Subject: suggestions for secondary structure -> protein structure prediction ?

From: "Jerome Baudry" <jerome-.at.-scs.uiuc.edu>
Date: Tue, 30 Mar 2004 08:48:31 -0600

Dear All

I have NMR information about the secondary structure(s) of several domains
of a protein. Is there a relatively fast way to propose (and rank) different
folding solutions for the complete protein, from the domains assigned with
secondary structures? I was thinking maybe about an homology-modeling-like
approach where PMF of several possible associations for these secondary
elements would be calculated, or a scoring function, or maybe a full
potential energy function, where the assembly of the secondary elements
rigid-body blocks would be automated and somehow combinatorialized....

I am not looking at a folding pathway/trajectory, but at somehow ranking
different final solutions.

Any suggestions of possible approaches/literature/software ?

Thanks a lot in advance...

----------------------------------------------------------
Jerome Baudry, Ph.D.       Senior Research Scientist, VizLab Manager.
School of Chemical Sciences    University of Illinois at Urbana-Champaign
505 S. Mathews Ave.; Box 2.1; Urbana, IL, 61801   Phone: (1) (217) 244 3210;
Fax: (1) (217) 333 3120;    e-mail: jerome-.at.-scs.uiuc.edu