Integrating computation and visualization for biomolecular analysis: an example using python and AVS.

M F Sanner; B S Duncan; C J Carrillo; A J Olson

doi:10.1142/9789814447300_0039

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Integrating computation and visualization for biomolecular analysis: an example using python and AVS.

M F Sanner·B S Duncan·C J Carrillo·A J Olson

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Abstract

One of the challenges in biocomputing is to enable the efficient use of a wide variety of fast-evolving computational methods to simulate, analyze, and understand the complex properties and interactions of molecular systems. Our laboratory investigates several areas including molecular visualization, protein-ligand docking, protein-protein docking, molecular surfaces, and the derivation of phenomenological potentials. In this paper we present an approach based on the Python programming language to achieve a high level of integration between these different computational methods and our primary visualization system AVS. This approach removes many limitations of AVS while increasing dramatically the inter-operability of our computational tools. Several examples are shown to illustrate how this approach enables a high level of integration and inter-operability between different tools, while retaining modularity and avoiding the creation of a large monolithic package that is difficult to extend and maintain.

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Capsid Computational Biology Computer Graphics Computing Methodologies Models, Molecular Programming Languages Protein Conformation Proteins Tobacco Mosaic Virus User-Computer Interface Comparative Study Journal Article Research Support, U.S. Gov't, Non-P.H.S.Research Support, U.S. Gov't, P.H.S.

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M F Sanner, B S Duncan, C J Carrillo, A J Olson. 1999. Integrating computation and visualization for biomolecular analysis: an example using python and AVS.. https://doi.org/10.1142/9789814447300_0039

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