DockingApp: a user friendly interface for facilitated docking simulations with AutoDock Vina

Muzio, Elena Di; Toti, Daniele; Polticelli, Fabio

doi:10.1007/s10822-016-0006-1

Cited by 97 publications

(51 citation statements)

References 13 publications

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“…Simulations were performed using DockingApp, a user friendly interface for the docking program AutoDock Vina . In all simulations, the search space (docking grid) included the whole HSA structure, to perform “blind” predictions of the cantharidin binding sites.…”

Section: Methodsmentioning

confidence: 99%

Cantharidin inhibits competitively heme‐Fe(III) binding to the FA1 site of human serum albumin

Polticelli

Leboffe

Tortosa

et al. 2017

J of Molecular Recognition

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Cantharidin, a monoterpene isolated from the insect blister beetle, has long been used as a medicinal agent in the traditional Chinese medicine. Cantharidin inhibits a subgroup of serine/threonine phosphatases, thus inducing cell growth inhibition and cytotoxicity. Cantharidin has anticancer activity in vitro, since it is able of inducing p53-dependent apoptosis and double-strand breakage of DNA in cancer cells. Although the toxicity of cantharidin to the gastrointestinal and urinary tracts prevents its medical use, it is a promising lead compound for chemical modification to develop new anticancer therapeutics. In fact, cantharidin does not cause myelosuppression and displays anticancer activity against cells with a multidrug resistance phenotype. Here, the competitive inhibitory effect of cantharidin on heme-Fe(III) binding to the fatty acid site 1 (FA1) of human serum albumin (HSA) is reported. Docking and molecular dynamics simulations support functional data indicating the preferential binding of cantharidin to the FA1 site of HSA. Present results may be relevant in vivo as HSA could transport cantharidin, which in turn could affect heme-Fe(III) scavenging by HSA.

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Section: Methodsmentioning

confidence: 99%

Cantharidin inhibits competitively heme‐Fe(III) binding to the FA1 site of human serum albumin

Polticelli

Leboffe

Tortosa

et al. 2017

J of Molecular Recognition

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“…Docking analyses were performed using the crystal structures of FA‐free HSA (PDB ID: 1AO6) and FA‐bound HSA (PDB ID: 3SQJ). Simulations were carried out using DockingApp , an user friendly interface for the docking program AutoDock Vina . The grid spacing was set to 1 Å per grid unit and the exhaustiveness parameter was increased from the default value of 8 to 24, as suggested by Autodock Vina developers for grid sizes larger than 27,000 Å 3 (see http://vina.scripps.edu/tutorial.html), which is the case for HSA simulations.…”

Section: Docking Simulations Of Cannabinoids Binding To Fa‐free and Fmentioning

confidence: 99%

Human serum albumin: A modulator of cannabinoid drugs

et al. 2017

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The endocannabinoid system is a unique neuromodulatory system that affects a wide range of biological processes and maintains the homeostasis in all mammal body systems. In recent years, several pharmacological tools to target endocannabinoid neurotransmission have been developed, including direct and indirect cannabinoid agonists and cannabinoid antagonists. Due to their hydrophobic nature, cannabinoid agonists and antagonists need to bind specific transporters to allow their distribution in body fluids. Human serum albumin (HSA), the most abundant plasma protein, is a key determinant of drug pharmacokinetics. As HSA binds both the endocannabinoid anandamide and the active ingredient of Cannabis sativa, Δ-9-tetrahydrocannabinol, we hypothesize that HSA can be the most important carrier of cannabinoid drugs. In silico docking observations strongly indicate that HSA avidly binds the indirect cannabinoid agonists URB597, AM5206, JZL184, JZL195, and AM404, the direct cannabinoid agonists WIN55,212-2 and CP55,940, and the prototypical cannabinoid antagonist/inverse agonist SR141716. Values of the free energy for cannabinoid drugs binding to HSA range between -5.4 kcal mol and -10.9 kcal mol . Accounting for the HSA concentration in vivo (∼ 7.5 × 10 M), values of the free energy here determined suggest that the formation of the HSA:cannabinoid drug complexes may occur in vivo. Therefore, HSA appears to be an important determinant for cannabinoid efficacy and may guide the choice of the drug dose regimen to optimize drug efficacy and to avoid drug-related toxicity. © 2017 IUBMB Life, 69(11):834-840, 2017.

