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Practical Innovation at BioCon 2003


Python for Structural Bioinformatics
Sophie Coon, The Scripps Research Institute
Michel Sanner, Ph.D., The Scripps Research Institute

Track: Bioinformatics 2003 Tutorial
Date: Monday, February 03
Time: 8:30am - 12:00pm
Location: Sierra

One of the challenges in bio-computing is to enable the efficient use of a wide variety of rapidly evolving computational methods to simulate, analyze, and understand the complex interactions of molecular systems. The MGL laboratory is interested in the development of novel computational technologies and the application of these technologies to the analysis and understanding of complex systems in structural molecular biology.

Over the past few years, we have developed a number of Python packages to deal with many aspects of structural bio-informatics. These extensions can be combined into a high-level application such as the Python-based Molecular Viewing environment (PMV). PMV is a general purpose molecular visualization and manipulation environment. New commands can be added to extend its capabilities, but more importantly, it has been built using a set of reusable software components, allowing the functionality available in PMV to be reused in other Python-based computational chemistry environments.

After a rapid introduction to the fundamental concepts implemented in PMV, we will walk attendees through the features of PMV. Basic commands as well as some capabilities that are unique to PMV (introspection, creation of new attributes on the fly, etc.) will be demonstrated using the HIV-protease and one of its inhibitors, indinavir.

In the second half of this tutorial, we will address two of the main components underlying PMV, MolKit and DejaVu, in greater detail; the scripting capabilities of PMV; and the addition of new functionality through commands. This tutorial is intended to get the user comfortable using PMV, and to demonstrate some of the features that set PMV apart from other typical molecular viewer programs.

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