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INTRODUCTION. Receptor-ligand molecular docking is a structure-based approach widely used by the scientific community in Medicinal Chemistry. The main objective is to assist the process of drug discovery, searching for new lead compounds against relevant therapeutic targets with known three-dimensional structures [1]. The program DockThor [2, 3], developed by the group GMMSB/LNCC, has obtained promising results in comparative studies with other well-established docking programs for predicting experimental binding modes, considering several molecular targets and chemical classes of ligands. The first version of the DockThor portal was firstly available for binding mode prediction and was strict to the docking of a single ligand at a time. Despite useful for pose prediction, the scoring function implemented in the first version of the DockThor portal was not suitable for predicting binding affinities, which is crucial for virtual screening studies. Recently, our research group developed new empirical scoring functions to predict protein-ligand binding affinities that demonstrated to be competitive with the best scoring functions reported in the literature [4]. Such encouraging results motivated the development of a new version of the Web server for virtual screening. The DockThor 2.0 portal utilizes the computational facilities provided by the SINAPAD Brazilian high-performance platform (www. lncc. br/sinapad) and the Santos Dumont supercomputer. MATERIALS AND METHODS. The DockThor program has implemented a grid-based method that employs a steady-state genetic algorithm for multiple solutions as the search engine and the …