![]() Secretaría de Ciencia y Técnica de la Universidad Nacional de Córdoba, FONCYT. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.ĭata Availability: All relevant data are within the paper and its Supporting Information files.įunding: This work was supported by CONICET- Consejo Nacional de Investigaciones Científicas y Tecnológicas, Secyt-UNC. ![]() Received: DecemAccepted: ApPublished: May 12, 2016Ĭopyright: © 2016 Quiroga, Villarreal. PLoS ONE 11(5):Įditor: Heinrich Sticht, Universität Erlangen-Nürnberg, GERMANY Precompiled binaries, source code, documentation and a tutorial for using Smina to run the Vinardo scoring function are available at the same address.Ĭitation: Quiroga R, Villarreal MA (2016) Vinardo: A Scoring Function Based on Autodock Vina Improves Scoring, Docking, and Virtual Screening. The Vinardo scoring function is available as an option within Smina, a fork of Vina, which is freely available under the GNU Public License v2.0 from. Vinardo outperforms Vina in all tests performed, for all datasets analyzed. This article provides an overview of the development of the Vinardo scoring function, highlights its differences with Vina, and compares the performance of the two scoring functions in scoring, docking and virtual screening applications. On the other hand, a combination of scoring, minimization, and re-docking on carefully curated training datasets allowed us to develop a simplified scoring function with optimum docking performance. We show that the traditional approach to train empirical scoring functions, using linear regression to optimize the correlation of predicted and experimental binding affinities, does not result in a function with optimal docking capabilities. Vinardo is based on Vina, and was trained through a novel approach, on state of the art datasets. Here we present a scoring function which we call Vinardo (Vina RaDii Optimized). Autodock Vina is a very popular, and highly cited, open source docking program. ![]()
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