I don't know whether your question is specifically for protein-ligand interactions, protein-protein interactions, internal protein interactions, etc., but one place to start is to look at some of the database tools already available on-line, including, for example, CREDO from Tom Blundell's group, which is a nice database of pairwise interactions (intra- and intermolecular) between ligands and proteins.
There are also commercial products that do interaction searches in the PDB, but they are quite expensive. ------------------------------------------------ P. Shing Ho, Ph.D. Professor & Chair Biochemistry & Molecular Biology 1870 Campus Delivery Colorado State University Fort Collins, CO 80523-1870 970-491-0569 (phone) From: Katherine Sippel <katherine.sip...@gmail.com<mailto:katherine.sip...@gmail.com>> Reply-To: Katherine Sippel <katherine.sip...@gmail.com<mailto:katherine.sip...@gmail.com>> Date: Monday, October 28, 2013 12:23 PM To: "CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>" <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> Subject: [ccp4bb] Data mining interactions in the PDB Hi all, I was wondering if anyone knew of a software or server to mine the PDB for a specific class of interactions? I've tried PDBeMotif without much luck and I thought I'd check to see if there was an alternative before I go re-inventing the wheel. Cheers, Katherine -- "Nil illegitimo carborundum" - Didactylos
