Subject: Cornell Theory Center Computational Biology Tools

From: Eugene Leitl <[email-masked]>
Date: Fri, 24 Sep 1999 17:42:13 -0700 (PDT)

http://www.tc.cornell.edu/reports/NIH/resource/CompBiologyTools/

The NIH "Parallel Processing Resource for Biomedical Scientists" at
the Cornell Theory Center announces a major release of computer
programs for molecular and protein modeling. The code was developed by
the groups of Ron Elber and Harold Scheraga and is released to the
public domain. Although the code is not copyrighted, we expect you to
reference the code to the extent that it helped you in your work. We
further expect that this code will NOT be used as a whole or as a part
of any commercial software.

This release includes the following: 

- protein folding 
The ECEPPAK package. A set of programs based on the ECEPP/3 force
field used to study the conformational properties of polypeptides and
proteins. Among others, ECEPPAK includes computational tools to carry
out global conformational searches at the all-atom level. A parallel
version of the code using MPI is available for an IBM SP.

- molecular dynamics 
The MOIL modeling package to simulate structure, dynamics, and
function of biological molecules at the atomic level of detail. Note
the availability of a Window version in the present release and a
parallel version for stochastic path simulations.

- protein recognition 
The LOOPP program (Linear Optimization Of Protein Potentials).  A
program for potential optimization and alignments. LOOPP aligns
sequence to sequence, sequence to structure, and structure to
structure. It further enables the optimization of potentials and
scoring functions for the above mentioned applications.

- process dihedral angle files 
The ANALYZE package to classify conformations obtained from a global
search into families and compute conformational characteristics such
as RMS deviations and interproton distances.  It can also estimate the
statistical weights of the conformations by fitting the theoretically
calculated average NOE intensities and coupling constants to the
respective experimental data.

A workshop will be held on the Cornell University campus November
15-16, 1999 to provide an in-depth description and hands-on experience
with the software packages that the resource just released to the
public domain. See

http://www.tc.cornell.edu/Events/1999/CompBiologyTools