MOPED: Method for optimizing physical energy parameters using decoys. - Chaok Seok; J. Ben Rosen; John D. Chodera; Ken A. Dill (J. Comput. Chem., 2003)

Long-Time Protein Folding Dynamics from Short-Time Molecular Dynamics Simulations. - John D. Chodera; William C. Swope; Jed W. Pitera; Ken A. Dill (Multiscale Model. Simul., 2006)

Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics. - Kai Wang; John D. Chodera; Yanzhi Yang; Michael R. Shirts (J. Comput. Aided Mol. Des., 2013)

Modeling error in experimental assays using the bootstrap principle: understanding discrepancies between assays using different dispensing technologies. - Sonya M. Hanson; Sean Ekins; John D. Chodera (J. Comput. Aided Mol. Des., 2015)

Introduction to the special issue: Data Part 2: Experimental Data. - Christian Kramer; John D. Chodera; Terry R. Stouch (J. Comput. Aided Mol. Des., 2015)

Measuring experimental cyclohexane-water distribution coefficients for the SAMPL5 challenge. - Ariën S. Rustenburg; Justin Dancer; Baiwei Lin; Jianwen A. Feng; Daniel F. Ortwine; David L. Mobley; John D. Chodera (J. Comput. Aided Mol. Des., 2016)

Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale. - Daniel L. Parton; Patrick B. Grinaway; Sonya M. Hanson; Kyle Beauchamp; John D. Chodera (PLoS Comput. Biol., 2016)

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics. - Peter K. Eastman; Jason M. Swails; John D. Chodera; Robert McGibbon; Yutong Zhao; Kyle Beauchamp; Lee-Ping Wang; Andrew C. Simmonett; Matthew P. Harrigan; Chaya D. Stern; Rafal P. Wiewiora; Bernard R. Brooks; et al. (PLoS Comput. Biol., 2017)

Quantifying Configuration-Sampling Error in Langevin Simulations of Complex Molecular Systems. - Josh Fass; David A. Sivak; Gavin E. Crooks; Kyle Beauchamp; Benedict J. Leimkuhler; John D. Chodera (Entropy, 2018)

pK a measurements for the SAMPL6 prediction challenge for a set of kinase inhibitor-like fragments. - Mehtap Isik; Dorothy Levorse; Ariën S. Rustenburg; Ikenna E. Ndukwe; Heather Wang; Xiao Wang; Mikhail Y. Reibarkh; Gary E. Martin; Alexey A. Makarov; David L. Mobley; Timothy Rhodes; John D. Chodera (J. Comput. Aided Mol. Des., 2018)

Overview of the SAMPL6 host-guest binding affinity prediction challenge. - Andrea Rizzi; Steven Murkli; John N. McNeill; Wei Yao 010; Matthew R. Sullivan; Michael K. Gilson; Michael Chiu; Lyle Isaacs; Bruce C. Gibb; David L. Mobley; John D. Chodera (J. Comput. Aided Mol. Des., 2018)

Graph Nets for Partial Charge Prediction. - Yuanqing Wang; Josh Fass; Chaya D. Stern; Kun Luo; John D. Chodera (CoRR, 2019)

Sharing Data from Molecular Simulations. - Mark James Abraham; Rossen Apostolov; Jonathan Barnoud; Paul Bauer; Christian Blau; Alexandre M. J. J. Bonvin; Matthieu Chavent; John D. Chodera; Karmen Condic-Jurkic; Lucie Delemotte; Helmut Grubmüller; Rebecca J. Howard; et al. (J. Chem. Inf. Model., 2019)

End-to-End Differentiable Molecular Mechanics Force Field Construction. - Yuanqing Wang; Josh Fass; John D. Chodera (CoRR, 2020)

Standard state free energies, not pKas, are ideal for describing small molecule protonation and tautomeric states. - Marilyn R. Gunner; Taichi Murakami; Ariën S. Rustenburg; Mehtap Isik; John D. Chodera (J. Comput. Aided Mol. Des., 2020)

Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II log P Challenge. - Mehtap Isik; Teresa Danielle Bergazin; Thomas Fox; Andrea Rizzi; John D. Chodera; David L. Mobley (J. Comput. Aided Mol. Des., 2020)

Octanol-water partition coefficient measurements for the SAMPL6 blind prediction challenge. - Mehtap Isik; Dorothy Levorse; David L. Mobley; Timothy Rhodes; John D. Chodera (J. Comput. Aided Mol. Des., 2020)

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; et al. (J. Comput. Aided Mol. Des., 2020)

Is Structure-Based Drug Design Ready for Selectivity Optimization? - Steven K. Albanese; John D. Chodera; Andrea Volkamer; Simon Keng; Robert Abel; Lingle Wang (J. Chem. Inf. Model., 2020)

