title: Vinardo: A Scoring Function Based on Autodock Vina Improves Scoring, Docking, and Virtual Screening.
abstract: Autodock Vina is a very popular, and highly cited, open source docking program. Here we present a scoring function which we call Vinardo (Vina RaDii Optimized). Vinardo is based on Vina, and was trained through a novel approach, on state of the art datasets. 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. 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. 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. Vinardo outperforms Vina in all tests performed, for all datasets analyzed. 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 http://smina.sf.net. Precompiled binaries, source code, documentation and a tutorial for using Smina to run the Vinardo scoring function are available at the same address.
authors.affiliation: Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), CONICET-Departamento de Matemática y Física, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Córdoba, Argentina.
authors.forename: Rodrigo
authors.identifier: 0000-0001-5015-0531
authors.initials: R
authors.lastname: Quiroga
authors.affiliation: Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), CONICET-Departamento de Matemática y Física, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Córdoba, Argentina.
authors.forename: Marcos A
authors.initials: MA
authors.lastname: Villarreal
mesh_terms: D019992:Databases as Topic; D004353:Drug Evaluation, Preclinical; D008024:Ligands; D062105:Molecular Docking Simulation; D012984:Software; D013816:Thermodynamics
chemical_list: D008024:Ligands