virtual screening.
With more and more efforts being made in this field, many free computational
software and web-servers are available for pocket identification and protein-ligand
binding site prediction. The goal of our metaPocket approach is to combine all these
free tools together and improve the ligand-binding site prediction success rate.
We believe that our web-server will provide the users a comprehensive web tool in
protein-ligand binding site prediction. In the future, we will continue working on it
and hope to include more and more algorithms and tools into our metaPocket server.
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