Conformational sampling by self-organization

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United States of America Patent

APP PUB NO 20060089808A1
SERIAL NO

10519638

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Abstract

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A self-organizing method, system, and computer program product for generating molecular conformations that are consistent with a set of distance and/or volume constraints. A stochastic proximity embedding (SPE) algorithm evaluates individual distance and/or volume constraints and adjusts the atomic coordinates to minimize violations of such constraints. The method scales linearly with thenumber of atoms, and produces many more unique conformations at a fraction of the time required by conventional distance geometry algorithms.

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Patent Owner(s)

Patent OwnerAddress
JOHNSON & JOHNSON PHARMACEUTICAL RESEARCH & DEVELOPMENT LLC920 ROUTE 202 BOX 300 RARITAN NJ 08869

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Inventor(s)

Inventor Name Address # of filed Patents Total Citations
Agrafiotis, DimitrisK Downington, PA 1 3
Izrailev, SergeiF New York, NY 1 3
Salemme, FrancisR Yardley, PA 1 3
Xu, Huafeng San Francisco, CA 5 13

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