Dear Jessica,
The Small Molecule Drug Discovery Suite and the Software "Maestro" of Schrödinger could be very useful. But it is not free. https://www.schrodinger.com/suites/small-molecule-drug-discovery-suite You could map or predict binding sites of your protein of interest and determine which amino acids could be part of the binding pocket. However, I don't think it will be considered a quantitative description of the binding pocket, because you will be using a static conformation of the protein if you use a crystal structure from the PDB. You could also try molecular docking and MM-GBSA calculations to predict which residues could interact with the ligand and indirectly quantify the electrostatic and hydrophobic contribution from each amino acid. Best, Pedro De la Torre. Sotomayor Lab. ________________________________ From: CCP4 bulletin board <[email protected]> on behalf of Jessica M. Carpenter <[email protected]> Sent: Tuesday, June 11, 2019 4:02 PM To: [email protected] Subject: [ccp4bb] Characterizing a binding pocket Dear all, Can any of you recommend softwares/web servers/programs to calculate the volume, hydrophobicity, and electrostatics of a binding pocket in a protein structure? I am trying to quantitatively describe the heme binding pocket of a protein by characterizing the residues surfacing the pocket/cavity. Thank you very much. Jessica Carpenter Graduate student Department of Chemistry Dartmouth College Hanover, NH 03755 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
