title: PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results.
abstract: We introduce PHASE, a highly flexible system for common pharmacophore identification and assessment, 3D QSAR model development, and 3D database creation and searching. The primary workflows and tasks supported by PHASE are described, and details of the underlying scientific methodologies are provided. Using results from previously published investigations, PHASE is compared directly to other ligand-based software for its ability to identify target pharmacophores, rationalize structure-activity data, and predict activities of external compounds.
authors.affiliation: Schrödinger, Inc., 120 W. 45th St., 29th Floor, New York, NY 10036, USA. dixon@schrodinger.com
authors.forename: Steven L
authors.initials: SL
authors.lastname: Dixon
authors.forename: Alexander M
authors.initials: AM
authors.lastname: Smondyrev
authors.forename: Eric H
authors.initials: EH
authors.lastname: Knoll
authors.forename: Shashidhar N
authors.initials: SN
authors.lastname: Rao
authors.forename: David E
authors.initials: DE
authors.lastname: Shaw
authors.forename: Richard A
authors.initials: RA
authors.lastname: Friesner
mesh_terms: D003198:Computer Simulation; D017076:Computer-Aided Design; D030562:Databases, Protein; D015195:Drug Design; D004353:Drug Evaluation, Preclinical; D005493:Folic Acid Antagonists / Q000737:chemistry / Q000494:pharmacology; D006801:Humans; D066298:In Vitro Techniques; D008024:Ligands; D008958:Models, Molecular; D011487:Protein Conformation; D021281:Quantitative Structure-Activity Relationship; D012984:Software; D013762:Tetrahydrofolate Dehydrogenase / Q000737:chemistry
chemical_list: D005493:Folic Acid Antagonists; D008024:Ligands; D013762:Tetrahydrofolate Dehydrogenase