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Molecular Docking

After identification of drug target, next challenge is to design drug or inhibitor against target. Molecular docking is not only important for designing drug against a target but also required for predicting binding between molecules. This page provides list of computational resources developed for molecular docking particularly for predicting inhibitors against drug targets.

Webservers for Molecular Docking (Raghava's Group)

  1. GDoQ: Model for prediction of GLMU inhibitors using QSAR and docking approach.
  2. KiDoQ: Prediction of inhibition constant using docking and QSAR.
  3. PLDbench: Benchmarking of docking software on peptide-ligand complexes. 
  4. PPDBench:  Benchmarking of docking software on protein-peptide complexes.

External Links to web servers developed/maintained by other groups

This section provides URL/links to important websites developed and maintained by other researchers. It exclude servers by Raghava's group, which is given in above section. 

  1. DOCKSCORE: a webserver for ranking protein-protein docked poses.
  2. DockYard: a repository to assist modeling of protein:protein docking.
  3. PIMADb: A Database of Protein-Protein Interactions in Huge Macromolecular Assemblies.
  4. PocketAnnotate: towards site:based function annotation.
  5. PocketDepth: a new depth based algorithm for identification of ligand binding sites in proteins.
  6. TPACM4: A fast empirical GAFF compatible partial atomic charge assignment scheme for modeling interactions of small molecules with biomolecular targets.