AMBER Archive (2003)

Subject: PSC Summer Workshop: Modeling from Protein Sequence to Structure

From: Troy Wymore (wymore_at_psc.edu)
Date: Thu Apr 24 2003 - 12:33:39 CDT

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PSC BIOMEDICAL INITIATIVE WORKSHOP 2003

               MODELING FROM PROTEIN SEQUENCE TO STRUCTURE:
               COMPUTATIONAL TOOLS FOR STRUCTURE PREDICTION
               June 2-5
               Application Deadline: April 30
               Primary Instructor: Prof. Charles Brooks (Scripps)

This workshop will introduce researchers to computational tools
(the MMTSB Tool Set available at http://mmtsb.scripps.edu) aimed
at predicting structure based on sequence alone, from identification
of suitable homology templates, or through application of secondary-structure
templated de novo folding, as well as refinement and energy calculations
on "ensembles" of molecular structures. This freely available tool set
comprises a perl-based library of applications that interface to the molecular
modeling packages CHARMM and AMBER, and the MONSSTER package for protein
structure prediction. Participants in the workshop will be presented
lectures on molecular modeling theory and practice, protein structure
prediction, loop modeling and energy-based structure refinement.
Advanced sampling methods such as replica-exchange molecular dynamics, as
utilized in structure prediction algorithms, will be discussed.
Practical tutorials exploring the use and application of the
MMTSB tool set will focus on conventional molecular mechanics calculations
of energy, minimization and dynamics as well as loop modeling and
refinement using replica-exchange molecular dynamics and hierarchical
protein structure prediction using de novo (or secondary structure templated) folding
algorithms in the MONSSTER and CHARMM packages. Web-based servers for
protein sequence alignment, secondary structure prediction and homology template
identification will be discussed in the context of their utility to the
overall structure prediction pipeline utilizing the MMTSB Tool Set.

For specific details, including an electronic application form, see:

http://www.psc.edu/biomed/training/workshops/2003/proteomics/index.html

If you have any questions, please contact Nancy Blankenstein at
blankens_at_psc.edu