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Postprocessing of Docked Protein−Ligand Complexes Using Implicit Solvation Models
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Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/(sici)1096-987x(19990130)20:2<217::aid-jcc4>3.0.co;2-aopenalex-snapshot
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