The input of COACH-D can either be the sequence or the structure of the query protein. Users can also submit a query ligand for docking.
As shown in Figure 1, the COACH-D workflow is as follows:
As shown in Figure 1, the COACH-D workflow is as follows:
(1) If the sequence of the query receptor (monomer only) is provided, the I-TASSER Suite or AlphaFold2 will be used to predict the receptor's structure.
(2.1) If the structure is a monomer, it will be processed by five individual methods (TM-SITE, S-SITE, COFACTOR, FINDSITE and ConCavity ) to predict the protein-ligand
binding pockets and residues. Four of these methods make predictions by searching the query structure/sequence through the Q-BioLiP and BioLiP template libraries.
(2.2) If the structure is a multimer, it will be processed by the quaternary-based method Q-SITE.
(3) Both template-searched ligands and user-submitted ligand are docked into the predicted binding pockets using the efficient docking algorithm AutoDock Vina.
(2.1) If the structure is a monomer, it will be processed by five individual methods (TM-SITE, S-SITE, COFACTOR, FINDSITE and ConCavity ) to predict the protein-ligand
binding pockets and residues. Four of these methods make predictions by searching the query structure/sequence through the Q-BioLiP and BioLiP template libraries.
(2.2) If the structure is a multimer, it will be processed by the quaternary-based method Q-SITE.
(3) Both template-searched ligands and user-submitted ligand are docked into the predicted binding pockets using the efficient docking algorithm AutoDock Vina.
Figure 1. The flowchart of the COACH-D algorithm.
Job submission guide:
(1) Input or upload a protein sequence in FASTA format(only supports single chain) or a protein structure in PDB, mmCIF format(supports single-chain & multi-chains).
(2) Provide the ligand file(optional).
(3) Choose whether to keep your results private.
(4) Submit.
Notice: Due to computing resource limitation, we now allow no more than 5 running/pending jobs per user at the same time.
(2) Provide the ligand file(optional).
(3) Choose whether to keep your results private.
(4) Submit.
Notice: Due to computing resource limitation, we now allow no more than 5 running/pending jobs per user at the same time.
Figure 2. The submission page of COACH-D.
There are separate download links for the following:
(1) The submitted protein
(2) The submitted ligand (optional)
(3) AZIP file containing the main results
(2) The submitted ligand (optional)
(3) A
Figure 3. The download link of COACH-D.
The COACH-D results are usually summarized in a web page that consists of three sections:
(1) The display frame of COACH-D results.
(2) The main results table of COACH-D.
(3) Summary of template ligands.
(1) The display frame of COACH-D results.
(2) The main results table of COACH-D.
(3) Summary of template ligands.
(1) The display frame of COACH-D results.
This section displays the predicted binding of five pockets to the ligand.
The "Predicted complex" box on the left visualizes the predicted binding sites and complex structure.
The "Current complex Information" box on the right summarizes the details of the current displayed structure.
This section displays the predicted binding of five pockets to the ligand.
The "Predicted complex" box on the left visualizes the predicted binding sites and complex structure.
The "Current complex Information" box on the right summarizes the details of the current displayed structure.
Figure 4. The display frame of COACH-D results.
(2) The main results table of COACH-D.
This section displays more details about prediction.
Rank : The predicitons are ranked by the C-score.
Poseu: The binding pose of the ligand submitted by user.
Poset: The binding pose of the ligand obtained from the PDB template.
Cscore: The confidence score of the prediction. C-score ranges [0-1], where a higher score indicates a more reliable prediction.
Cluster Size : The number of protein template in a cluster.
P Template : The representative protein template in a cluster.
L Template: The representative ligand template in a cluster.
Predicted binding residues: The consensus prediciton based on spatial clustering of the predicted binding sites from individual methods.
Poseu: The binding pose of the ligand submitted by user.
Poset: The binding pose of the ligand obtained from the PDB template.
Cscore: The confidence score of the prediction. C-score ranges [0-1], where a higher score indicates a more reliable prediction.
Cluster Size : The number of protein template in a cluster.
P Template : The representative protein template in a cluster.
L Template: The representative ligand template in a cluster.
Predicted binding residues: The consensus prediciton based on spatial clustering of the predicted binding sites from individual methods.
Figure 5. The main results table of COACH-D.
(3) Summary of template ligands.
This section displays the ligand information for the "Rank 1" model from the table above, excluding the representative ligands listed in the "L Template" column.
Rank: The ligands are ranked by their frequencies in the cluster.
Ligand: Click on the ligand ID to view more information in the Q-BioLiP database and click the button to download the SDF file.
Frequency: The total number of times the ligand occuring in the cluster.
PDB template: The PDB structures in the cluster that bind the ligand. At most 20 templates are listed for each ligand.
Visualization: A visualization of the ligand.
Ligand: Click on the ligand ID to view more information in the Q-BioLiP database and click the button to download the SDF file.
Frequency: The total number of times the ligand occuring in the cluster.
PDB template: The PDB structures in the cluster that bind the ligand. At most 20 templates are listed for each ligand.
Visualization: A visualization of the ligand.
Figure 6. Summary table of template ligands.
Please cite the following article when you use the COACH-D server:
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).
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).
If you have more questions or comments about the server, please email yangjy@sdu.edu.cn.