Abstract
Despite the increasing capability of supercomputers and new algorithms, sufficient conformational sampling of slow molecular processes remains daunting in molecular dynamics simulations. One such problem arises in studying antibiotic permeation through the outer membrane (OM) porins of multi-drug resistant Gram-negative pathogens, because the narrow constriction region of these porins hinders translation and rotation of antibiotics. To improve sampling of antibiotic conformations, we developed a grid-based workflow to create a comprehensive dataset of discrete antibiotic poses.
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