On 09:50 Tue 14 Sep , Dirk Kostrewa wrote: > I would spend some time in improving the search model, first. If there > are more than one possible search molecules in the PDB, I usually do a > structural alignment (ssm superposition) to get an idea about the > flexibility of the search molecules. Then I remove all parts that I > suspect to be flexible (usually N- and C-termini, long loops), until I > get a very compact search model.
Dirk, If you aren't already doing this automatically, you could save some time next time around by using the MUSTANG-MR server <http://pxgrid.med.monash.edu.au:8080/mustangserver/>. It does the second part (finding conserved structural regions) automatically with a variety of RMSD cutoffs. We've recently had some success on a difficult case by coupling the SSM and MUSTANG-MR servers, using the top ~10 SSM results (up to ~3 Å RMSD on common regions) and a 1.4 Å MUSTANG cutoff. -- Thanks, Donnie Donald S. Berkholz, Ph.D. Research Fellow James R. Thompson lab, Physiology & Biomedical Engineering Grazia Isaya lab, Pediatric & Adolescent Medicine Medical Sciences 2-66 Mayo Clinic College of Medicine 200 First Street SW Rochester, MN 55905 office: 507-538-6924 cell: 612-991-1321
pgpgKe946izdO.pgp
Description: PGP signature
