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    Structure Prediction

    Reliable and Accurate Solution to the Induced Fit Docking Problem for Protein–Ligand Binding
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    • Edward B. Miller
      Edward B. Miller
      Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
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    • Robert B. Murphy
      Robert B. Murphy
      Schrödinger, Inc., 10201 Wateridge Circle, San Diego, California 92121, United States
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      Daniel Sindhikara
      Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
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      Kenneth W. Borrelli
      Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
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      Matthew J. Grisewood
      Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
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      Fabio Ranalli
      Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
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      Steven L. Dixon
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      Steven Jerome
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      Nicholas A. Boyles
      Schrödinger, Inc., 101 SW Main Street, Portland, Oregon 97204, United States
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    • Sayan Mondal
      Sayan Mondal
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      Salma B. Rafi
      Schrödinger, Inc., 101 SW Main Street, Portland, Oregon 97204, United States
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      Dawn M. Troast
      Morphic Therapeutic, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
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      Robert Abel
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    • Richard A. Friesner*
      Richard A. Friesner
      Department of Chemistry, Columbia University, 3000 Broadway, MC 3110, New York, New York 10036, United States
      *Phone: 212-854-7606. Fax: 212-854-7454. Email: [email protected]
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    Journal of Chemical Theory and Computation

    Cite this: J. Chem. Theory Comput. 2021, 17, 4, 2630–2639
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    https://doi.org/10.1021/acs.jctc.1c00136
    Published March 29, 2021
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    Abstract

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    We present a reliable and accurate solution to the induced fit docking problem for protein–ligand binding by combining ligand-based pharmacophore docking, rigid receptor docking, and protein structure prediction with explicit solvent molecular dynamics simulations. This novel methodology in detailed retrospective and prospective testing succeeded to determine protein–ligand binding modes with a root-mean-square deviation within 2.5 Å in over 90% of cross-docking cases. We further demonstrate these predicted ligand–receptor structures were sufficiently accurate to prospectively enable predictive structure-based drug discovery for challenging targets, substantially expanding the domain of applicability for such methods.

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    • Detailed methodology as well as performance of individual components of algorithm and scoring function, additional tables listing complete composition of data sets, and parameter values for composite scoring function (PDF)

    • Coordinates of public retrospective predictions (ZIP)

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    Cite this: J. Chem. Theory Comput. 2021, 17, 4, 2630–2639
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