Binding site characteristics in structure-based virtual screening: evaluation of current docking tools
Publication type: Journal Article
Publication date: 2003-01-14
scimago Q3
wos Q3
SJR: 0.376
CiteScore: 3.8
Impact factor: 2.5
ISSN: 16102940, 09485023
PubMed ID:
12638011
Catalysis
Organic Chemistry
Inorganic Chemistry
Physical and Theoretical Chemistry
Computer Science Applications
Computational Theory and Mathematics
Abstract
Two new docking programs FRED (OpenEye Scientific Software) and Glide (Schrödinger, Inc.) in combination with various scoring functions implemented in these programs have been evaluated against a variety of seven protein targets (cyclooxygenase-2, estrogen receptor, p38 MAP kinase, gyrase B, thrombin, gelatinase A, neuraminidase) in order to assess their accuracy in virtual screening. Sets of known inhibitors were added to and ranked relative to a random library of drug-like compounds. Performance was compared in terms of enrichment factors and CPU time consumption. Results and specific features of the two new tools are discussed and compared to previously published results using FlexX (Tripos, Inc.) as a docking engine. In addition, general criteria for the selection of docking algorithms and scoring functions based on binding-site characteristics of specific protein targets are proposed. Figure Enrichment factors obtained with FlexX, Glide and FRED docking engines in combination with different scoring functions for seven selected targets with highly variable binding sites
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Total citations:
167
Citations from 2024:
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(1.8%)
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Schulz-Gasch T., Stahl M. Binding site characteristics in structure-based virtual screening: evaluation of current docking tools // Journal of Molecular Modeling. 2003. Vol. 9. No. 1. pp. 47-57.
GOST all authors (up to 50)
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Schulz-Gasch T., Stahl M. Binding site characteristics in structure-based virtual screening: evaluation of current docking tools // Journal of Molecular Modeling. 2003. Vol. 9. No. 1. pp. 47-57.
Cite this
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TY - JOUR
DO - 10.1007/s00894-002-0112-y
UR - https://doi.org/10.1007/s00894-002-0112-y
TI - Binding site characteristics in structure-based virtual screening: evaluation of current docking tools
T2 - Journal of Molecular Modeling
AU - Schulz-Gasch, Tanja
AU - Stahl, Martin
PY - 2003
DA - 2003/01/14
PB - Springer Nature
SP - 47-57
IS - 1
VL - 9
PMID - 12638011
SN - 1610-2940
SN - 0948-5023
ER -
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BibTex (up to 50 authors)
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@article{2003_Schulz-Gasch,
author = {Tanja Schulz-Gasch and Martin Stahl},
title = {Binding site characteristics in structure-based virtual screening: evaluation of current docking tools},
journal = {Journal of Molecular Modeling},
year = {2003},
volume = {9},
publisher = {Springer Nature},
month = {jan},
url = {https://doi.org/10.1007/s00894-002-0112-y},
number = {1},
pages = {47--57},
doi = {10.1007/s00894-002-0112-y}
}
Cite this
MLA
Copy
Schulz-Gasch, Tanja, and Martin Stahl. “Binding site characteristics in structure-based virtual screening: evaluation of current docking tools.” Journal of Molecular Modeling, vol. 9, no. 1, Jan. 2003, pp. 47-57. https://doi.org/10.1007/s00894-002-0112-y.