title: Conformation mining: an algorithm for finding biologically relevant conformations.
abstract: Discovering essential features shared by active compounds, an important step in drug-design, is complicated by conformational flexibility. We present a new algorithm to efficiently mine the conformational space of multiple actives and find small subsets of conformations likely to be biologically relevant. The approach identifies chemical and steric similarities between actives, providing insight into features important for binding when structural data are absent. Validation studies (thrombin and CDK2 data) produce alignments similar to protein-based alignments.
authors.affiliation: Rational Discovery LLC, 555 Bryant Street #467, Palo Alto, California 94301, USA. sputta@rationaldiscovery.com
authors.forename: Santosh
authors.initials: S
authors.lastname: Putta
authors.forename: Gregory A
authors.initials: GA
authors.lastname: Landrum
authors.forename: Julie E
authors.initials: JE
authors.lastname: Penzotti
mesh_terms: D000465:Algorithms; D042846:CDC2-CDC28 Kinases / Q000037:antagonists & inhibitors / Q000737:chemistry; D018360:Crystallography, X-Ray; D051357:Cyclin-Dependent Kinase 2; D008024:Ligands; D008958:Models, Molecular; D008968:Molecular Conformation; D011506:Proteins / Q000737:chemistry*; D013917:Thrombin / Q000037:antagonists & inhibitors / Q000737:chemistry
chemical_list: D008024:Ligands; D011506:Proteins; D042846:CDC2-CDC28 Kinases; D051357:Cyclin-Dependent Kinase 2; D013917:Thrombin