John D. Chodera

38 papers A* 1Journal 37

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	A Computational Community Blind Challenge on Pan-Coronavirus Drug Discovery Data. J. Chem. Inf. Model. Hugo MacDermott-Opeskin, Jenke Scheen, Cas Wognum, Joshua T. Horton, Devany West, Alexander Matthew Payne, Maria A. Castellanos, Sean Colby, Edward J. Griffen, David Cousins, Jessica Stacey, Lauren Reid, Jasmin Cara Aschenbrenner, Daren Fearon, Blake Balcomb, Peter Marples, Charles W. E. Tomlinson, Ryan Lithgo, Andre S. Godoy, Max Winokan, Haim Barr, Noa Lahav, Michael Lavi, Shirley Duberstein, Galit Cohen, Gwendolyn Fate, Bruce Lefker, Ralph Robinson, Tamas Szommer, Nick Lynch, David D. L. Minh, Van Ngoc Thuy La, Lulu Kang, Kate Huddleston, Ryan Renslow, Mallory Tollefson, W. Patrick Walters, Cynthia Xu, Jonny Hsu, Julien St-Laurent, Honore Etsmoberg, Lu Zhu, Andrew Quirke, Mohamed Iliyas Abdul Haleem, Irfan Alibay, Gunjan Baid, Benjamin Birnbaum, Kevin P. Bishop, Hugo-Javier Bohórquez, Ashmita Bose, C. J. Brown, Jackson W. Burns, Lianjin Cai, Ruel Cedeno, Stephane de Cesco, Vladimir I. Chupakhin, Finlay Clark, Daniel J. Cole, Carles Corbi-Verge, Muhammad Danial, Alec Davi, Wim Dehaen, Niklas Piet Doering, Alexis Dougha, Marie-Pierre Dréanic, Bryce Eakin, Anatol Ehrlich, Rokas Elijosius, Jozef Fülöp, Anthony Gitter, Kenneth Goossens, Yaowen Gu, Teresa Head-Gordon, Laurent Hoffer, Johan Hofmans, Ellena Jiang, Benjamin Kaminow, Sina Khosravi, Asma Feriel Khoualdi, Eelke B. Lenselink, Zhirong Liu, Yue Liu, Sijie Liu, Yizhou Ma, Patrick Maher, Imke Mayer, Oscar Mendez-Lucio, Antonia S. J. S. Mey, Julien Michel, Floriane Montanari, Taoyu Niu, Ryusei Ogino, Ashok Palaniappan, Xiaolin Pan, Auro Patnaik, Long-Hung Dinh Pham, Luis Pinto, Justin Purnomo, Alex Rich, Lars L. Schaaf, Christoph Schran, Rajeev Kumar Singh, Mounika Srilakshmi, Satya Pratik Srivastava, Kunyang Sun, Zhaoxi Sun, Valerij Talagayev, Balamurugan Thirukonda Subramanian Balakrishnan, Ida Titus, Alexandre Tkatchenko, Wojtek Treyde, Giovanni Tricarico, Austin Tripp, Nopsinth Vithayapalert, Yingze Wang, Azmine Toushik Wasi, Steffen Wedig, Gerhard Wolber, Bofei Xu, Weijun Zhou, Frank von Delft, Alpha Lee, Karla Kirkegaard, Peter Sjö, James S. Fraser, John D. Chodera
2026	J	`jnl`	Blind Challenges Let Us See the Path Forward for Predictive Models. J. Chem. Inf. Model. John D. Chodera, W. Patrick Walters, Sriram Kosuri, James S. Fraser
2025	J	`jnl`	The Need for Continuing Blinded Pose- and Activity Prediction Benchmarks. J. Chem. Inf. Model. 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
2024	J	`jnl`	Benchmarking Cross-Docking Strategies in Kinase Drug Discovery. J. Chem. Inf. Model. David Schaller, Clara D. Christ, John D. Chodera, Andrea Volkamer
2024	J	`jnl`	Enhancing Protein-Ligand Binding Affinity Predictions Using Neural Network Potentials. J. Chem. Inf. Model. Francesc Sabanés Zariquiey, Raimondas Galvelis, Emilio Gallicchio, John D. Chodera, Thomas E. Markland, Gianni De Fabritiis
2024	J	`jnl`	Nutmeg and SPICE: Models and Data for Biomolecular Machine Learning. CoRR Peter K. Eastman, Benjamin P. Pritchard, John D. Chodera, Thomas E. Markland
