PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results
By Steve Dixon, A. Smondyrev, E. Knoll, S. Rao, David E. Shaw, Richard A. Friesner. 2006
1,140 citations recorded by the source corpus.
Subfields: Computational Theory and Mathematics, Pharmacology, Computational Chemistry & Drug Discovery
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Computational Theory and Mathematics
- Dina Schneidman-Duhovny
- Haim J. Wolfson
- Ruth Nussinov
- Glaucius Oliva
- L. Ferreira
- Ricardo N Dos Santos
- Sun Choi
- Woody Sherman
In Pharmacology
- Ruth Nussinov
- Krzysztof Rataj
- Stefan Mordalski
- Andrzej J. Bojarski
- Adriano Defini Andricopulo
- Insung S. Choi
- Hyeoncheol Cho
In Computational Chemistry & Drug Discovery
- Dina Schneidman-Duhovny
- Sun Choi
- Glaucius Oliva
- Woody Sherman
- Haim J. Wolfson
- Ruth Nussinov
- Krzysztof Rataj
- Stefan Mordalski
Citations in the corpus
- Molecular Docking and Structure-Based Drug Design Strategies (2015, background): “…[154,155] HypoGen [141] ALADDIN [156] HypoRefine [141] RAPID [157] GASP [142,143] DANTE [158] DiscoTech [143,144] APOLLO [159] GALAHAD [143,145] CLEW [160] LigandScout [146,147] MPHIL [161] MOE [148,149] GAMMA [162] PHASE [150,151] SCAMPI [163] XED [152,153] Apex-3D [164] LigBuilder [165,166]”
- ConfGen: A Conformational Search Method for Efficient Generation of Bioactive Conformers (2010, methodology): “For some applications, such as pharmacophore modeling, rmsd values of 2.0 Å may be adequate, as can be inferred in the work by Dixon et al. 5 where conformations aligned using accurate pharmacophore hypotheses have in most cases rmsd values larger than 2.0 Å. 34 However, for other applications,…”
- GPCRdb: the G protein‐coupled receptor database – an introduction (2016, background): “Ligand fragments can be automatically matched and superimposed in the GPCRdb. Pharmacophore elements: orange, aromatic; green, hydrophobic; blue, cationic; and light blue, hydrogen bond donor, were here assigned with Phase (Dixon et al., 2006). infrastructure centres like NCBI and EMBL-EBI, they typ”
- Role of computer-aided drug design in modern drug discovery (2015, methodology): “Several commonly used programs for automatic pharmacophore generation include Discovery Studio, PHASE (Dixon et al. 2006a, b), LigandScout (Wolber and Langer 2005), and MOE.”
- PharmaGist: a webserver for ligand-based pharmacophore detection (2008, methodology): “Examples for such methods include RAPID (8), MPHIL (9) and the commercial programs DISCO (10), Phase (11) of Schrodinger and HipHop and HypoGen, which are part of the Catalyst software package of Accelrys (12–16).”