John D Chodera (John Chodera)

ORCID

Publication Activity (10 Years)

Years Active: 2015-2024
Publications (10 Years): 79

Top Venues

Journal of chemical theory and computation

Journal of chemical information and modeling

The journal of physical chemistry. B

Journal of computer-aided molecular design

Memorial Sloan Kettering Cancer Center

University of California San Francisco (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Memorial Sloan Kettering Cancer Center Feb 03 2019

United States

Associate Member :: Computational and Systems Biology

Memorial Sloan-Kettering Cancer Center Nov 01 2012 - Feb 02 2019

United States

Assistant Member :: Computational Biology

University of California Berkeley Oct 01 2008 - Oct 31 2012

United States

QB3-Berkeley Distinguished Postdoctoral Fellow :: California Institute for Quantitative Biology (QB3)

Stanford University Jan 01 2007 - Oct 01 2008

United States

Postdoctoral Fellow :: Chemistry

Education History

University of California San Francisco - Dec 31 2006

United States

PHD :: Biophysics

California Institute of Technology

United States

BSC :: Biology

Publications

Francesc Sabanés Zariquiey, Raimondas Galvelis, Emilio Gallicchio, John D Chodera, Thomas E Markland, Gianni De Fabritiis
Enhancing Protein-Ligand Binding Affinity Predictions Using Neural Network Potentials. Journal of chemical information and modeling 64 (5) (2024)
Michael Retchin, Yuanqing Wang, Kenichiro Takaba, John D Chodera
DrugGym: A testbed for the economics of autonomous drug discovery. bioRxiv : the preprint server for biology (2024)
Yuanqing Wang, Iván Pulido, Kenichiro Takaba, Benjamin Kaminow, Jenke Scheen, Lily Wang, John D Chodera
EspalomaCharge: Machine Learning-Enabled Ultrafast Partial Charge Assignment. The journal of physical chemistry. A 128 (20) (2024)
Kenichiro Takaba, Anika J Friedman, Chapin E Cavender, Pavan Kumar Behara, Iván Pulido, Michael M Henry, Hugo I MacDermott-Opeskin, Christopher R Iacovella, Arnav M Nagle, Alexander Matthew Payne, Michael R Shirts, David L Mobley, John D Chodera, Yuanqing Wang
Machine-learned molecular mechanics force fields from large-scale quantum chemical data. Chemical science 15 (32) (2024)
Michael Retchin, Yuanqing Wang, Kenichiro Takaba, John D Chodera
DrugGym: A testbed for the economics of autonomous drug discovery. bioRxiv : the preprint server for biology (2024)
Francesc Sabanés Zariquiey, Raimondas Galvelis, Emilio Gallicchio, John D Chodera, Thomas E Markland, Gianni De Fabritiis
Enhancing Protein-Ligand Binding Affinity Predictions Using Neural Network Potentials. Journal of chemical information and modeling 64 (5) (2024)
Yuanqing Wang, Iván Pulido, Kenichiro Takaba, Benjamin Kaminow, Jenke Scheen, Lily Wang, John D Chodera
EspalomaCharge: Machine Learning-Enabled Ultrafast Partial Charge Assignment. The journal of physical chemistry. A (2024)
Kenichiro Takaba, Anika J Friedman, Chapin E Cavender, Pavan Kumar Behara, Iván Pulido, Michael M Henry, Hugo I MacDermott-Opeskin, Christopher R Iacovella, Arnav M Nagle, Alexander Matthew Payne, Michael R Shirts, David L Mobley, John D Chodera, Yuanqing Wang
Machine-learned molecular mechanics force fields from large-scale quantum chemical data. Chemical science 15 (32) (2024)
Michael Retchin, Yuanqing Wang, Kenichiro Takaba, John D Chodera
DrugGym: A testbed for the economics of autonomous drug discovery. bioRxiv : the preprint server for biology (2024)
Ivy Zhang, Dominic A Rufa, Iván Pulido, Michael M Henry, Laura E Rosen, Kevin Hauser, Sukrit Singh, John D Chodera
Correction to Identifying and Overcoming the Sampling Challenges in Relative Binding Free Energy Calculations of a Model Protein:Protein Complex. Journal of chemical theory and computation (2024)
Michael Retchin, Yuanqing Wang, Kenichiro Takaba, John D Chodera
DrugGym: A testbed for the economics of autonomous drug discovery. bioRxiv : the preprint server for biology (2024)
Francesc Sabanés Zariquiey, Raimondas Galvelis, Emilio Gallicchio, John D Chodera, Thomas E Markland, Gianni De Fabritiis
Enhancing Protein-Ligand Binding Affinity Predictions Using Neural Network Potentials. Journal of chemical information and modeling 64 (5) (2024)
