Hi Rams, You could consider using LigPlot+, generate LigPlots for all 'n' PDB files, and then also superimpose all the plots to see the variations in the protein-ligand interactions of the same ligand bound to different proteins.
Alternatively, you could try to write a program using Coot's lsq ligand; CCP4MG Superpose equivalent ligand (might take some time to do manually or few/many at a time but easy to execute and visualize); try with LSQKAB; or CSD Ligand Overlay (used for ligand-based design when protein structures are unknown). Best, Debanu On Sat, Jul 15, 2023 at 6:56 AM Boaz Shaanan <bshaa...@bgu.ac.il> wrote: > Hi Rams, > It's also worth looking into the Cambridge CSD suit. I'm pretty sure that > there is a routine there for superimposing small molecules, i.e. ligands > which will produce the matrices you need. How to put it on a script is > another question. > Cheers, > Boaz > > Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben Gurion University > Beer Sheva, Israel > > On Jul 15, 2023 15:09, "Subramanian, Ramaswamy" <subra...@purdue.edu> > wrote: > Thanks Boaz, > > The proteins are all completely different in folds and structures! > > > Rams > subra...@purdue.edu > > > > On Jul 15, 2023, at 8:04 AM, Boaz Shaanan <bshaa...@bgu.ac.il> wrote: > > ---- *External Email*: Use caution with attachments, links, or sharing > data ---- > Hi, > -You may want to send a query to the UCSF chimerax/chimera people. They > may suggest how to this using scripts. > - I have not done this on 50 structures, only on few ones. In my > experience, if the proteins are sufficiently similar there is a good chance > that superimposing the proteins will also bring the ligands to near > superposition. > -Using chimera/chimerax you can select protein residues within certain > radius from the ligands, write out the pdb's and then perhaps superimpose > those smaller pdb's. I have not tried this. > Sorry I can't be of more help. > Cheers, > Boaz > > > > > > > > > > > > *Boaz Shaanan, Ph.D. Dept. of > Life Sciences Ben-Gurion University > of the Negev Beer-Sheva > 84105 > Israel > > E-mail: bshaa...@bgu.ac.il <bshaa...@bgu.ac.il> Phone: 972-8-647-2220 > Fax: 972-8-647-2992 or 972-8-646-1710 * > > > > > > > ------------------------------ > *From:* CCP4 bulletin board on behalf of Subramanian, Ramaswamy > *Sent:* Friday, July 14, 2023 10:49 PM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* [ccp4bb] Ligand superposition! > > Hi All, > > I have over 50 pdb files that I have downloaded from PDB that all have the > same ligand bound. > > I wamt to superpose the ligands (and move the protein coordinates using > that matrix). The goal is for me to see how difference in ligand > environments in different complexes. > > Is there an easy way to do it? I am sure it has been done before and I do > not want to reinvent the wheel. > > Thanks. > > > > Rams > subra...@purdue.edu > > > > > ------------------------------ > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > ------------------------------ > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