2023	J	`jnl`	Espaloma-0.3.0: Machine-learned molecular mechanics force field for the simulation of protein-ligand systems and beyond. CoRR Kenichiro Takaba, Iván Pulido, Mike Henry, Hugo MacDermott-Opeskin, John D. Chodera, Yuanqing Wang
2023	J	`jnl`	EspalomaCharge: Machine learning-enabled ultra-fast partial charge assignment. CoRR Yuanqing Wang, Iván Pulido, Kenichiro Takaba, Benjamin Kaminow, Jenke Scheen, Lily Wang, John D. Chodera
2023	J	`jnl`	NNP/MM: Accelerating Molecular Dynamics Simulations with Machine Learning Potentials and Molecular Mechanics. J. Chem. Inf. Model. Raimondas Galvelis, Alejandro Varela-Rial, Stefan Doerr, Roberto Fino, Peter K. Eastman, Thomas E. Markland, John D. Chodera, Gianni De Fabritiis
2023	J	`jnl`	OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. CoRR 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, Andreas Krämer, Julien Michel, Joshua A. Mitchell, Vijay S. Pande, João P. G. L. M. Rodrigues, Jaime Rodríguez-Guerra, Andrew C. Simmonett, Jason M. Swails, Ivy Zhang, John D. Chodera, Gianni De Fabritiis, Thomas E. Markland
2023	A*	`conf`	Spatial Attention Kinetic Networks with E(n)-Equivariance. ICLR Yuanqing Wang, John D. Chodera
2023	J	`jnl`	Spatial Attention Kinetic Networks with E(n)-Equivariance. CoRR Yuanqing Wang, John D. Chodera
2022	J	`jnl`	Bayesian-Inference-Driven Model Parametrization and Model Selection for 2CLJQ Fluid Models. J. Chem. Inf. Model. Owen Madin, Simon Boothroyd, Richard A. Messerly, Josh Fass, John D. Chodera, Michael R. Shirts
2022	J	`jnl`	NNP/MM: Fast molecular dynamics simulations with machine learning potentials and molecular mechanics. CoRR Raimondas Galvelis, Alejandro Varela-Rial, Stefan Doerr, Roberto Fino, Peter K. Eastman, Thomas E. Markland, John D. Chodera, Gianni De Fabritiis
2022	J	`jnl`	Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization at Scale. J. Chem. Inf. Model. 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, Daniel J. Cole
2022	J	`jnl`	SAMPL7 protein-ligand challenge: A community-wide evaluation of computational methods against fragment screening and pose-prediction. J. Comput. Aided Mol. Des. Harold Grosjean, Mehtap Isik Bennett, Anthony Aimon, David L. Mobley, John D. Chodera, Frank von Delft, Philip C. Biggin
2022	J	`jnl`	SPICE, A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials. CoRR 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
2021	J	`jnl`	Automated high throughput pK J. Comput. Aided Mol. Des. Matthew N. Bahr, Aakankschit Nandkeolyar, John K. Kenna, Neysa Nevins, Luigi Da Vià, Mehtap Isik Bennett, John D. Chodera, David L. Mobley
2021	J	`jnl`	Overview of the SAMPL6 pK J. Comput. Aided Mol. Des. Mehtap Isik Bennett, Ariën S. Rustenburg, Andrea Rizzi, Marilyn R. Gunner, David L. Mobley, John D. Chodera
2020	J	`jnl`	Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II log P Challenge. J. Comput. Aided Mol. Des. Mehtap Isik Bennett, Teresa Danielle Bergazin, Thomas Fox, Andrea Rizzi, John D. Chodera, David L. Mobley
2020	J	`jnl`	End-to-End Differentiable Molecular Mechanics Force Field Construction. CoRR Yuanqing Wang, Josh Fass, John D. Chodera
2020	J	`jnl`	Is Structure-Based Drug Design Ready for Selectivity Optimization? J. Chem. Inf. Model. Steven K. Albanese, John D. Chodera, Andrea Volkamer, Simon Keng, Robert Abel, Lingle Wang
