PMID: 8603055Oct 1, 1995Paper

Biomolecular visualization using AVS

Journal of Molecular Graphics
B S DuncanA J Olson

Abstract

Dataflow systems for scientific visualization are becoming increasingly sophisticated in their architecture and functionality. AVS, from Advanced Visual Systems Inc., is a powerful dataflow environment that has been applied to many computation and visualization tasks. An important, yet complex, application area is molecular modeling and biomolecular visualization. Problems in biomolecular visualization tax the capability of dataflow systems because of the diversity of operations that are required and because many operations do not fit neatly into the dataflow paradigm. Here we describe visualization strategies and auxiliary programs developed to enhance the applicability of AVS for molecular modelling. Our visualization strategy is to use general-purpose AVS modules and a small number of chemistry-specific modules. We have developed methods to control AVS using AVS-tool, a programmable interface to the AVS Command Line Interpreter (CLI), and have also developed NAB, a C-like language for writing AVS modules that has extensions for operating on proteins and nucleic acids. This strategy provides a flexible and extensible framework for a wide variety of molecular modeling tasks.

References

Jan 1, 1977·Annual Review of Biophysics and Bioengineering·F M Richards
May 25, 1977·Journal of Molecular Biology·F C BernsteinM Tasumi
Nov 1, 1992·Scientific American·A J Olson, D S Goodsell
Jan 1, 1990·Proteins·D S Goodsell, A J Olson
Dec 1, 1994·Journal of Molecular Graphics·J Walton
Feb 1, 1995·Journal of Molecular Graphics·K Flurchick, L Bartolotti
Jun 1, 1994·Journal of Molecular Graphics·M TeschnerJ Brickmann
Feb 1, 1993·Biopolymers·B S Duncan, A J Olson
Aug 1, 1995·Journal of Molecular Graphics·B S Duncan, A J Olson
Aug 1, 1995·Journal of Molecular Graphics·B S Duncan, A J Olson
Oct 25, 1991·Science·D Collis

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Citations

Aug 6, 1999·Journal of Molecular Graphics & Modelling·T J MackeA J Olson
May 20, 1998·Structure·T A LarsenD S Goodsell
Feb 9, 2010·Molecular and Cellular Endocrinology·Rosamaria LappanoMarcello Maggiolini

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