Yuanqing Wang, Iván Pulido, Kenichiro Takaba, Benjamin Kaminow, Jenke Scheen, Lily Wang, John D Chodera
EspalomaCharge: Machine Learning-Enabled Ultrafast Partial Charge Assignment. The journal of physical chemistry. A 128 (20) (2024)
Francesc Sabanés Zariquiey, Raimondas Galvelis, Emilio Gallicchio, John D Chodera, Thomas E Markland, Gianni De Fabritiis
Enhancing Protein-Ligand Binding Affinity Predictions Using Neural Network Potentials. Journal of chemical information and modeling 64 (5) (2024)
Yuanqing Wang, Iván Pulido, Kenichiro Takaba, Benjamin Kaminow, Jenke Scheen, Lily Wang, John D Chodera
EspalomaCharge: Machine Learning-Enabled Ultrafast Partial Charge Assignment. The journal of physical chemistry. A 128 (20) (2024)
Francesc Sabanés Zariquiey, Raimondas Galvelis, Emilio Gallicchio, John D Chodera, Thomas E Markland, Gianni De Fabritiis
Enhancing Protein-Ligand Binding Affinity Predictions Using Neural Network Potentials. Journal of chemical information and modeling (2024)
Francesc Sabanés Zariquiey, Raimondas Galvelis, Emilio Gallicchio, John D Chodera, Thomas E Markland, Gianni De Fabritiis
Enhancing Protein-Ligand Binding Affinity Predictions Using Neural Network Potentials. Journal of chemical information and modeling (2024)
Ivy Zhang, Dominic A Rufa, Iván Pulido, Michael M Henry, Laura E Rosen, Kevin Hauser, Sukrit Singh, John D Chodera
Correction to Identifying and Overcoming the Sampling Challenges in Relative Binding Free Energy Calculations of a Model Protein:Protein Complex. Journal of chemical theory and computation 20 (2) (2024)
Kenichiro Takaba, Anika J Friedman, Chapin E Cavender, Pavan Kumar Behara, Iván Pulido, Michael M Henry, Hugo I MacDermott-Opeskin, Christopher R Iacovella, Arnav M Nagle, Alexander Matthew Payne, Michael R Shirts, David L Mobley, John D Chodera, Yuanqing Wang
Machine-learned molecular mechanics force fields from large-scale quantum chemical data. Chemical science 15 (32) (2024)
Francesc Sabanés Zariquiey, Raimondas Galvelis, Emilio Gallicchio, John D Chodera, Thomas E Markland, Gianni De Fabritiis
Enhancing Protein-Ligand Binding Affinity Predictions Using Neural Network Potentials. Journal of chemical information and modeling 64 (5) (2024)
Kenichiro Takaba, Anika J Friedman, Chapin E Cavender, Pavan Kumar Behara, Iván Pulido, Michael M Henry, Hugo I MacDermott-Opeskin, Christopher R Iacovella, Arnav M Nagle, Alexander Matthew Payne, Michael R Shirts, David L Mobley, John D Chodera, Yuanqing Wang
Machine-learned molecular mechanics force fields from large-scale quantum chemical data. Chemical science 15 (32) (2024)
Michael Retchin, Yuanqing Wang, Kenichiro Takaba, John D Chodera
DrugGym: A testbed for the economics of autonomous drug discovery. bioRxiv : the preprint server for biology (2024)
Raimondas Galvelis, Alejandro Varela-Rial, Stefan Doerr, Roberto Fino, Peter Eastman, Thomas E Markland, John D Chodera, Gianni De Fabritiis
NNP/MM: Accelerating Molecular Dynamics Simulations with Machine Learning Potentials and Molecular Mechanics. Journal of chemical information and modeling (2023)
Peter Eastman, Raimondas Galvelis, Raul P Pelaez, 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 Pedregal, Andrew C Simmonett, Sukrit Singh, Jason Swails, Philip Turner, Yuanqing Wang, Ivy Zhang, John D Chodera, Gianni De Fabritiis, Thomas E Markland
OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. The journal of physical chemistry. B 128 (1) (2023)
Ian R Outhwaite, Sukrit Singh, Benedict-Tilman Berger, Stefan Knapp, John D Chodera, Markus A Seeliger
Death by a Thousand Cuts â€" Combining Kinase Inhibitors for Selective Target Inhibition and Rational Polypharmacology. bioRxiv : the preprint server for biology (2023)
Peter Eastman, Raimondas Galvelis, Raul P Pelaez, 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 Pedregal, Andrew C Simmonett, Sukrit Singh, Jason Swails, Philip Turner, Yuanqing Wang, Ivy Zhang, John D Chodera, Gianni De Fabritiis, Thomas E Markland
OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. The journal of physical chemistry. B 128 (1) (2023)
