Webina: an open-source library and web app that runs AutoDock Vina entirely in the web browser.

Yuri Kochnev,Jacob D Durrant,Erich Hellemann,Kevin C Cassidy,Yann Ponty

doi:10.1093/bioinformatics/btaa579

Abstract

MotivationMolecular docking is a computational technique for predicting how a small molecule might bind a macromolecular target. Among docking programs, AutoDock Vina is particularly popular. Like many docking programs, Vina requires users to download/install an executable file and to run that file from a command-line interface. Choosing proper configuration parameters and analyzing Vina output is also sometimes challenging. These issues are particularly problematic for students and novice researchers.ResultsWe created Webina, a new version of Vina, to address these challenges. Webina runs Vina entirely in a web browser, so users need only visit a Webina-enabled webpage. The docking calculations take place on the user’s own computer rather than a remote server.Availability and implementationA working version of the open-source Webina app can be accessed free of charge from http://durrantlab.com/webina.Supplementary information Supplementary data are available at Bioinformatics online.

Highlights

To facilitate use, we created a web app with a convenient GUI interface so users can configure and run Webina on their own receptor/ligand systems of interest
Webina has the same ability to consume CPUs and memory, but many users will wish to adjust these parameters to avoid impacting the performance of other programs and browser tabs
The "Advanced Parameters" subsection allows users to specify the many additional parameters that are available via command-line Vina (Figure 1D)

Summary

Introduction

We created a web app with a convenient GUI interface so users can configure and run Webina on their own receptor/ligand systems of interest. The same app allows users to visualize Webina-docked poses in their browsers. Webina will be a useful tool for the CADD research and educational communities. The web-app source code and compiled Webina library are available at http://durrantlab.com/webina-download. We release both under the terms of the open-source Apache License, Version 2.0. A working version of the app can be accessed free of charge from http://durrantlab.com/webina

Methods

Results

Conclusion