PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results

• Published in: Journal of computer-aided molecular design Vol. 20; no. 10-11; pp. 647 - 671
• Main Authors: Dixon, Steven L, Smondyrev, Alexander M, Knoll, Eric H, Rao, Shashidhar N, Shaw, David E, Friesner, Richard A
• Format: Journal Article
• Language: English
• Published: Netherlands Springer Nature B.V 01-10-2006
• Subjects: Assessments; Computer programs; Computer Simulation; Computer-Aided Design; Databases, Protein; Drug Design; Drug Evaluation, Preclinical; Folic Acid Antagonists - chemistry; Folic Acid Antagonists - pharmacology; Humans; In Vitro Techniques; Ligands; Mathematical models; Methodology; Models, Molecular; Molecular biology; Perception; Pharmacology; Protein Conformation; Quantitative Structure-Activity Relationship; Software; Tasks; Tetrahydrofolate Dehydrogenase - chemistry; Three dimensional
• ISSN: 0920-654X; 1573-4951
• DOI: 10.1007/s10822-006-9087-6

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.