Re: [ccp4bb] SCA

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: incorrect linkage definitions ?
From: Ethan Merritt merritt {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2010-01-18

Next message:
Subject: Re: incorrect linkage definitions ?
From: Engin Ozkan eozkan {- at -} STANFORD {- dot -} EDU
Date: 2010-01-18

Subject: Re: SCA
From: Tommi Kajander tommi {- dot -} kajander {- at -} HELSINKI {- dot -} FI
Date: 2010-01-18

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" :

> 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-keller2@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

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: incorrect linkage definitions ?
From: Ethan Merritt merritt {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2010-01-18

Next message:
Subject: Re: incorrect linkage definitions ?
From: Engin Ozkan eozkan {- at -} STANFORD {- dot -} EDU
Date: 2010-01-18