The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
Fast, accurate, and reliable molecular docking with QuickVina 2
Open accessAbstract
Motivation: The need for efficient molecular docking tools for high-throughput screening is growing alongside the rapid growth of drug-fragment databases. AutoDock Vina (‘Vina’) is a widely used docking tool with parallelization for speed. QuickVina (‘QVina 1’) then further enhanced the speed via a heuristics, requiring high exhaustiveness. With low exhaustiveness, its accuracy was compromised. We present in this article the latest version of QuickVina (‘QVina 2’) that inherits both the speed of QVina 1 and the reliability of the original Vina. Results: We tested the efficacy of QVina 2 on the core set of PDBbind 2014. With the default exhaustiveness level of Vina (i.e. 8), a maximum of 20.49-fold and an average of 2.30-fold acceleration with a correlation coefficient of 0.967 for the first mode and 0.911 for the sum of all modes were attained over the original Vina. A tendency for higher acceleration with increased number of rotatable bonds as the design variables was observed. On the accuracy, Vina wins over QVina 2 on 30% of the data with average energy difference of only 0.58 kcal/mol. On the same dataset, GOLD produced RMSD smaller than 2 Å on 56.9% of the data while QVina 2 attained 63.1%. Availability and implementation: The C++ source code of QVina 2 is available at (www.qvina.org). Contact: aalhossary@pmail.ntu.edu.sg Supplementary information: Supplementary data are available at Bioinformatics online.
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Trott, O., & Olson, A. J. (2010) · Journal of Computational Chemistry · doi:10.1002/jcc.21334 · Cited by 38,412
The PDBbind database: methodologies and updates
Wang, R., Fang, X., Lu, Y., Yang, C.-Y., & Wang, S. (2005) · Journal of Medicinal Chemistry · doi:10.1021/jm048957q · Cited by 933
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Metadata
- Authors
- Alhossary, A., Handoko, S. D., Mu, Y., & Kwoh, C.-K.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2015-02-24
- Volume
- 31
- Issue
- 13
- Pages
- 2214-2216
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2108389384
- Cited by
- 375
- References
- 2
- FWCI
- 3.66
- Type
- journal article
- Language
- en
- Open access
- bronze
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