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:

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, in press (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).