Motivation Molecular 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. Results We 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 A 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.

Protein structure determines biological function. Accurately conceptualizing 3D protein/ ligand structures is thus vital to scientific research and education. Virtual reality (VR) enables protein visualization in stereoscopic 3D, but many VR molecular-visualization programs are expensive and challenging to use; work only on specific VR headsets; rely on complicated model-preparation software; and/or require the user to install separate programs or plugins. Here we introduce ProteinVR, a web-based application that works on various VR setups and operating systems. ProteinVR displays molecular structures within 3D environments that give useful biological context and allow users to situate themselves in 3D space. Our web-based implementation is ideal for hypothesis generation and education in research and large-classroom settings. We release ProteinVR under the open-source BSD-3-Clause license.

Highlights d Simulations and experiments provide insight into how LARP1 binds TOP mRNA d Key residues contribute to cap recognition dynamics and mRNA specificity d Druggable LARP1 pockets suggest avenues for anti-cancer drug discovery

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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