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John D. Chodera

Active 1992–2025

127
Papers
25,274
Citations
69
h-index
118
i10-index

Citations

Citations per year for John D. Chodera1970: 2 citations1973: 2 citations1974: 1 citations1983: 1 citations1986: 1 citations1992: 3 citations1993: 2 citations1996: 4 citations1999: 1 citations2000: 1 citations2001: 1 citations2003: 2 citations2004: 1 citations2005: 11 citations2006: 6 citations2007: 40 citations2008: 63 citations2009: 111 citations2010: 153 citations2011: 180 citations2012: 184 citations2013: 181 citations2014: 234 citations2015: 236 citations2016: 309 citations2017: 293 citations2018: 340 citations2019: 708 citations2020: 847 citations2021: 1,222 citations2022: 992 citations2023: 809 citations2024: 1,031 citations2025: 705 citations2026: 95 citations1971–1972: no citations, so these years are not shown1975–1982: no citations, so these years are not shown1984–1985: no citations, so these years are not shown1987–1991: no citations, so these years are not shown1994–1995: no citations, so these years are not shown1997–1998: no citations, so these years are not shown2002: no citations, so this year is not shown

Citation sources

Countries

World map of the countries and regions citing this authorUnited States: 3,108 citing papers, 31.7% of this breakdownChina: 854 citing papers, 8.7% of this breakdownGermany: 759 citing papers, 7.7% of this breakdownUnited Kingdom: 687 citing papers, 7% of this breakdownFrance: 359 citing papers, 3.7% of this breakdownItaly: 325 citing papers, 3.3% of this breakdownSwitzerland: 312 citing papers, 3.2% of this breakdownCanada: 246 citing papers, 2.5% of this breakdownSpain: 219 citing papers, 2.2% of this breakdownIndia: 203 citing papers, 2.1% of this breakdownJapan: 194 citing papers, 2% of this breakdownSweden: 191 citing papers, 2% of this breakdown
0%31.7%Other 23.9%

Institutions

Fields

  • Biochemistry, Genetics and Molecular Biology43.9%
  • Medicine20.2%
  • Computer Science14.7%
  • Physics and Astronomy6.1%
  • Materials Science5.6%
  • Chemistry3.5%
  • Other6%

Topics

  • Protein Structure and Dynamics13.8%
  • Computational Drug Discovery Methods8.4%
  • SARS-CoV-2 and COVID-19 Research4%
  • Enzyme Structure and Function3.4%
  • Machine Learning in Materials Science3.4%
  • Spectroscopy and Quantum Chemical Studies3.2%
  • Other63.8%

Coauthors

All papers

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  1. Statistically optimal analysis of samples from multiple equilibrium states

    Authors: Michael R. Shirts, John D. Chodera - The Journal of Chemical Physics 2008 cited by 1,992

  2. Markov models of molecular kinetics: Generation and validation

    Authors: Jan-Hendrik Prinz, Hao Wu, Marco Sarich, Bettina G. Keller, Martin Senne, Martin Held, John D. Chodera, Christof Schütte, Frank Noé - The Journal of Chemical Physics 2011 cited by 1,347

  3. MEN1 mutations mediate clinical resistance to menin inhibition

    Authors: Florian Perner, Eytan M. Stein, Daniela V. Wenge, Sukrit Singh, Jeonghyeon Kim, Athina Apazidis, Homa Rahnamoun, Disha Anand, Christian Marinaccio, Charlie Hatton, Yanhe Wen, Richard M. Stone, David Schaller, Shoron Mowla, Wenbin Xiao, Holly A. Gamlen, Aaron J. Stonestrom, Sonali Persaud, Elizabeth T. Ener, Jevon Cutler, John G. Doench, Gerard M. McGeehan, Andrea Volkamer, John D. Chodera, Radosław P. Nowak, Eric S. Fischer, Ross L. Levine, Scott A. Armstrong, Sheng F. Cai - Nature 2023 cited by 243

