FYI, CCP4 release 2.0.6 does not seem to have 'SC' (a very useful program indeed) in the list of programs in the GUI. This is on Linux (Generic)Fortunately, the program itself is still included and is perfectly runnable from command line old-school style :)
Artem On Thu, Nov 11, 2010 at 3:57 PM, Mike Lawrence <lawre...@wehi.edu.au> wrote: > Dear Francois, Intekhab > > the correct reference for the Sc statistic is > > Lawrence, M. C. & Colman, P. M. (1993). Shape complementarity at > protein/protein interfaces. J. Mol. Biol. 234, 946-950. > > You can also find a description in the March 2001 CCP4 newsletter (#39). > > I am not certain why you cannot find it within the Windows version - it > should simply be called "SC". > > sincerely > > Mike > > 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 > > > > > > > > > Hi, > > > > This is the first time I read about "shape complementarity statistics". > > > > According to: > > "A structural basis for the activity of retro-Diels–Alder catalytic > > antibodies: Evidence for a catalytic aromatic residue" > > > > As seen here: > > http://www.pnas.org/content/99/15/9674.full > > > > --- > > [...] compute the SHAPE COMPLEMENTARITY STATISTICS index (Sc). This > > statistics index measures the geometric surface complementarity via the > > use of normal products, and the extent to which the interacting surface > > elements are brought into proximity via an exponential distance > > separation term. Sc values usually range from 0.70 to 0.76 for > > proteinase–protein inhibitor surfaces, from 0.64 to 0.68 for > > antigen–antibody complexes, and from 0.45 to 0.70 for MHC–peptide > > complexes (30). > > --- > > > > I am frightened. :( > > I don't think this is in my book "The cartoon guide > > to statistics". Despite the book is really nice. > > > > Regards, > > F. > > > > intekhab alam wrote: > >> I want to calculate the shape comlementarity statitics (SC) of a dimeric > >> protein using CCp4. I am using CCP4 6.1.3 on windows but the SC program > >> is not available in that suite. > >> Which version of CCP4 has that program. Are there any other programs > >> that can calculate that. > >> > >> Thanks > >> > >> -- > >> INTEKHAB ALAM > >> LABORATORY OF STRUCTURAL BIOINFORMATICS > >> KOREA UNIVERSITY, SEOUL > > > > > > ______________________________________________________________________ > 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. > ______________________________________________________________________ >
