Publications by authors named "John D Chodera"

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Trastuzumab Deruxtecan (T-DXd) Resistance via Loss of HER2 Expression and Binding.
Wanyi Chen, Avantika Gupta, Nicholas Mai, Sharanya Nag, Joshua S Lau, John D Chodera

Cancer Discov· November 2025

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How many crystal structures do you need to trust your docking results?
Alexander Matthew Payne, Benjamin Kaminow, Hugo MacDermott-Opeskin, Iván Pulido, Jenke Scheen, John D Chodera

bioRxiv· September 2025

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A Structure-Based Computational Pipeline for Broad-Spectrum Antiviral Discovery.
Maria A Castellanos, Alexander M Payne, Jenke Scheen, Hugo MacDermott-Opeskin, Iván Pulido, John D Chodera

bioRxiv· July 2025

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Prospective Evaluation of Structure-Based Simulations Reveal Their Ability to Predict the Impact of Kinase Mutations on Inhibitor Binding.
Sukrit Singh, Vytautas Gapsys, Matteo Aldeghi, David Schaller, Aziz M Rangwala, John D Chodera

J Phys Chem B· March 2025

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Prospective evaluation of structure-based simulations reveal their ability to predict the impact of kinase mutations on inhibitor binding.
Sukrit Singh, Vytautas Gapsys, Matteo Aldeghi, David Schaller, Aziz M Rangwala, John D Chodera

bioRxiv· March 2025

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Fine-tuning molecular mechanics force fields to experimental free energy measurements.
Dominic Rufa, Joshua Fass, John D Chodera

bioRxiv· January 2025

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Benchmarking Cross-Docking Strategies in Kinase Drug Discovery.
David A Schaller, Clara D Christ, John D Chodera, Andrea Volkamer

J Chem Inf Model· December 2024

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Nutmeg and SPICE: Models and Data for Biomolecular Machine Learning.
Peter Eastman, Benjamin P Pritchard, John D Chodera, Thomas E Markland

J Chem Theory Comput· October 2024

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Lessons learned during the journey of data: from experiment to model for predicting kinase affinity, selectivity, polypharmacology, and resistance.
Raquel López-Ríos de Castro, Jaime Rodríguez-Guerra, David Schaller, Talia B Kimber, Corey Taylor, John D Chodera

bioRxiv· September 2024

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Machine-learned molecular mechanics force fields from large-scale quantum chemical data.
Kenichiro Takaba, Anika J Friedman, Chapin E Cavender, Pavan Kumar Behara, Iván Pulido, John D Chodera

Chem Sci· August 2024

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DrugGym: A testbed for the economics of autonomous drug discovery.
Michael Retchin, Yuanqing Wang, Kenichiro Takaba, John D Chodera

bioRxiv· June 2024

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EspalomaCharge: Machine Learning-Enabled Ultrafast Partial Charge Assignment.
Yuanqing Wang, Iván Pulido, Kenichiro Takaba, Benjamin Kaminow, Jenke Scheen, John D Chodera

J Phys Chem A· May 2024

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Enhancing Protein-Ligand Binding Affinity Predictions Using Neural Network Potentials.
Francesc Sabanés Zariquiey, Raimondas Galvelis, Emilio Gallicchio, John D Chodera, Thomas E Markland

J Chem Inf Model· March 2024

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Enhancing Protein-Ligand Binding Affinity Predictions using Neural Network Potentials.
Francesc Sabanes Zariquiey, Raimondas Galvelis, Emilio Gallicchio, John D Chodera, Thomas E Markland

ArXiv· February 2024

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OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials.
Peter Eastman, Raimondas Galvelis, Raúl P Peláez, Charlles R A Abreu, Stephen E Farr, John D Chodera

J Phys Chem B· January 2024

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Correction to Identifying and Overcoming the Sampling Challenges in Relative Binding Free Energy Calculations of a Model Protein:Protein Complex.
Ivy Zhang, Dominic A Rufa, Iván Pulido, Michael M Henry, Laura E Rosen, John D Chodera

J Chem Theory Comput· January 2024

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Death by a thousand cuts through kinase inhibitor combinations that maximize selectivity and enable rational multitargeting.
Ian R Outhwaite, Sukrit Singh, Benedict-Tilman Berger, Stefan Knapp, John D Chodera

Elife· December 2023

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Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors.
Melissa L Boby, Daren Fearon, Matteo Ferla, Mihajlo Filep, Lizbé Koekemoer, John D Chodera

Science· November 2023

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OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials.
Peter Eastman, Raimondas Galvelis, Raúl P Peláez, Charlles R A Abreu, Stephen E Farr, John D Chodera

ArXiv· November 2023

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NNP/MM: Accelerating Molecular Dynamics Simulations with Machine Learning Potentials and Molecular Mechanics.
Raimondas Galvelis, Alejandro Varela-Rial, Stefan Doerr, Roberto Fino, Peter Eastman, John D Chodera

J Chem Inf Model· September 2023

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Benchmarking Cross-Docking Strategies for Structure-Informed Machine Learning in Kinase Drug Discovery.
David Schaller, Clara D Christ, John D Chodera, Andrea Volkamer

bioRxiv· September 2023

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Identifying and Overcoming the Sampling Challenges in Relative Binding Free Energy Calculations of a Model Protein:Protein Complex.
Ivy Zhang, Dominic A Rufa, Iván Pulido, Michael M Henry, Laura E Rosen, John D Chodera

J Chem Theory Comput· August 2023

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Identifying and overcoming the sampling challenges in relative binding free energy calculations of a model protein:protein complex.
Ivy Zhang, Dominic A Rufa, Iván Pulido, Michael M Henry, Laura E Rosen, John D Chodera

bioRxiv· June 2023

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Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field.
Simon Boothroyd, Pavan Kumar Behara, Owen C Madin, David F Hahn, Hyesu Jang, John D Chodera

J Chem Theory Comput· June 2023

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MEN1 mutations mediate clinical resistance to menin inhibition.
Florian Perner, Eytan M Stein, Daniela V Wenge, Sukrit Singh, Jeonghyeon Kim, John D Chodera

Nature· March 2023

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