The SAMPL6 SAMPLing challenge: Assessing the reliability and efficiency of binding free energy calculations

Andrea Rizzi; Travis Jensen; David R. Slochower; Matteo Aldeghi; Vytautas Gapsys; Dimitris Ntekoumes; Stefano Bosisio; Michail Papadourakis; Niel M. Henriksen; Bert L. de Groot; Zoe Cournia; Alex Dickson; Julien Michel; Michael K. Gilson; Michael R. Shirts; David L. Mobley; John D. Chodera

doi:10.1101/795005

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The SAMPL6 SAMPLing challenge: Assessing the reliability and efficiency of binding free energy calculations

View ORCID ProfileAndrea Rizzi, Travis Jensen, View ORCID ProfileDavid R. Slochower, View ORCID ProfileMatteo Aldeghi, View ORCID ProfileVytautas Gapsys, Dimitris Ntekoumes, Stefano Bosisio, Michail Papadourakis, View ORCID ProfileNiel M. Henriksen, View ORCID ProfileBert L. de Groot, View ORCID ProfileZoe Cournia, View ORCID ProfileAlex Dickson, View ORCID ProfileJulien Michel, View ORCID ProfileMichael K. Gilson, View ORCID ProfileMichael R. Shirts, View ORCID ProfileDavid L. Mobley, View ORCID ProfileJohn D. Chodera

doi: https://doi.org/10.1101/795005

Andrea Rizzi

Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY 10065

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Travis Jensen

Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80309

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David R. Slochower

Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA

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Matteo Aldeghi

Max Planck Institute for Biophysical Chemistry, Computational Biomolecular Dynamics Group, Göttingen, Germany

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Vytautas Gapsys

Max Planck Institute for Biophysical Chemistry, Computational Biomolecular Dynamics Group, Göttingen, Germany

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Dimitris Ntekoumes

Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece

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Stefano Bosisio

EaStCHEM School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, UK

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Michail Papadourakis

EaStCHEM School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, UK

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Niel M. Henriksen

Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USAAtomwise, 717 Market St Suite 800, San Francisco, CA 94103

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Bert L. de Groot

Max Planck Institute for Biophysical Chemistry, Computational Biomolecular Dynamics Group, Göttingen, Germany

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Zoe Cournia

Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece

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Alex Dickson

Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USADepartment of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI, USA

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Julien Michel

EaStCHEM School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, UK

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Michael K. Gilson

Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA

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Michael R. Shirts

Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80309

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David L. Mobley

Department of Pharmaceutical Sciences and Department of Chemistry, University of California, Irvine, California 92697, USA

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For correspondence: dmobley@uci.edu john.chodera@choderalab.org

John D. Chodera

Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065

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For correspondence: dmobley@uci.edu john.chodera@choderalab.org

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Posted October 07, 2019.

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The SAMPL6 SAMPLing challenge: Assessing the reliability and efficiency of binding free energy calculations

Andrea Rizzi, Travis Jensen, David R. Slochower, Matteo Aldeghi, Vytautas Gapsys, Dimitris Ntekoumes, Stefano Bosisio, Michail Papadourakis, Niel M. Henriksen, Bert L. de Groot, Zoe Cournia, Alex Dickson, Julien Michel, Michael K. Gilson, Michael R. Shirts, David L. Mobley, John D. Chodera

bioRxiv 795005; doi: https://doi.org/10.1101/795005

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