Peter Eastman, Raimondas Galvelis, Raul P Pelaez, 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 Pedregal, Andrew C Simmonett, Sukrit Singh, Jason Swails, Philip Turner, Yuanqing Wang, Ivy Zhang, John D Chodera, Gianni De Fabritiis, Thomas E Markland
OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. The journal of physical chemistry. B 128 (1) (2023)
Peter Eastman, Raimondas Galvelis, Raul P Pelaez, 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 Pedregal, Andrew C Simmonett, Sukrit Singh, Jason Swails, Philip Turner, Yuanqing Wang, Ivy Zhang, John D Chodera, Gianni De Fabritiis, Thomas E Markland
OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. The journal of physical chemistry. B 128 (1) (2023)
Peter Eastman, Raimondas Galvelis, Raul P Pelaez, 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 Pedregal, Andrew C Simmonett, Sukrit Singh, Jason Swails, Philip Turner, Yuanqing Wang, Ivy Zhang, John D Chodera, Gianni De Fabritiis, Thomas E Markland
OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. The journal of physical chemistry. B (2023)
Simon Boothroyd, Pavan Kumar Behara, Owen C Madin, David F Hahn, Hyesu Jang, Vytautas Gapsys, Jeffrey R Wagner, Joshua T Horton, David L Dotson, Matthew W Thompson, Jessica Maat, Trevor Gokey, Lee-Ping Wang, Daniel J Cole, Michael K Gilson, John D Chodera, Christopher I Bayly, Michael R Shirts, David L Mobley
Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field. Journal of chemical theory and computation (2023)
Peter Eastman, Raimondas Galvelis, Raul P Pelaez, 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 Pedregal, Andrew C Simmonett, Sukrit Singh, Jason Swails, Philip Turner, Yuanqing Wang, Ivy Zhang, John D Chodera, Gianni De Fabritiis, Thomas E Markland
OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. The journal of physical chemistry. B 128 (1) (2023)
Peter Eastman, Raimondas Galvelis, Raul P Pelaez, 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 Pedregal, Andrew C Simmonett, Sukrit Singh, Jason Swails, Philip Turner, Yuanqing Wang, Ivy Zhang, John D Chodera, Gianni De Fabritiis, Thomas E Markland
OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. The journal of physical chemistry. B (2023)
David Schaller, Clara D Christ, John D Chodera, Andrea Volkamer
Benchmarking Cross-Docking Strategies for Structure-Informed Machine Learning in Kinase Drug Discovery. bioRxiv : the preprint server for biology (2023)
Melissa L Boby, Daren Fearon, Matteo Ferla, Mihajlo Filep, Lizbé Koekemoer, Matthew C Robinson, null null, John D Chodera, Alpha A Lee, Nir London, Annette von Delft, Frank von Delft, Hagit Achdout, Anthony Aimon, Dominic S Alonzi, Robert Arbon, Jasmin C Aschenbrenner, Blake H Balcomb, Elad Bar-David, Haim Barr, Amir Ben-Shmuel, James 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 Cox, Tristan Ian Croll, Milan Cvitkovic, Steven De Jonghe, Alex Dias, Kim Donckers, David L Dotson, Alice Douangamath, Shirly Duberstein, Tim Dudgeon, Louise E Dunnett, Peter Eastman, Noam Erez, Charles J Eyermann, Michael Fairhead, Gwen Fate, Oleg Fedorov, Rafaela S Fernandes, Lori Ferrins, Richard Foster, Holly Foster, Laurent Fraisse, Ronen Gabizon, Adolfo García-Sastre, Victor O Gawriljuk, Paul Gehrtz, Carina Gileadi, Charline Giroud, William G Glass, Robert C Glen, Itai Glinert, Andre S Godoy, Marian Gorichko, Tyler Gorrie-Stone, Ed J Griffen, Amna Haneef, Storm Hassell Hart, Jag Heer, Michael Henry, Michelle Hill, Sam Horrell, Qiu Yu Judy Huang, Victor D Huliak, Matthew F D Hurley, Tomer Israely, Andrew Jajack, Jitske Jansen, Eric Jnoff, Dirk Jochmans, Tobias John, Benjamin Kaminow, Lulu Kang, Anastassia L Kantsadi, Peter W Kenny, J L Kiappes, Serhii O Kinakh, Boris Kovar, Tobias Krojer, Van Ngoc Thuy La, Sophie Laghnimi-Hahn, Bruce A Lefker, Haim Levy, Ryan M Lithgo, Ivan G Logvinenko, Petra Lukacik, Hannah Bruce Macdonald, Elizabeth M MacLean, Laetitia L Makower, Tika R Malla, Peter G Marples, Tatiana Matviiuk, Willam McCorkindale, Briana L McGovern, Sharon Melamed, Kostiantyn P Melnykov, Oleg Michurin, Pascal Miesen, Halina Mikolajek, Bruce F Milne, David Minh, Aaron