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“…Many of these interact with command-line Vina “under the hood.” For example, PyRx [3], now a commercial program, provides a helpful wizard-like interface for Vina docking. Programs such as DockingApp [4] and AUDocker LE [5] are somewhat similar (albeit less feature rich) open-source alternatives. Other GUI programs aim to simplify specific steps in the standard docking protocol.…”

Section: Resultsmentioning

confidence: 99%

Webina: An Open-Source Library and Web App that Runs AutoDock Vina Entirely in the Web Browser

Kochnev

Hellemann

Cassidy

et al. 2019

Preprint

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1 1 Abstract 7 Molecular docking is a computational technique for predicting how a small molecule might bind a macromolecular 8 target. Among docking programs, AutoDock Vina is particularly popular. Like many docking programs, Vina 9 requires users to download/install an executable file and to run that file from a Unix-or DOS-like command-line 10 interface. Choosing proper configuration parameters and analyzing Vina output is also sometimes challenging. 11 These issues are particularly problematic for students and novice researchers. We have created Webina, a new 12 version of Vina, to address these challenges. Webina is a JavaScript/WebAssembly library that runs AutoDock 13 Vina entirely in a web browser. To use Webina, users need only visit a Webina-enabled webpage. The docking 14 calculations take place on the user's own computer rather than a remote server. To encourage use, we have incorporated 15 the Webina library into our own Webina web app. The app includes a convenient interface so users can easily 16 setup their docking runs and analyze the results. Webina will be a useful open-source tool for the research and 17 educational communities. A working version of the app can be accessed free of charge from http://durrantlab.com/webina. 18 2 Introduction 19 Molecular docking is a popular computer-aided drug discovery (CADD) technique for predicting non-covalent 20 small-molecule/macromolecular binding. By accelerating lead identification, docking aims to streamline the 21 early-stage drug-discovery process. A docking program first predicts the 3D geometries ("poses") with which 22 virtual-library compounds might bind a given macromolecular target. Second, a scoring function evaluates the 23 predicted geometries to estimate binding affinities [1]. The top-scoring compounds are then recommended for 24 experimental testing. The resulting hit rates are far from 100%, but they tend to be better than those obtained 25 from more costly high-throughput experimental screens [2]. 26 Among docking programs, AutoDock Vina is particularly popular [1]. Vina is an open-source program written 27 in C++ that runs on all major desktop operating systems. Its strengths include speed and relative ease of use. 28 But like many CADD programs, Vina has some notable shortcomings. Users must download and install the 29 program to use it on their own machines. Choosing proper configuration parameters and analyzing Vina output 30 is also sometimes challenging. And absent third-party graphical user interface (GUI) wrappers [3-7], Vina is 31 only accessible from a Unix-or DOS-like command-line interface. These limitations are particularly impactful 32 in educational settings, where expecting students to download, install, and use a command-line program is often 33 impractical. 34To address these challenges, we have created Webina, a WebAssembly (Wasm) library that runs AutoDock 35 Vina entirely in a web browser. Wasm is an emerging web technology that allows developers to run compiled 36 code without requiring the installation of a...

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DockingApp: a user friendly interface for facilitated docking simulations with AutoDock Vina

Cited by 97 publications

References 13 publications

Cantharidin inhibits competitively heme‐Fe(III) binding to the FA1 site of human serum albumin

Cantharidin inhibits competitively heme‐Fe(III) binding to the FA1 site of human serum albumin

Human serum albumin: A modulator of cannabinoid drugs

Webina: An Open-Source Library and Web App that Runs AutoDock Vina Entirely in the Web Browser

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