COACH
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COACH
Is it possible to use COACH to find the active site of a protein by giving it a docked model of a protein pdb?
Re: COACH
Yes, by providing a docked model of a protein PDB, COACH can analyze the structure and predict the potential ligand binding sites, including the active site where the ligand interacts with the protein. This can be valuable for understanding the mechanism of action of a protein and designing new drugs or therapeutics.MERT YENEN wrote: ↑Mon Aug 19, 2024 7:24 am Is it possible to use COACH to find the active site of a protein by gmoto x3miving it a docked model of a protein pdb?
Re: COACH
COACH is a web server designed for the prediction of protein-ligand binding sites. It integrates multiple predictions and features to provide a consensus result for the likely active site or binding pocket on a protein. To use COACH for predicting the active site based on a protein model, you would typically follow this process:
1. **Prepare the Protein Structure**: You'll need to have the protein structure in PDB format. This means you should already have the docked model of your protein ready.
2. **Submit to COACH**: You would then submit the PDB file to the COACH server. This is usually done through their web interface.
3. **Receive Predictions**: COACH will analyze the submitted model, integrating predictions from multiple methods like COFACTOR and TM-SITE, to identify potential binding sites.
4. **Review Results**: The output will generally highlight potential ligand binding sites, which may correlate with the protein's active site.
While COACH is designed to identify binding pockets, these pockets can often overlap with active sites, especially if the active site of the protein is where ligand binding occurs connections game.
If you're unable to use the COACH server directly, you might want to explore local software that incorporates similar functionalities or reach out to someone who can access the COACH server. Also, note that COACH is best used for predictive purposes; experimental validation is usually required to confirm active sites for specific proteins.
1. **Prepare the Protein Structure**: You'll need to have the protein structure in PDB format. This means you should already have the docked model of your protein ready.
2. **Submit to COACH**: You would then submit the PDB file to the COACH server. This is usually done through their web interface.
3. **Receive Predictions**: COACH will analyze the submitted model, integrating predictions from multiple methods like COFACTOR and TM-SITE, to identify potential binding sites.
4. **Review Results**: The output will generally highlight potential ligand binding sites, which may correlate with the protein's active site.
While COACH is designed to identify binding pockets, these pockets can often overlap with active sites, especially if the active site of the protein is where ligand binding occurs connections game.
If you're unable to use the COACH server directly, you might want to explore local software that incorporates similar functionalities or reach out to someone who can access the COACH server. Also, note that COACH is best used for predictive purposes; experimental validation is usually required to confirm active sites for specific proteins.