COACH-D: protein-ligand binding site prediction with refiend ligand pose by molecular docking

COACH-D

Introduction

COACH-D is an improved version of the COACH server 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

Submit

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

Or upload the protein structure file:

Provide the ligand file (optional)

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

Other information (optional)

Email: (Optional, where the results will be sent to)

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

Keep my results private (check this box if you want to keep your job private. A key will be assigned for you to access the results)

References

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).

J Yang, A Roy, Y Zhang, Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment, Bioinformatics, 29: 2588-2595 (2013).