  4. SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape

    Authors: Tyler N. Starr, Nadine Czudnochowski, Zhuoming Liu, Fabrizia Zatta, Young‐Jun Park, Amin Addetia, Dora Pinto, Martina Beltramello, Patrick Hernandez, Allison J. Greaney, Roberta Marzi, William G. Glass, Ivy Zhang, Adam S. Dingens, John E. Bowen, M. Alejandra Tortorici, Alexandra C. Walls, Jason A. Wojcechowskyj, Anna De Marco, Laura E. Rosen, Jiayi Zhou, Martin Montiel-Ruiz, Hannah Kaiser, Josh R. Dillen, Heather Tucker, Jessica Bassi, Chiara Silacci-Fregni, Michael P. Housley, Julia di Iulio, Gloria Lombardo, Maria L. Agostini, Nicole Sprugasci, Katja Culap, Stefano Jaconi, Marcel Meury, Exequiel Dellota, Rana Abdelnabi, Caroline S. Foo, Elisabetta Cameroni, Spencer Stumpf, Tristan I. Croll, Jay C. Nix, Colin Havenar‐Daughton, Luca Piccoli, Fabio Benigni, Johan Neyts, Amalio Telenti, Florian A. Lempp, Matteo Samuele Pizzuto, John D. Chodera, Christy M. Hebner, Herbert W. Virgin, Sean P. J. Whelan, David Veesler, Davide Corti, Jesse D. Bloom, Gyorgy Snell - Nature 2021 cited by 600

  5. Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors

    Authors: Melissa L. Boby, D. Fearon, Matteo P. Ferla, Mihajlo Filep, L. Koekemoer, Matthew C. Robinson, John D. Chodera, Alpha A. Lee, Nir London, Annette von Delft, F. von Delft, Hagit Achdout, A. Aimon, Dominic S. Alonzi, Robert Arbon, J.C. Aschenbrenner, Blake Balcomb, Elad Bar-David, Haim Barr, Amir Ben‐Shmuel, James M. Bennett, Vitaliy A. Bilenko, Bruce Borden, Pascale Boulet, Gregory R. Bowman, Lennart Brewitz, Juliane Brun, Sarma BVNBS, Mark Calmiano, Anna Carbery, Daniel W. Carney, Emma Cattermole, Edcon Chang, Eugene Chernyshenko, Austin Clyde, Joseph E. Coffland, Galit Cohen, Jason C. Cole, Alessandro Contini, Lisa Sanderson Cox, Tristan I. Croll, Milan Cvitkovic, Steven De Jonghe, Alex Dias, Kim Donckers, David Dotson, A. Douangamath, Shirly Duberstein, Tim Dudgeon, Louise E. Dunnett, Peter Eastman, Noam Erez, Charles J. Eyermann, M. Fairhead, Gwen Fate, O. Fedorov, R.S. Fernandes, Lori Ferrins, Richard Foster, Holly Foster, Laurent Fraisse, Ronen Gabizon, Adolfo García‐Sastre, Victor O. Gawriljuk, Paul Gehrtz, C. Gileadi, Charline Giroud, William G. Glass, Robert C. Glen, Itai Glinert, André S. Godoy, Marian V. Gorichko, T.J. Gorrie-Stone, Ed Griffen, Amna Haneef, Storm Hassell Hart, Jag Heer, Michael M. Henry, Michelle L. Hill, Sam Horrell, Qiu Yu J. Huang, Victor D. Huliak, Matthew F. D. Hurley, Tomer Israely, Andrew J. Jajack, Jitske Jansen, Eric Jnoff, Dirk Jochmans, Tobias John, Benjamin Kaminow, Lulu Kang, A.L. Kantsadi, Peter W. Kenny, J. L. Kiappes, Serhii O. Kinakh, Boris Kovar, T. Krojer, Van Ngoc Thuy La, Sophie Laghnimi-Hahn, Bruce A. Lefker and 118 more - Science 2023 cited by 175

  6. Best Practices for Alchemical Free Energy Calculations [Article v1.0].

    Authors: Antonia S. J. S. Mey, Bryce K. Allen, Hannah E. Bruce Macdonald, John D. Chodera, David F. Hahn, Maximilian Kühn, Julien Michel, David L. Mobley, Levi N. Naden, Samarjeet Prasad, Andrea Rizzi, Jenke Scheen, Michael R. Shirts, Gary Tresadern, Huafeng Xu - Living Journal of Computational Molecular Science 2019 cited by 270

  7. Current Status of the AMOEBA Polarizable Force Field

    Authors: Jay W. Ponder, Chuanjie Wu, Pengyu Ren, Vijay S. Pande, John D. Chodera, Michael J. Schnieders, Imran S. Haque, David L. Mobley, Daniel S. Lambrecht, Robert A. DiStasio, Martin Head‐Gordon, Gary N. I. Clark, Margaret E. Johnson, Teresa Head‐Gordon - The Journal of Physical Chemistry B 2010 cited by 1,481

  8. Ensemble Docking in Drug Discovery

    Authors: Rommie E. Amaro, Jérôme Baudry, John D. Chodera, Özlem Demir, J. Andrew McCammon, Yinglong Miao, Jeremy C. Smith - Biophysical Journal 2018 cited by 496

