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

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 provide...

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Published in:Journal of computer-aided molecular design 2006-10, Vol.20 (10-11), p.647-671
Main Authors: Dixon, Steven L, Smondyrev, Alexander M, Knoll, Eric H, Rao, Shashidhar N, Shaw, David E, Friesner, Richard A
Format: Article
Language:English
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
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cited_by cdi_FETCH-LOGICAL-c456t-166a40f6512045223178e57f61e1b7799759428a3d3e5bdcff6646c5c8b1948a3
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container_issue 10-11
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container_title Journal of computer-aided molecular design
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creator Dixon, Steven L
Smondyrev, Alexander M
Knoll, Eric H
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Shaw, David E
Friesner, Richard A
description 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.
doi_str_mv 10.1007/s10822-006-9087-6
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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
title PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results
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