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Poonam Mahapatra

Poonam Mahapatra

Bioinformatics Researcher

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Binding Site Prediction in Protein !: Revision

Binding Site Prediction in Protein !

Binding Site Prediction in Protein !

Last updated 2434 days ago by Poonam Mahapatra

The interaction between proteins and other molecules is fundamental to all biological functions. In this section we include tools that can assist in prediction of interaction sites on protein surface and tools for predicting the structure of the intermolecular complex formed between two or more molecules (docking).

Pockets Identification

open in new windowCASTp

Automatic Identification of pockets and cavities in proteins structure, and quantitation of their volumes using Delaunay triangulation. Available also as PyMOL plugin

open in new windowPocket-Finder

Automatic identification of pockets and cavities in proteins structure, and quantitation of their volumes.

open in new windowPocketPicker

Grid-based technique for the analysis of protein pockets. PocketPicker available as a plugin for PyMOL
 

Binding Site Prediction

open in new windowConSurf

 
Identification of functional regions in proteins by surface-mapping of phylogenetic informationopen in new windowCRESCENDO
 
Identification protein interaction sites. It uses sequence conservation patterns in homologous proteins to distinguish between residues that are conserved due to structural restraints from those due to functional restraints.  
 
Ligand Binding Sites
 
The server utilizes protein-structure prediction to provide structural models of the binding site. Ligands bound to structures are superimposed onto the model and use to predict the binding site.
 
 
A threading-based method for ligand-binding site prediction and functional annotation based on binding-site similarity across superimposed groups of threading templates.
 

LIGSITEcsc

Prediction of binding site by pocket identification using the Connolly surface and degree of conservation

 
metaPocketA meta server for ligand-binding site prediction. metaPocket use LIGSITEcsc, PASS, Q-SiteFinder and SURFNET
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