QuickVina: Accelerating AutoDock Vina Using Gradient-Based Heuristics for Global Optimization

Handoko, Stephanus Daniel; Ouyang, Xuchang; Su, Chinh Tran-To; Kwoh, Chee Keong; Ong, Yew Soon

doi:10.1109/tcbb.2012.82

Cited by 60 publications

(55 citation statements)

References 11 publications

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“…Geometry-based generation of initial ligand conformations in conformational space annealing global optimization [5] HYBRID Utilization of the knowledge of bound ligands [26] LiGenDock Capacity to conduct de novo design [51] PRL-Dock Increased speed, probabilistic relaxation labelling algorithm to search for potential intermolecular hydrogen bonding [100] QuickVina Increased speed, improvements in the local search algorithm via heuristic prevention of some intermediate points undergoing local search [213] S4MPLE Hybrid genetic algorithm, ability to and handle intramolecular and intermolecular degrees of freedom and an arbitrary number of independent species [8,50] VinaLC Increased speed, a mixed parallel scheme combining message passing interface and multithreading…”

Section: On-the-fly Methodsmentioning

confidence: 99%

Improvements, trends, and new ideas in molecular docking: 2012–2013 in review

Yuriev

Holien

Ramsland

2015

J of Molecular Recognition

246

165

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Molecular docking is a computational method for predicting the placement of ligands in the binding sites of their receptor(s). In this review, we discuss the methodological developments that occurred in the docking field in 2012 and 2013, with a particular focus on the more difficult aspects of this computational discipline. The main challenges and therefore focal points for developments in docking, covered in this review, are receptor flexibility, solvation, scoring, and virtual screening. We specifically deal with such aspects of molecular docking and its applications as selection criteria for constructing receptor ensembles, target dependence of scoring functions, integration of higher-level theory into scoring, implicit and explicit handling of solvation in the binding process, and comparison and evaluation of docking and scoring methods.

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Section: On-the-fly Methodsmentioning

confidence: 99%

Improvements, trends, and new ideas in molecular docking: 2012–2013 in review

Yuriev

Holien

Ramsland

2015

J of Molecular Recognition

246

165

View full text Add to dashboard Cite

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“…Before docking, protein structures were minimized and optimized using the same protocol as described elsewhere [14,23,24,31]. For Molecular docking, AutoDock Vina was employed, which follows a gradient optimization method in its local optimization procedure to rank the ligands based on empirical binding free energy (∆G in kcal/mol) function [32,33]. The overall docking procedure was first evaluated by re-docking of the co-crystallized inhibitor into the respective binding site of PPA and PPL, and root-mean-square-deviations were estimated.…”

Section: Molecular Docking Analysis and Molecular Dynamics Simulationsmentioning

confidence: 99%

In Vitro Antidiabetic, Anti-Obesity and Antioxidant Analysis of Ocimum basilicum Aerial Biomass and in Silico Molecular Docking Simulations with Alpha-Amylase and Lipase Enzymes

Noor

Ahmed

Rehman

et al. 2019

Biology

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The present study explored phytochemicals, porcine pancreatic α-amylase (PPA) and lipase (PPL) inhibitory activities and antioxidant potential of polar and nonpolar extracts of the leaves and flowers of Ocimum basilicum and the in-silico mode of interaction between these enzymes and the major chemical constituents of the herb. The hexane extract (HE) and hydro-ethanolic extract (EE) obtained sequentially were used to estimate PPA and PPL inhibitory and antioxidant activities, total phenolic content (TPC) and total flavonoid content (TFC). Chemical constituents of the essential oils and HE were determined by GC-MS (Gas Chromatography-Mass Spectrometry). For PPA inhibition, IC50 (µg/mL) of the extracts were 0.27–0.37, which were close to 0.24 of acarbose, while for PPL inhibition, IC50 (µg/mL) of the extracts were 278.40–399.65, and that of Orlistat 145.72. The flowers EE was most potent antioxidant followed by leaves EE. The leaves EE had highest TPC and TFC followed of flowers EE. The essential oil of flowers had higher estragole (55%) than linalool (37%), while the essential oil of the leaves had higher linalool (42%) than estragole (38%). The HE of the flowers contained higher estragole (42%) than linalool (23%), while of the HE of the leaves too had higher estragole (65%) than linalool (18%). The in-silico molecular docking study showed linalool and estragole to have considerable PPA and PPL binding potential, which were further investigated through molecular dynamics simulations and binding free energy calculations. The PPA and PPL inhibitory activities of O. basilicum extracts and their notable antioxidant potential propose the herb as a multi-target complimentary medicine for diabetes, obesity and oxidative stress.

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“…Структуру белка gp120 ВИЧ-1 в кристалле использовали в приближении жесткого рецептора для проведения молекулярного докинга с соединениями, идентифицированными в базах данных веб-ресурса Pharmit. Докинг осуществляли с учетом конформационной подвижности лигандов с помощью программы QuickVina 2 [28]. В качестве положительного контроля использовали ингибиторы проникновения ВИЧ-1 NBD-11021 [29] и (+)-DMJ-II-121 [30,31], представляющие новый класс полных функциональных антагонистов клеточного рецептора CD4 (рис.…”

Section: методы исследованияunclassified

In silico Identification of High-Affinity Ligands of the Hiv-1 Gp120 Protein, Potential Peptidomimetics of Neutralizing Antibody N6

Andrianov¹,

Nikolaev²,

Kornoushenko³

et al. 2019

Math.Biol.Bioinf.

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Six potential peptidomimetics of the cross-reactive neutralizing anti-HIV-1 antibody N6 that are able to mimic the pharmacophoric features of this immunoglobulin by specific and effective interactions with the CD4-binding site of the viral gp120 protein were identified by virtual screening and molecular modeling. The key role in the interaction of these compounds with gp120 is shown to play multiple van der Waals contacts with conserved residues of the gp120 Phe-43 cavity critical for the HIV binding to cellular receptor CD4, as well as hydrogen bond with Asp-368gp120 that increase the chemical affinity without activating unwanted allosteric effect. According to the data of molecular dynamics, the complexes of the identified ligands with gp120 are energetically stable and show the lower values of binding free energy compared with the HIV-1 inhibitors NBD-11021 and DMJ-II-121 used in the calculations as a positive control. Based on the data obtained, it was concluded that the identified compounds may be considered as promising candidates for detailed experimental studies to their further use in the design of novel antiviral drugs presenting HIV-1 inhibitors that block the early stages of the development of HIV infection.

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QuickVina: Accelerating AutoDock Vina Using Gradient-Based Heuristics for Global Optimization

Cited by 60 publications

References 11 publications

Improvements, trends, and new ideas in molecular docking: 2012–2013 in review

Improvements, trends, and new ideas in molecular docking: 2012–2013 in review

In Vitro Antidiabetic, Anti-Obesity and Antioxidant Analysis of Ocimum basilicum Aerial Biomass and in Silico Molecular Docking Simulations with Alpha-Amylase and Lipase Enzymes

In silico Identification of High-Affinity Ligands of the Hiv-1 Gp120 Protein, Potential Peptidomimetics of Neutralizing Antibody N6

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