Please use this identifier to cite or link to this item: https://hdl.handle.net/10356/89044
Title: Protein-Ligand Blind Docking Using QuickVina-W With Inter-Process Spatio-Temporal Integration
Authors: Hassan, Nafisa Mohamed
Alhossary, Amr Ali
Mu, Yuguang
Kwoh, Chee-Keong
Keywords: Docking
QuickVina-W
Issue Date: 2017
Source: Hassan, N. M., Alhossary, A. A., Mu. Y., & Kwoh, C.-K. (2017). Protein-Ligand Blind Docking Using QuickVina-W With Inter-Process Spatio-Temporal Integration. Scientific Reports, 7, 15451-.
Series/Report no.: Scientific Reports
Abstract: “Virtual Screening” is a common step of in silico drug design, where researchers screen a large library of small molecules (ligands) for interesting hits, in a process known as “Docking”. However, docking is a computationally intensive and time-consuming process, usually restricted to small size binding sites (pockets) and small number of interacting residues. When the target site is not known (blind docking), researchers split the docking box into multiple boxes, or repeat the search several times using different seeds, and then merge the results manually. Otherwise, the search time becomes impractically long. In this research, we studied the relation between the search progression and Average Sum of Proximity relative Frequencies (ASoF) of searching threads, which is closely related to the search speed and accuracy. A new inter-process spatio-temporal integration method is employed in Quick Vina 2, resulting in a new docking tool, QuickVina-W, a suitable tool for “blind docking”, (not limited in search space size or number of residues). QuickVina-W is faster than Quick Vina 2, yet better than AutoDock Vina. It should allow researchers to screen huge ligand libraries virtually, in practically short time and with high accuracy without the need to define a target pocket beforehand.
URI: https://hdl.handle.net/10356/89044
http://hdl.handle.net/10220/44804
ISSN: 2045-2322
DOI: 10.1038/s41598-017-15571-7
Rights: © 2017 The Author(s) (Nature Publishing Group). This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. Te images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
Fulltext Permission: open
Fulltext Availability: With Fulltext
Appears in Collections:SCSE Journal Articles

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