The experimental procedures of drug design, proven to be time-consuming and costly, are successfully complemented with computer-aided (in silico) approaches nowadays. Virtual ligand screening (VLS) is one of the most promising approaches when searching for new hit compounds. The efficiency of VLS procedures might be improved via post-docking optimization. In the focus of this investigation is AMMOS (Automatic Molecular Mechanics Optimization for in silico Screening) developed as multi-step structure-based procedure for efficient computational refinement of protein-ligand complexes at different levels of protein flexibility. Their performance has been assessed by the recently developed InterCriteria Analysis (ICrA), elaborated as multi-criterion decision-making approach to reveal possible relations in the behavior of pairs of criteria when multiple objects are considered. The capacity of ICrA as a supporting tool to assess the effect of applying different levels of protein flexibility in the post-docking optimization via AMMOS has been investigated and analyzed.
