title: Conformational sampling by self-organization.
abstract: A new stochastic algorithm for conformational sampling is described. The algorithm generates molecular conformations that are consistent with a set of geometric constraints, which include interatomic distance bounds and chiral volumes derived from the molecular connectivity table. The algorithm repeatedly selects individual geometric constraints at random and updates the respective atomic coordinates toward satisfying the chosen constraint. When compared to a conventional distance geometry algorithm based on the same set of geometric constraints, our method is faster and generates conformations that are more diverse and more energetically favorable.
authors.affiliation: 3-Dimensional Pharmaceuticals, Inc., 665 Stockton Drive, Exton, Pennsylvania 19341, USA.
authors.forename: Huafeng
authors.initials: H
authors.lastname: Xu
authors.forename: Sergei
authors.initials: S
authors.lastname: Izrailev
authors.forename: Dimitris K
authors.initials: DK
authors.lastname: Agrafiotis
mesh_terms: D000465:Algorithms; D004744:Enkephalin, Methionine / Q000737:chemistry; D008956:Models, Chemical; D008958:Models, Molecular; D008968:Molecular Conformation; D009020:Morphine / Q000737:chemistry; D020849:Raloxifene Hydrochloride / Q000737:chemistry
chemical_list: D020849:Raloxifene Hydrochloride; D004744:Enkephalin, Methionine; D009020:Morphine