Automated high throughput pKa and distribution coefficient measurements of pharmaceutical compounds for the SAMPL8 blind prediction challenge. - Matthew N. Bahr; Aakankschit Nandkeolyar; John K. Kenna; Neysa Nevins; Luigi Da Vià; Mehtap Isik; John D. Chodera; David L. Mobley (J. Comput. Aided Mol. Des., 2021)

Overview of the SAMPL6 pKa challenge: evaluating small molecule microscopic and macroscopic pKa predictions. - Mehtap Isik; Ariën S. Rustenburg; Andrea Rizzi; Marilyn R. Gunner; David L. Mobley; John D. Chodera (J. Comput. Aided Mol. Des., 2021)

NNP/MM: Fast molecular dynamics simulations with machine learning potentials and molecular mechanics. - Raimondas Galvelis; Alejandro Varela-Rial; Stefan Doerr; Roberto Fino; Peter K. Eastman; Thomas E. Markland; John D. Chodera; Gianni De Fabritiis (CoRR, 2022)

SPICE, A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials. - Peter K. Eastman; Pavan Kumar Behara; David L. Dotson; Raimondas Galvelis; John E. Herr; Josh T. Horton; Yuezhi Mao; John D. Chodera; Benjamin P. Pritchard; Yuanqing Wang; Gianni De Fabritiis; Thomas E. Markland (CoRR, 2022)

SAMPL7 protein-ligand challenge: A community-wide evaluation of computational methods against fragment screening and pose-prediction. - Harold Grosjean; Mehtap Isik; Anthony Aimon; David L. Mobley; John D. Chodera; Frank von Delft; Philip C. Biggin (J. Comput. Aided Mol. Des., 2022)

Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization at Scale. - Joshua T. Horton; Simon Boothroyd; Jeffrey Wagner; Joshua A. Mitchell; Trevor Gokey; David L. Dotson; Pavan Kumar Behara; Venkata Krishnan Ramaswamy; Mark Mackey; John D. Chodera; Jamshed Anwar; David L. Mobley; et al. (J. Chem. Inf. Model., 2022)

Bayesian-Inference-Driven Model Parametrization and Model Selection for 2CLJQ Fluid Models. - Owen Madin; Simon Boothroyd; Richard A. Messerly; Josh Fass; John D. Chodera; Michael R. Shirts (J. Chem. Inf. Model., 2022)

Spatial Attention Kinetic Networks with E(n)-Equivariance. - Yuanqing Wang; John D. Chodera (ICLR, 2023)

EspalomaCharge: Machine learning-enabled ultra-fast partial charge assignment. - Yuanqing Wang; Iván Pulido; Kenichiro Takaba; Benjamin Kaminow; Jenke Scheen; Lily Wang; John D. Chodera (CoRR, 2023)

Espaloma-0.3.0: Machine-learned molecular mechanics force field for the simulation of protein-ligand systems and beyond. - Kenichiro Takaba; Iván Pulido; Mike Henry; Hugo MacDermott-Opeskin; John D. Chodera; Yuanqing Wang (CoRR, 2023)

OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. - Peter K. Eastman; Raimondas Galvelis; Raúl P. Peláez; Charlles R. A. Abreu; Stephen E. Farr; Emilio Gallicchio; Anton Gorenko; Michael M. Henry; Frank Hu; Jing Huang 004; Andreas Krämer; Julien Michel; et al. (CoRR, 2023)

NNP/MM: Accelerating Molecular Dynamics Simulations with Machine Learning Potentials and Molecular Mechanics. - Raimondas Galvelis; Alejandro Varela-Rial; Stefan Doerr; Roberto Fino; Peter K. Eastman; Thomas E. Markland; John D. Chodera; Gianni De Fabritiis (J. Chem. Inf. Model., 2023)

Nutmeg and SPICE: Models and Data for Biomolecular Machine Learning. - Peter K. Eastman; Benjamin P. Pritchard; John D. Chodera; Thomas E. Markland (CoRR, 2024)

Benchmarking Cross-Docking Strategies in Kinase Drug Discovery. - David Schaller 002; Clara D. Christ; John D. Chodera; Andrea Volkamer (J. Chem. Inf. Model., 2024)

Enhancing Protein-Ligand Binding Affinity Predictions Using Neural Network Potentials. - Francesc Sabanés Zariquiey; Raimondas Galvelis; Emilio Gallicchio; John D. Chodera; Thomas E. Markland; Gianni De Fabritiis (J. Chem. Inf. Model., 2024)

The Need for Continuing Blinded Pose- and Activity Prediction Benchmarks. - Christian Kramer; John D. Chodera; Kelly L. Damm-Ganamet; Michael K. Gilson; Judith Guenther; Uta F. Lessel; Richard A. Lewis; David L. Mobley; Eva Nittinger; Adam Pecina; Matthieu Schapira; W. Patrick Walters (J. Chem. Inf. Model., 2025)