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There is a server at the Yale site, but if you want to play around more with the parameters, you can download the whole package and run it locally without too much trouble. There are some options which are not available through the server. The documentation is not great, however. The Gerstein package also contains the entropy-based methods (at least some). My problem is really knowing where to go once one gets the results... Jacob ******************************************* Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: [log in to unmask] ******************************************* ----- Original Message ----- From: "Tommi Kajander" <[log in to unmask]> To: <[log in to unmask]> Sent: Monday, January 18, 2010 4:10 PM Subject: Re: [ccp4bb] SCA yes, other people can comment probably but i think entropy based estimates are better (as i remember less dependent on sample set size). and indeed yale has a server. which may or may not do what you want. secondly its not proper to distributed ohter people's software w/o their permission (actuaally its abs wrong, if not illegal, availibility is anohter question of course...). i would advise to look at papers on entropy based measures of coupling and write to the authors. my two cents..., tommi Quoting "Jacob Keller" <[log in to unmask]>: > Hi Azadeh, > > I looked into this and other related methods extensively once, and came > out with the understanding that SCA is not really the best of this type > of analysis (you can read some of the papers out there which analyze the > several methods). I found that the java package from Mark Gerstein's > group at Yale does any/all of the analyses in parallel (if you want) and > is relatively easy to set up. The best, as I recall, was the one based > on: > > Gobel,U. et al. (1994) Correlated mutations and residue contacts in > proteins. > Proteins: Struct. Funct.Genet., 18, 309-317. > > I think you need an MTA for the actual SCA software, as well. > > Jacob > > ******************************************* > Jacob Pearson Keller > Northwestern University > Medical Scientist Training Program > Dallos Laboratory > F. Searle 1-240 > 2240 Campus Drive > Evanston IL 60208 > lab: 847.491.2438 > cel: 773.608.9185 > email: [log in to unmask] > ******************************************* > > ----- Original Message ----- > From: Azadeh Shahsavar > To: [log in to unmask] > Sent: Monday, January 18, 2010 4:25 AM > Subject: [ccp4bb] SCA > > > Dear all, > > Does anyone have the current (or old) version of SCA? (SCA: statistical > coupling analysis) > It should be as a toolbox of Matlab software. > > Thank you in advance, > Azadeh > -- Tommi Kajander, Ph.D. Macromolecular X-ray Crystallography Research Program in Structural Biology and Biophysics Institute of Biotechnology P.O. Box 65 (Street address: Viikinkaari 1, 4th floor) University of Helsinki FIN-00014 Helsinki, Finland Tel. +358-9-191 58903 Fax +358-9-191 59940