Re: [ccp4bb] Data mining interactions in the PDB
If you are interested in finding other interactions that look like one particular one, rather than just classifying things (e.g., is this cyan, sea-foam, turquoise or teal?), then I'd recommend the substructure searching capabilities of the DrugSite server You can specify any arbitrary segments of an existing structure (by residue ranges, small or large) and find all other structures that have the same backbone geometry. If the target residue segments are from different molecules in a known complex, it will find similar complexes. The server returns coordinates overlaid using only the residues in your defined target. https://drugsite.msi.umn.edu/ Barry C. Finzel Medicinal Chemistry Department University of Minnesota finze...@umn.edu On Oct 28, 2013, at 1:23 PM, Katherine Sippel wrote: 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
[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
Re: [ccp4bb] Data mining interactions in the PDB
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.commailto:katherine.sip...@gmail.com Reply-To: Katherine Sippel katherine.sip...@gmail.commailto:katherine.sip...@gmail.com Date: Monday, October 28, 2013 12:23 PM To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK CCP4BB@JISCMAIL.AC.UKmailto: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
Re: [ccp4bb] Data mining interactions in the PDB
Katherine I am not exactly sure what sort of tool you would like to use, but there are a couple of options found here... http://www.ebi.ac.uk/pdbe-as/pdbetemplate/ The last option DB search http://www.ebi.ac.uk/pdbe-as/pdbesearch/ allows you upload a fragment of structure - a small number of residues that are arranged in space, typically an active site. For example, you can upload an example of the catalytic triad (or quartet) as a PDB file. You need only provide the atom records for 6 or less residues cut out of a normal PDB file from any source. This will search the entire PDB for this arrangement of residues based on the CA atoms or side chain atoms; the latter is slower and can take a minute. The search will either match residue type exactly with geometry, or match similar residues (ie acid to acid). The three other tools from the main page http://www.ebi.ac.uk/pdbe-as/pdbetemplate/ allow you carry out various analysis of the PDB using a pre calculated set of residue arrangements such as the catalytic triad / quartet. These 1972 residue arrangements (some are active sites) were generated by statistical data mining using a Bayesian statistical methods to identify these residue patterns. You can browse these: http://www.ebi.ac.uk/pdbe-as/pdbetemplate/DMfragmentsBrowse.jsp search 1 protein with 1 fragment : http://www.ebi.ac.uk/pdbe-as/pdbetemplate/DMSingleFit.jsp or label a single protein with all the 1972 data mined fragments. A sort of auto-annotation of a structure with predefined fragments. You should be aware that the fragment database was calculated using a mathematical target which does not say what biological role of the fragments in the data. They are provided as a means to carry out your own research. Tom 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 No virus found in this message. Checked by AVG - www.avg.com http://www.avg.com Version: 2014.0.4158 / Virus Database: 3614/6764 - Release Date: 10/19/13
Re: [ccp4bb] Data mining interactions in the PDB
On 10/29/2013 03:23 AM, Katherine Sippel wrote: 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. Maybe this one (SuMo): http://sumo-pbil.ibcp.fr/cgi-bin/sumo-welcome paper: http://bioinformatics.oxfordjournals.org/content/21/20/3929.full Or this one (Drugsite): https://drugsite.msi.umn.edu. paper: http://pubs.acs.org/doi/abs/10.1021/ci4002537 Cheers, Katherine -- Nil illegitimo carborundum/- /Didactylos -- Best regards, Francois Berenger. https://www.linkedin.com/in/fberenger
Re: [ccp4bb] Data mining interactions in the PDB
How about this server http://iris.physics.iisc.ernet.in/psap/ On 10/29/2013 03:23 AM, Katherine Sippel wrote: 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. Maybe this one (SuMo): http://sumo-pbil.ibcp.fr/cgi-bin/sumo-welcome paper: http://bioinformatics.oxfordjournals.org/content/21/20/3929.full Or this one (Drugsite): https://drugsite.msi.umn.edu. paper: http://pubs.acs.org/doi/abs/10.1021/ci4002537 Cheers, Katherine -- Nil illegitimo carborundum/- /Didactylos -- Best regards, Francois Berenger. https://www.linkedin.com/in/fberenger -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. Could you kindly confirm the safe receipt of the mail please. All best wishes and regards, Yours sincerely, Dr. K. Sekar, Ph.D. Associate Professor Supercomputer Education and Research Centre Room No. 341, old Ecological Sciences Building (Second Floor) Indian Institute of Science Bangalore 560 012 INDIA E-mail:se...@physics.iisc.ernet.in se...@serc.iisc.ernet.in Tel: 91-(0)80-22933059/22933060/23600551 Fax: 91-(0)80-23600085 Home page: http://www.physics.iisc.ernet.in/~dichome/sekhome/index.html -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
