A genetic algorithm for flexible molecular overlay and pharmacophore elucidation. Export

@article{citeulike:940943, abstract = {A genetic algorithm (GA) has been developed for the superimposition of sets of flexible molecules. Molecules are represented by a chromosome that encodes angles of rotation about flexible bonds and mappings between hydrogen-bond donor proton, acceptor lone pair and ring centre features in pairs of molecules. The molecule with the smallest number of features in the data set is used as a template, onto which the remaining molecules are fitted with the objective of maximising structural equivalences. The fitness function of the GA is a weighted combination of: (i) the number and the similarity of the features that have been overlaid in this way; (ii) the volume integral of the overlay; and (iii) the van der Waals energy of the molecular conformations defined by the torsion angles encoded in the chromosomes. The algorithm has been applied to a number of pharmacophore elucidation problems, i.e., angiotensin II receptor antagonists, Leu-enkephalin and a hybrid morphine molecule, 5-HT1D agonists, benzodiazepine receptor ligands, 5-HT3 antagonists, dopamine D2 antagonists, dopamine reuptake blockers and FKBP12 ligands. The resulting pharmacophores are generated rapidly and are in good agreement with those derived from alternative means.}, address = {Department of Information Studies, University of Sheffield, Western Bank, UK.}, author = {Jones, G. and Willett, P. and Glen, R. C.}, citeulike-article-id = {940943}, citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/8789195}, citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=8789195}, issn = {0920-654X}, journal = {J Comput Aided Mol Des}, keywords = {algorithm, genetic, overlay}, month = {December}, number = {6}, pages = {532--549}, posted-at = {2007-12-04 09:18:10}, priority = {2}, title = {A genetic algorithm for flexible molecular overlay and pharmacophore elucidation.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/8789195}, volume = {9}, year = {1995} }

TY - JOUR ID - citeulike:940943 L3 - citeulike-article-id:940943 N2 - A genetic algorithm (GA) has been developed for the superimposition of sets of flexible molecules. Molecules are represented by a chromosome that encodes angles of rotation about flexible bonds and mappings between hydrogen-bond donor proton, acceptor lone pair and ring centre features in pairs of molecules. The molecule with the smallest number of features in the data set is used as a template, onto which the remaining molecules are fitted with the objective of maximising structural equivalences. The fitness function of the GA is a weighted combination of: (i) the number and the similarity of the features that have been overlaid in this way; (ii) the volume integral of the overlay; and (iii) the van der Waals energy of the molecular conformations defined by the torsion angles encoded in the chromosomes. The algorithm has been applied to a number of pharmacophore elucidation problems, i.e., angiotensin II receptor antagonists, Leu-enkephalin and a hybrid morphine molecule, 5-HT1D agonists, benzodiazepine receptor ligands, 5-HT3 antagonists, dopamine D2 antagonists, dopamine reuptake blockers and FKBP12 ligands. The resulting pharmacophores are generated rapidly and are in good agreement with those derived from alternative means. IS - 6 JF - J Comput Aided Mol Des SN - 0920-654X AD - Department of Information Studies, University of Sheffield, Western Bank, UK. EP - 549 TI - A genetic algorithm for flexible molecular overlay and pharmacophore elucidation. VL - 9 SP - 532 KW - algorithm KW - genetic KW - overlay AU - Jones, G AU - Willett, P AU - Glen, RC PY - 1995/12// UR - http://view.ncbi.nlm.nih.gov/pubmed/8789195 ER -