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 it

SUBMITTER: Quiroga R 

PROVIDER: S-EPMC4865195 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature