From owner-chemistry@ccl.net Sun Nov 13 13:17:01 2005 From: "Dr. Csaba Hetenyi csaba:-:ovrisc.mdche.u-szeged.hu" To: CCL Subject: CCL: AutoDock3 and shuffled peptide sequences Message-Id: <-29957-051113084511-32037-FZTTgN0XTxTZiNiJgQRmpg++server.ccl.net> X-Original-From: "Dr. Csaba Hetenyi" Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Sun, 13 Nov 2005 14:00:59 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: "Dr. Csaba Hetenyi" [csaba[#]ovrisc.mdche.u-szeged.hu] Hi, For larger peptides larger number of energy evaluations and population size may be necessary. For validation of the parameters of LGA it is necessary to measure RMSD between the X-ray position and the docked peptide. Grid spacing of .3 A helps in some cases. You may trust your results and actual LGA (grid) parameter setup after validation. Best, Csaba On Sat, 12 Nov 2005, Starr Hazard hazards+*+musc.edu wrote: > Sent to CCL by: Starr Hazard [hazards|-|musc.edu] > Folks, > > I am examining the docking of a hexapeptide to a protein with AutoDock3. I > generated some initial results and sought to examine specificity. I > shuffled the sequence (ie left amino acid content constant and altered the > sequence order) and tried to AutoDock3 again. In many cases the shuffled > sequences show better scores than the original sequences. > > The shuffled and "wildtype" sequences were docked under similar ie mostly > default conditions. Have I shown that the binding is none specific or have > just got a sampling error? > > Starr > > > Starr> > > > ------ Csaba Hetenyi, MSc, PhD Dept. of Medical Chemistry, University of Szeged, 8 Dom ter, Szeged 6720, Hungary