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Biological and Medicinal Chemistry

Working Paper

Open Science Discovery of Oral Non-Covalent SARS-CoV-2 Main Protease Inhibitors

The COVID Moonshot Consortium, John Chodera, Alpha Lee, Nir London, Frank von Delft

Version 2 posted 19 October 2021

2,202

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4

Citations

Theoretical and Computational Chemistry

Working Paper

Toward Learned Chemical Perception of Force Field Typing Rules

Camila Zanette, Caitlin C. Bannan, Christopher I. Bayly, Josh Fass, Michael Gilson, Michael R. Shirts, John Chodera, David Mobley

Version 3 posted 15 October 2018

1,279

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Theoretical and Computational Chemistry

Working Paper

Sharing Data from Molecular Simulations

Mark J. Abraham, Rossen Apostolov, Jonathan Barnoud, Paul Bauer, Christian Blau, Alexandre M.J.J. Bonvin, matthieu chavent, John Chodera, Karmen Condic-Jurkic, Lucie Delemotte, Helmut Grubmüller, Rebecca J. Howard, E joseph jordan, Erik Lindahl, Samuli Ollila, Jana Selent, Daniel Smith, Phillip J. Stansfeld, Johanna Tiemann, Mikael Trellet, Christopher Woods, Artem Zhmurov

Version 1 posted 09 September 2019

1,203

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Theoretical and Computational Chemistry

Working Paper

Automated High Throughput pKa and Distribution Coefficient Measurements of Pharmaceutical Compounds for the SAMPL8 Blind Prediction Challenge

Matthew Bahr, Aakankschit Nandkeolyar, John Kenna, Luigi DaVia, Neysa Nevins, Mehtap Isik, John Chodera, David Mobley

Version 1 posted 01 October 2021

583

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Theoretical and Computational Chemistry

Working Paper

Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes Using Nonequilibrium Candidate Monte Carlo

Samuel Gill, Nathan M. Lim, Patrick Grinaway, Ariën S. Rustenburg, Josh Fass, Gregory Ross, John D. Chodera, David Mobley

Version 5 posted 23 February 2018

3,458

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Theoretical and Computational Chemistry

Working Paper

Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization At Scale

Joshua Horton, Simon Boothroyd, Jeffrey Wagner, Joshua Mitchell, Trevor Gokey, David Dotson, Pavan Behara, Venkata Ramaswamy, Mark Mackey, John Chodera, Jamshed Anwar, David Mobley, Daniel Cole

Version 1 posted 09 September 2022

534

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1

Citations

Theoretical and Computational Chemistry

Working Paper

Development and Benchmarking of Open Force Field v1.0.0, the Parsley Small Molecule Force Field

Yudong Qiu, Daniel Smith, Simon Boothroyd, Hyesu Jang, Jeffrey Wagner, Caitlin C. Bannan, Trevor Gokey, Victoria T. Lim, Chaya Stern, Andrea Rizzi, Xavier Lucas, Bryon Tjanaka, Michael R. Shirts, Michael Gilson, John Chodera, Christopher I. Bayly, David Mobley, Lee-Ping Wang

Version 4 posted 09 August 2021

1,829

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1

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Theoretical and Computational Chemistry

Working Paper

CACHE (Critical Assessment of Computational Hit-finding Experiments): A public-private partnership benchmarking initiative to enable the development of computational methods for hit-finding

Suzanne Ackloo, Rima Al-awar, Rommie E. Amaro, Cheryl H. Arrowsmith, Hatylas Azevedo, Robert A. Batey, Yoshua Bengio, Ulrich A.K. Betz, Cristian G. Bologa, John D. Chodera, Wendy D. Cornell, Ian Dunham, Gerhard F. Ecker, Kristina Edfeldt, Aled M. Edwards, Michael K. Gilson, Claudia R. Gordijo, Gerhard Hessler, Alexander Hillisch, Anders Hogner, John J. Irwin, Johanna M. Jansen, Daniel Kuhn, Andrew R. Leach, Alpha A. Lee, Uta Lessel, John Moult, Ingo Muegge, Tudor I. Oprea, Benjamin G. Perry, Patrick Riley, Kumar Singh Saikatendu, Vijayaratnam Santhakumar, Matthieu Schapira, Cora Scholten, Matthew H. Todd, Masoud Vedadi, Andrea Volkamer, Timothy M. Willson

Version 1 posted 22 October 2021

2,223

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Theoretical and Computational Chemistry

Working Paper

Binding thermodynamics of host-guest systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative

David Slochower, Niel Henriksen, Lee-Ping Wang, John Chodera, David Mobley, Michael Gilson

Version 2 posted 06 September 2019

1,625

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Theoretical and Computational Chemistry

Working Paper

The Open Force Field Evaluator: An automated, efficient, and scalable framework for the estimation of physical properties from molecular simulation

Simon Boothroyd, Lee-Ping Wang, David Mobley, John Chodera, Michael Shirts

Version 1 posted 05 August 2021

713

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1

Citations

Refine Search

12 results in John Chodera in Authors: John Chodera

Open Science Discovery of Oral Non-Covalent SARS-CoV-2 Main Protease Inhibitors

Toward Learned Chemical Perception of Force Field Typing Rules

Sharing Data from Molecular Simulations

Automated High Throughput pKa and Distribution Coefficient Measurements of Pharmaceutical Compounds for the SAMPL8 Blind Prediction Challenge

Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes Using Nonequilibrium Candidate Monte Carlo

Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization At Scale

Development and Benchmarking of Open Force Field v1.0.0, the Parsley Small Molecule Force Field

CACHE (Critical Assessment of Computational Hit-finding Experiments): A public-private partnership benchmarking initiative to enable the development of computational methods for hit-finding

Binding thermodynamics of host-guest systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative

The Open Force Field Evaluator: An automated, efficient, and scalable framework for the estimation of physical properties from molecular simulation

12 results in Authors: John Chodera