PME &LES MOLECULAR DYNAMICS FOR STUDY OF SEQUENCE SPECIFIC DNA &RNA STRUCTURE

$39,522P41FY2000RRNIH

University Of California San Francisco, San Francisco CA

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Abstract

We are applying the AMBER force field with Particle Mesh Ewald (PME) treatment of electrostatics and the Locally Enhanced Sampling (LES) method to predict the sequence specific structure of DNA and RNA duplexes. Results obtained from unrestrained molecular dynamics are compared against structures generated using NMR data. The Computer Graphics Laboratory facilities are instrumental to the visualization of the results.

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