Introduction

COACH-D is a template-based algorithm for protein-ligand binding site prediction. First, five individual methods are used to predict the ligand-binding pockets and residues. Then the ligands (from the templates or the user) are the docked into the binding pockets. One of the major improvements of COACH-D over COACH are the ligand-binding poses are refined to make them physically more realistic, using the efficient molecular docking algorithm AutoDock Vina. In addition, COACH-D has a new option to accept the submission of ligand. Read more about the COACH-D algorithm...

The major results returned by COACH-D include:

• One predicted 3D structure model for the submissions with protein sequence
• The top five protein-ligand binding pockets and the binding residues in each pocket
• The top five protein-ligand complex structures docked with the submitted ligand
• The top five protein-ligand complex structures docked with the ligands from the template structures
• A summary of ligands that are possible to bind the protein

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Provide the protein data (mandatory)

Input protein data below: (either structure in PDB format or sequence in FASTA format).   Click for an example PDB input,    Click for an example FASTA input

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Upload your ligand file below (in MOL2, PDB or SDF format). Download an example input in MOL2,   PDB,   SDF

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Target name: (Optional, your given name to this target)

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Reference

Q Wu, Z Peng, Y Zhang, J Yang, COACH-D: improved protein-ligand binding site prediction with refined ligand-binding poses through molecular docking, Nucleic Acids Research, 46: W438–W442 (2018).