From chemistry-request[ AT ]server.ccl.net Fri Jun 2 22:04:06 2000 Received: from relay2.scripps.edu (relay2.scripps.edu [137.131.200.30]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id WAA00652 for ; Fri, 2 Jun 2000 22:04:06 -0400 Received: from goliath.scripps.edu (goliath.scripps.edu [137.131.108.88]) by relay2.scripps.edu (8.9.3/TSRI-3.2.0r) with ESMTP id TAA21174; Fri, 2 Jun 2000 19:02:01 -0700 (PDT) Received: from goliath (goliath [137.131.108.88]) by goliath.scripps.edu (8.9.2/TSRI-3.0.1) with ESMTP id TAA280734; Fri, 2 Jun 2000 19:02:00 -0700 (PDT) Date: Fri, 2 Jun 2000 19:02:00 -0700 From: "Garrett M. Morris" To: Simon Cross cc: chemistry(+ at +)ccl.net Subject: Re: CCL:AUTODOCK 3.0 In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Simon, On Fri, 2 Jun 2000, Simon Cross wrote: > Has anyone used soft potentials with Autodock 3.0, or used other AutoGrid 3.1 has not yet been released, but it has a new form of pairwise potential smoothing, which ramps the potential to a finite value at separation zero. This finite value can be varied by the user, and so could help dramatically in the early stages of the docking. > methods to overcome problems with 'gating' in a fixed receptor? I > am specifically working on antibodies and find that Autodock can > only reproduce the ligand location in the crystal structure if it > is initiated within the binding pocket - if the ligand is placed Are you using SA (simulated annealing) to do this? You can only start the ligand at a pre-defined position using SA and LS (Solis and Wets). The GA and LGA start from a population of random initial genomes. > outside the binding pocket it docks in the correct location but > only 'half in' the pocket, presumably due to the lack of > flexibility of the antibody in this system. The LGA is the most efficient search method: SA seems to be the least efficient. You should get better results with the LGA than with the SA, for the same number of energy evaluations. We found this even though both were started from random initial states or populations of states. If you are using LGA, with a population size of 50, an elitism number of 1, and a crossover rate of 0.80, you might want to try increasing elitism to 5. Then there is a 20% chance that one of the top five do not experience crossover, and thus will survive into the next generation. Another pointer: increase the maxium number of evaluations, by a factor of 10. This might help to improve the search results. > I am trying to get around this by using soft potentials but am not > entirely sure how to do this. Any comments much appreciated. > > ----------------------------------------- > > Simon Cross > School of Chemistry > University of Nottingham > tel. 0115 9514193 > Email: pcxsc "-at-" nottingham.ac.uk > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY#* at *#ccl.net -- To Everybody | CHEMISTRY-REQUEST#* at *#ccl.net -- To Admins > MAILSERV ^%at%^ ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH -A_T- ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl.,at,.ccl.net I hope this helps, Garrett ___ Dr Garrett M. Morris, MA, DPhil The Scripps Research Institute, tel: (858) 784-2292 Dept. Molecular Biology, MB-5, fax: (858) 784-2860 10550 North Torrey Pines Road, email: garrett |-at-| scripps.edu La Jolla, CA 92037-1000, USA. www.scripps.edu/pub/olson-web/gmm