  9. Markov state models of biomolecular conformational dynamics

    Authors: John D. Chodera, Frank Noé - Current Opinion in Structural Biology 2014 cited by 836

  10. Hypoxia Induces Production of L-2-Hydroxyglutarate

    Authors: Andrew M. Intlekofer, Raymond G. Dematteo, Sriram Venneti, Lydia W.S. Finley, Chao Lü, Alexander R. Judkins, Ariën S. Rustenburg, Patrick Grinaway, John D. Chodera, Justin R. Cross, Craig B. Thompson - Cell Metabolism 2015 cited by 510

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

    Authors: Suzanne Ackloo, Rima Al‐awar, Rommie E. Amaro, C.H. Arrowsmith, Hatylas Azevedo, Robert A. Batey, Yoshua Bengio, Ulrich A. K. Betz, Cristian Bologa, John D. Chodera, Wendy D. Cornell, Ian Dunham, Gerhard F. Ecker, Kristina Edfeldt, A.M. Edwards, Michael K. Gilson, Cláudia R. Gordijo, Gerhard Heßler, Alexander Hillisch, Anders Hogner, John J. Irwin, Johanna M. Jansen, Daniel Kühn, Andrew R. Leach, Alpha A. Lee, Uta Lessel, Maxwell R. Morgan, John Moult, Ingo Muegge, Tudor I. Oprea, Benjamin Perry, Patrick Riley, Sophie A. L. Rousseaux, Kumar Singh Saikatendu, Vijayaratnam Santhakumar, Matthieu Schapira, Cora Scholten, Matthew H. Todd, Masoud Vedadi, Andrea Volkamer, Timothy M. Willson - Nature Reviews Chemistry 2022 cited by 102

  12. OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

    Authors: 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 - PLoS Computational Biology, PLoS Comput. Biol. 2016 cited by 2,763

  13. SARS-CoV-2 simulations go exascale to predict dramatic spike opening and cryptic pockets across the proteome

    Authors: Maxwell I. Zimmerman, Justin R. Porter, Michael D. Ward, Sukrit Singh, Neha Vithani, Artur Meller, Upasana L. Mallimadugula, Catherine E. Kuhn, Jonathan Borowsky, Rafal Wiewiora, Matthew F. D. Hurley, Aoife M. Harbison, Carl A. Fogarty, Joseph E. Coffland, Elisa Fadda, Vincent A. Voelz, John D. Chodera, Gregory R. Bowman - Nature Chemistry 2021 cited by 301

  14. OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

    Authors: Peter Eastman, Mark S. Friedrichs, John D. Chodera, Randall J. Radmer, Christopher M. Bruns, Joy P. Ku, Kyle A. Beauchamp, Thomas J. Lane, Lee‐Ping Wang, Diwakar Shukla, Tony Tye, Mike Houston, Timo Stich, Christoph Klein, Michael R. Shirts, Vijay S. Pande - Journal of Chemical Theory and Computation 2012 cited by 750

  15. INK4 Tumor Suppressor Proteins Mediate Resistance to CDK4/6 Kinase Inhibitors

    Authors: Qing Li, Baishan Jiang, Jiaye Guo, Hong Shao, Isabella Del Priore, Qing Chang, Rei Kudo, Zhiqiang Li, Pedram Razavi, Bo Liu, Andrew S. Boghossian, Matthew G. Rees, Melissa M. Ronan, Jennifer A. Roth, Katherine A. Donovan, Marta Palafox, Jorge S. Reis‐Filho, Elisa de Stanchina, Eric S. Fischer, Neal Rosen, Violeta Serra, Andrew Koff, John D. Chodera, Nathanael S. Gray, Sarat Chandarlapaty - Cancer Discovery 2021 cited by 165

  16. NNP/MM: Accelerating Molecular Dynamics Simulations with Machine Learning Potentials and Molecular Mechanics

    Authors: Raimondas Galvelis, Alejandro Varela-Rial, Stefan Doerr, Roberto Fino, Peter K. Eastman, Thomas E. Markland, John D. Chodera, Gianni De Fabritiis - Journal of Chemical Information and Modeling, J. Chem. Inf. Model. 2023 cited by 90

  17. Alchemical free energy methods for drug discovery: progress and challenges

    Authors: John D. Chodera, David L. Mobley, Michael R. Shirts, R. W. Dixon, Kim Branson, Vijay S. Pande - Current Opinion in Structural Biology 2011 cited by 586

