Self-organizing superimposition algorithm for conformational sampling

Abstract: A novel self-organizing algorithm for conformational sampling is introduced, in which precomputed conformations 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 demonstrated to achieve good performance and promises potential applications on more challenging modeling problems. q 2007 Wiley Periodicals, Inc. J Comput Chem 28: 1234–1239, 2007 Key words: self-organizing superimposition; self-organization; self-organizing; conformational sampling; conformational analysis; distance geometry; molecular fragment; superimposition; stochastic proximity embedding

• Type: Journal
• Year: 2007
• Where: JCC
• Authors: Fangqiang Zhu, Dimitris K. Agrafiotis
• Keywords: Algorithm, Conformational Sampling, JCC 2007, Self-organizing