COACH-D: template-based protein-ligand binding site prediction

COACH-D

Introduction

COACH-D is a template-based algorithm for protein-ligand binding site prediction. Ligand-binding pockets are first predicted using homologous templates from the Q-BioLiP database. Then ligands (from templates or user submission) are docked into the predicted binding pockets using AutoDock Vina. In the 2024 update, the template search procedure has been accelerated by at least two times using Foldseek, without loss of precision. In addition, both monomeric and multimeric structures are supported. It takes 0.5-3 hours to complete the prediction for an input structures of about 300 residues. Read more about the COACH-D algorithm...

The supported input formats for protein include:

Monomeric structure or sequence
Multimeric structure

The output results include:

The top five protein-ligand complex structures with submitted ligand
The top five protein-ligand complex structures with template ligands
A summary of ligands that may potentially bind to the protein

Submit

Provide the protein data (mandatory)

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

Or upload the protein structure/sequence file:

Provide the ligand file (optional)

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

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).