Improving ligand‐ranking of AutoDock Vina by changing the empirical parameters

AutoDock Vina (Vina) achieved a very high docking‐success rate, p^, but give a rather low correlation coefficient, R, for binding affinity with respect to experiments. This low correlation can be an obstacle for ranking of ligand‐binding affinity, which is the main objective of docking simulations....

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Vydáno v:Journal of computational chemistry Ročník 43; číslo 3; s. 160 - 169
Hlavní autoři: Pham, T. Ngoc Han, Nguyen, Trung Hai, Tam, Nguyen Minh, Y. Vu, Thien, Pham, Nhat Truong, Huy, Nguyen Truong, Mai, Binh Khanh, Tung, Nguyen Thanh, Pham, Minh Quan, V. Vu, Van, Ngo, Son Tung
Médium: Journal Article
Jazyk:angličtina
Vydáno: Hoboken, USA John Wiley & Sons, Inc 30.01.2022
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Témata:
Affinity
AutoDock Vina
Binding
binding affinity
Correlation coefficients
Docking
empirical parameter
Hydrogen bonds
Ligands
Mathematical analysis
modified Vina
Parameters
Ranking
screening
binding affinity
screening
empirical parameter
AutoDock Vina
modified Vina
ISSN:0192-8651, 1096-987X, 1096-987X
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Popis
Shrnutí:AutoDock Vina (Vina) achieved a very high docking‐success rate, p^, but give a rather low correlation coefficient, R, for binding affinity with respect to experiments. This low correlation can be an obstacle for ranking of ligand‐binding affinity, which is the main objective of docking simulations. In this context, we evaluated the dependence of Vina R coefficient upon its empirical parameters. R is affected more by changing the gauss2 and rotation than other terms. The docking‐success rate p^ is sensitive to the alterations of the gauss1, gauss2, repulsion, and hydrogen bond parameters. Based on our benchmarks, the parameter set1 has been suggested to be the most optimal. The testing study over 800 complexes indicated that the modified Vina provided higher correlation with experiment Rset1=0.556±0.025 compared with RDefault=0.493±0.028 obtained by the original Vina and RVina1.2=0.503±0.029 by Vina version 1.2. Besides, the modified Vina can be also applied more widely, giving R≥0.500 for 32/48 targets, compared with the default package, giving R≥0.500 for 31/48 targets. In addition, validation calculations for 1036 complexes obtained from version 2019 of PDBbind refined structures showed that the set1 of parameters gave higher correlation coefficient (Rset1=0.617±0.017) than the default package (RDefault=0.543±0.020) and Vina version 1.2 (RVina1.2=0.540±0.020). The version of Vina with set1 of parameters can be downloaded at https://github.com/sontungngo/mvina. The outcomes would enhance the ranking of ligand‐binding affinity using Autodock Vina. A new set of empirical parameters of AutoDock Vina was proposed. The accuracy of affinity prediction was significantly increased from RDefault=0.493±0.028 to Rset1=0.556±0.025 over 800 testing complexes. Over 1036 validating complexes, the proposed parameter formed Rset1=0.617±0.017, which is rigidly larger than the default package (RDefault=0.543±0.020) and Vina version 1.2 (RVina1.2=0.540±0.020).
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ISSN:0192-8651
1096-987X
1096-987X
DOI:10.1002/jcc.26779