  18. Development and Benchmarking of Open Force Field v1.0.0—the Parsley Small-Molecule Force Field

    Authors: Yudong Qiu, Daniel G. A. Smith, Simon Boothroyd, Hyesu Jang, David F. Hahn, Jeffrey Wagner, Caitlin C. Bannan, Trevor Gokey, Victoria T. Lim, Chaya Stern, Andrea Rizzi, Bryon Tjanaka, Gary Tresadern, Xavier Lucas, Michael R. Shirts, Michael K. Gilson, John D. Chodera, Christopher I. Bayly, David L. Mobley, Lee‐Ping Wang - Journal of Chemical Theory and Computation 2021 cited by 170

  19. L-2-Hydroxyglutarate production arises from noncanonical enzyme function at acidic pH

    Authors: Andrew M. Intlekofer, Bo Wang, Hui Liu, Hardik Shah, Carlos Carmona‐Fontaine, Ariën S. Rustenburg, Salah Salah, M. R. Gunner, John D. Chodera, Justin R. Cross, Craig B. Thompson - Nature Chemical Biology 2017 cited by 270

  20. Entropy-Enthalpy Compensation: Role and Ramifications in Biomolecular Ligand Recognition and Design

    Authors: John D. Chodera, David L. Mobley - Annual Review of Biophysics 2013 cited by 537

  21. End-to-end differentiable construction of molecular mechanics force fields

    Authors: Yuanqing Wang, Josh Fass, Benjamin Kaminow, John E. Herr, Dominic A. Rufa, Ivy Zhang, Iván Pulido, Michael M. Henry, Hannah E. Bruce Macdonald, Kenichiro Takaba, John D. Chodera - Chemical Science 2022 cited by 90

  22. Acquired resistance to IDH inhibition through trans or cis dimer-interface mutations

    Authors: Andrew M. Intlekofer, Alan H. Shih, Bo Wang, Abbas Nazir, Ariën S. Rustenburg, Steven K. Albanese, Minal Patel, Christopher Famulare, Fabian Correa, Naofumi Takemoto, Vidushi Durani, Hui Liu, Justin Taylor, Noushin Farnoud, Elli Papaemmanuil, Justin R. Cross, Martin S. Tallman, Maria E. Arcila, Mikhail Roshal, Gregory A. Petsko, Bin Wu, Sung Choe, Zenon Konteatis, Scott A. Biller, John D. Chodera, Craig B. Thompson, Ross L. Levine, Eytan M. Stein - Nature 2018 cited by 280

  23. Best Practices for Constructing, Preparing, and Evaluating Protein-Ligand Binding Affinity Benchmarks [Article v1.0]

    Authors: David F. Hahn, Christopher I. Bayly, Melissa L. Boby, Hannah E. Bruce Macdonald, John D. Chodera, Vytautas Gapsys, Antonia S. J. S. Mey, David L. Mobley, Laura Pérez‐Benito, Christina Schindler, Gary Tresadern, Gregory L. Warren - Living Journal of Computational Molecular Science 2022 cited by 81

  24. Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity

    Authors: Emma C. Thomson, Laura E. Rosen, James G. Shepherd, Roberto Spreafico, Ana da Silva Filipe, Jason A. Wojcechowskyj, Christopher Davis, Luca Piccoli, David J. Pascall, Josh R. Dillen, Spyros Lytras, Nadine Czudnochowski, Rajiv Shah, Marcel Meury, Natasha Jesudason, Anna De Marco, Kathy Li, Jessica Bassi, Áine O’Toole, Dora Pinto, Rachel Colquhoun, Katja Culap, Ben Jackson, Fabrizia Zatta, Andrew Rambaut, Stefano Jaconi, Vattipally B. Sreenu, Jay C. Nix, Ivy Zhang, Ruth F. Jarrett, William G. Glass, Martina Beltramello, Kyriaki Nomikou, Matteo Samuele Pizzuto, L. Tong, Elisabetta Cameroni, Tristan I. Croll, Natasha Johnson, Julia di Iulio, Arthur Wickenhagen, Alessandro Ceschi, Aoife M. Harbison, Daniel Mair, Paolo Ferrari, Katherine Smollett, Federica Sallusto, Stephen Carmichael, Christian Garzoni, Jenna Nichols, Massimo Galli, Joseph Hughes, Agostino Riva, Antonia Ho, Marco Schiuma, Malcolm G. Semple, Peter Openshaw, Elisa Fadda, J. Kenneth Baillie, John D. Chodera, Suzannah J. Rihn, Samantha Lycett, Herbert W. Virgin, Amalio Telenti, Davide Corti, David L. Robertson, Gyorgy Snell - Cell 2021 cited by 660