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Self-Organizing Superimposition Algorithm for Conformational Sampling

Summary: Self-Organizing Superimposition Algorithm for
Conformational Sampling
Johnson & Johnson Pharmaceutical Research & Development, L.L.C., 665 Stockton Drive,
Exton, Pennsylvania 19341
Received 25 August 2006; Accepted 18 October 2006
DOI 10.1002/jcc.20622
Published online 13 February 2007 in Wiley InterScience (www.interscience.wiley.com).
Abstract: A novel self-organizing algorithm for conformational sampling is introduced, in which precomputed con-
formations of rigid fragments are used as templates to enforce the desired geometry. Starting from completely random
coordinates, the algorithm repeatedly superimposes the templates to adjust the positions of the atoms, thereby gradually
refining the conformation of the molecule. Combined with pair-wise adjustments of the atoms to resolve steric clashes,
conformations that satisfy all geometric constraints can be generated from this procedure. The algorithm is demon-
strated to achieve good performance and promises potential applications on more challenging modeling problems.
q 2007 Wiley Periodicals, Inc. J Comput Chem 28: 12341239, 2007
Key words: self-organizing superimposition; self-organization; self-organizing; conformational sampling; conforma-
tional analysis; distance geometry; molecular fragment; superimposition; stochastic proximity embedding
Conformational sampling, the generation of low-energy three-
dimensional (3D) conformations of organic molecules, is a prob-


Source: Agrafiotis, Dimitris K. - Molecular Design and Informatics Group, Johnson & Johnson Pharmaceutical Research and Development
Goddard III, William A. - Materials and Process Simulation Center & Department of Chemistry, California Institute of Technology


Collections: Chemistry; Computer Technologies and Information Sciences; Materials Science