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: j-kell...@northwestern.edu
*******************************************
----- Original Message -----
From: "Tommi Kajander" <tommi.kajan...@helsinki.fi>
To: <CCP4BB@JISCMAIL.AC.UK>
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" <j-kell...@md.northwestern.edu>:
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: j-kell...@northwestern.edu
*******************************************
----- Original Message -----
From: Azadeh Shahsavar
To: CCP4BB@JISCMAIL.AC.UK
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
