Conformational Optimization and Sampling Along Natural Coordinates

Peter Minary
Stanford University

In the present talk we introduce various applications of a novel method that facilitate the use of ‘Natural Moves’ or arbitrary degrees of freedom which may give rise to collective rearrangements in the tertiary or even higher level structure of biological assemblies. While the method may open various new avenues in the modeling of biological structures, here we only present a few applications including the conformational sampling of large nucleic acid (nucleosome, fractal like RNA) molecules and fitting into cryo-EM density maps of protein assemblies such as the Fatty Acid Synthase. The was supported by NIH Grant GM41455 GM63817 and HFSP award RGP0024/2008.

Presentation (PowerPoint File)

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