Hello MODELLERs,

The following workshop should be of interest to researchers subsribing to this list; especially those wanting to refine structures generated with MODELLER.

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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@psc.edu