2020	J	`jnl`	Octanol-water partition coefficient measurements for the SAMPL6 blind prediction challenge. J. Comput. Aided Mol. Des. Mehtap Isik Bennett, Dorothy Levorse, David L. Mobley, Timothy Rhodes, John D. Chodera
2020	J	`jnl`	Standard state free energies, not pK J. Comput. Aided Mol. Des. Marilyn R. Gunner, Taichi Murakami, Ariën S. Rustenburg, Mehtap Isik Bennett, John D. Chodera
2020	J	`jnl`	The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations. J. Comput. Aided Mol. Des. 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
2019	J	`jnl`	Graph Nets for Partial Charge Prediction. CoRR Yuanqing Wang, Josh Fass, Chaya D. Stern, Kun Luo, John D. Chodera
2019	J	`jnl`	Sharing Data from Molecular Simulations. J. Chem. Inf. Model. 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, E. Joseph Jordan, Erik Lindahl, Samuli Ollila, Jana Selent, Daniel G. A. Smith, Phillip J. Stansfeld, Johanna K. S. Tiemann, Mikaël Trellet, Christopher J. Woods, Artem A. Zhmurov
2018	J	`jnl`	Overview of the SAMPL6 host-guest binding affinity prediction challenge. J. Comput. Aided Mol. Des. Andrea Rizzi, Steven Murkli, John N. McNeill, Wei Yao, Matthew R. Sullivan, Michael K. Gilson, Michael Chiu, Lyle Isaacs, Bruce C. Gibb, David L. Mobley, John D. Chodera
2018	J	`jnl`	Quantifying Configuration-Sampling Error in Langevin Simulations of Complex Molecular Systems. Entropy Josh Fass, David A. Sivak, Gavin E. Crooks, Kyle Beauchamp, Benedict J. Leimkuhler, John D. Chodera
2018	J	`jnl`	pK a measurements for the SAMPL6 prediction challenge for a set of kinase inhibitor-like fragments. J. Comput. Aided Mol. Des. Mehtap Isik Bennett, 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
2017	J	`jnl`	OpenMM 7: Rapid development of high performance algorithms for molecular dynamics. PLoS Comput. Biol. 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, Vijay S. Pande
2016	J	`jnl`	Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale. PLoS Comput. Biol. Daniel L. Parton, Patrick B. Grinaway, Sonya M. Hanson, Kyle Beauchamp, John D. Chodera
2016	J	`jnl`	Measuring experimental cyclohexane-water distribution coefficients for the SAMPL5 challenge. J. Comput. Aided Mol. Des. Ariën S. Rustenburg, Justin Dancer, Baiwei Lin, Jianwen A. Feng, Daniel F. Ortwine, David L. Mobley, John D. Chodera
2015	J	`jnl`	Introduction to the special issue: Data Part 2: Experimental Data. J. Comput. Aided Mol. Des. Christian Kramer, John D. Chodera, Terry R. Stouch
2015	J	`jnl`	Modeling error in experimental assays using the bootstrap principle: understanding discrepancies between assays using different dispensing technologies. J. Comput. Aided Mol. Des. Sonya M. Hanson, Sean Ekins, John D. Chodera
2013	J	`jnl`	Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics. J. Comput. Aided Mol. Des. Kai Wang, John D. Chodera, Yanzhi Yang, Michael R. Shirts
2006	J	`jnl`	Long-Time Protein Folding Dynamics from Short-Time Molecular Dynamics Simulations. Multiscale Model. Simul. John D. Chodera, William C. Swope, Jed W. Pitera, Ken A. Dill
2003	J	`jnl`	MOPED: Method for optimizing physical energy parameters using decoys. J. Comput. Chem. Chaok Seok, J. Ben Rosen, John D. Chodera, Ken A. Dill