Hi Brett, SC was not developed for this purpose and hence may not be very useful with its default parametrization. Nevertheless, it could be useful for cross-comparing the complementarity of different inhibitors to the same site, but I have not experimented this. The TRIM parameter may need to be reduced in order to allow interrogation of a large percentage of the solvent inaccesible surface. If you try this, please let me know how well it works.
sincerely Mike Lawrence, PhD Associate Professor and WEHI Fellow Division of Structural Biology Walter and Eliza Hall Institute of Medical Research 1G Royal Parade, Parkville Victoria 3052, AUSTRALIA Tel. 61-3-9345-2693 Fax 61-3-9345-2686 Email: lawre...@wehi.edu.au On 11/09/2013, at 6:56 AM, Brett, Thomas wrote: > Hi all: > If have used SC previously to calculate shape complimentarity for > macromolecular complexes. Can this also be used to calculate shape > complimentarity for a (say) protein/small molecule inhibitor complex? Or is > there some other metric/software that can/should be used to quantitate how > well a small molecule fits a pocket? > thanks > -tom > > > Tom J. Brett, PhD > Assistant Professor of Medicine > Division of Pulmonary and Critical Care > Washington University School of Medicine > Campus Box 8052, 660 S. Euclid > Saint Louis, MO 63110 > http://brettlab.dom.wustl.edu/ ______________________________________________________________________ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. ______________________________________________________________________
