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Exploring Complex Protein−Ligand Recognition Mechanisms with Coarse Metadynamics
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/(sici)1096-987x(19981115)19:14<1639::aid-jcc10>3.0.co;2-bopenalex-snapshot
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inferredcites →https://doi.org/10.1002/1096-987x(200009)21:12<1049::aid-jcc3>3.0.co;2-fopenalex-snapshot
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inferredcites →https://doi.org/10.1002/1521-3773(20020802)41:15<2644::aid-anie2644>3.0.co;2-oopenalex-snapshot
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inferredcites →https://doi.org/10.1002/jcc.20035openalex-snapshot
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inferredcites →https://doi.org/10.1002/jcc.20289openalex-snapshot
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inferredcites →https://doi.org/10.1002/jcc.540150503openalex-snapshot
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inferredcites →https://doi.org/10.1002/med.20067openalex-snapshot
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inferredcites →https://doi.org/10.1002/pro.5560040611openalex-snapshot
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inferredcites →https://doi.org/10.1002/prot.10028openalex-snapshot
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inferredcites →https://doi.org/10.1002/prot.10115openalex-snapshot
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inferredcites →https://doi.org/10.1002/prot.20088openalex-snapshot
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inferredcites →https://doi.org/10.1002/prot.21082openalex-snapshot
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inferredcites →https://doi.org/10.1006/jcph.1996.0001openalex-snapshot
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inferredcites →https://doi.org/10.1016/0021-9991(77)90098-5openalex-snapshot
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inferredcites →https://doi.org/10.1016/0022-2836(89)90609-8openalex-snapshot
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inferredcites →https://doi.org/10.1016/j.tibs.2003.12.004openalex-snapshot
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Incoming claims: where this work appears in other papers’ reference lists and arguments.
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