Morris, Garrett M Morris, Melody Jane Morwitzer, Demetri Moustakas, Charles E Mowbray, Aline M Nakamura, Jose Brandao Neto, Johan Neyts, Luong Nguyen, Gabriela D Noske, Vladas Oleinikovas, Glaucius Oliva, Gijs J Overheul, C David Owen, Ruby Pai, Jin Pan, Nir Paran, Alexander Matthew Payne, Benjamin Perry, Maneesh Pingle, Jakir Pinjari, Boaz Politi, Ailsa Powell, Vladimír Pšenák, Iván Pulido, Reut Puni, Victor L Rangel, Rambabu N Reddi, Paul Rees, St Patrick Reid, Lauren Reid, Efrat Resnick, Emily Grace Ripka, Ralph P Robinson, Jaime Rodriguez-Guerra, Romel Rosales, Dominic A Rufa, Kadi Saar, Kumar Singh Saikatendu, Eidarus Salah, David Schaller, Jenke Scheen, Celia A Schiffer, Christopher J Schofield, Mikhail Shafeev, Aarif Shaikh, Ala M Shaqra, Jiye Shi, Khriesto Shurrush, Sukrit Singh, Assa Sittner, Peter Sjö, Rachael Skyner, Adam Smalley, Bart Smeets, Mihaela D Smilova, Leonardo J Solmesky, John Spencer, Claire Strain-Damerell, Vishwanath Swamy, Hadas Tamir, Jenny C Taylor, Rachael E Tennant, Warren Thompson, Andrew Thompson, Susana Tomásio, Charles W E Tomlinson, Igor S Tsurupa, Anthony Tumber, Ioannis Vakonakis, Ronald P van Rij, Laura Vangeel, Finny S Varghese, Mariana Vaschetto, Einat B Vitner, Vincent Voelz, Andrea Volkamer, Martin A Walsh, Walter Ward, Charlie Weatherall, Shay Weiss, Kris M White, Conor Francis Wild, Karolina D Witt, Matthew Wittmann, Nathan Wright, Yfat Yahalom-Ronen, Nese Kurt Yilmaz, Daniel Zaidmann, Ivy Zhang, Hadeer Zidane, Nicole Zitzmann, Sarah N Zvornicanin
Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors. Science (New York, N.Y.) 382 (6671) (2023)
Ian R Outhwaite, Sukrit Singh, Benedict-Tilman Berger, Stefan Knapp, John D Chodera, Markus A Seeliger
Death by a thousand cuts through kinase inhibitor combinations that maximize selectivity and enable rational multitargeting. eLife 12 (2023)
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 James Stonestrom, Sonali Persaud, Elizabeth T Ener, Jevon A 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
MEN1 mutations mediate clinical resistance to menin inhibition. Nature (2023)
Ivy Zhang, Dominic A Rufa, Iván Pulido, Michael M Henry, Laura E Rosen, Kevin Hauser, Sukrit Singh, John D Chodera
Identifying and overcoming the sampling challenges in relative binding free energy calculations of a model protein:protein complex. bioRxiv : the preprint server for biology (2023)
Peter Eastman, Raimondas Galvelis, Raul P Pelaez, 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 Pedregal, Andrew C Simmonett, Sukrit Singh, Jason Swails, Philip Turner, Yuanqing Wang, Ivy Zhang, John D Chodera, Gianni De Fabritiis, Thomas E Markland
OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. The journal of physical chemistry. B 128 (1) (2023)
Ivy Zhang, Dominic A Rufa, Iván Pulido, Michael M Henry, Laura E Rosen, Kevin Hauser, Sukrit Singh, John D Chodera
Identifying and Overcoming the Sampling Challenges in Relative Binding Free Energy Calculations of a Model Protein:Protein Complex. Journal of chemical theory and computation (2023)
Harold Grosjean, Mehtap Işık, Anthony Aimon, David L Mobley, John D Chodera, Frank von Delft, Philip Charles Biggin
SAMPL7 protein-ligand challenge: A community-wide evaluation of computational methods against fragment screening and pose-prediction. Journal of computer-aided molecular design 36 (4) (2022)
Owen C Madin, Simon Boothroyd, Richard A Messerly, Josh Fass, John D Chodera, Michael R Shirts
Bayesian-Inference-Driven Model Parametrization and Model Selection for 2CLJQ Fluid Models. Journal of chemical information and modeling 62 (4) (2022)
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
Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization at Scale. Journal of chemical information and modeling 62 (22) (2022)
Simon Boothroyd, Lee-Ping Wang, David L Mobley, John D Chodera, Michael R Shirts
Open Force Field Evaluator: An Automated, Efficient, and Scalable Framework for the Estimation of Physical Properties from Molecular Simulation. Journal of chemical theory and computation 18 (6) (2022)
David F Hahn, Christopher I Bayly, Hannah E Bruce Macdonald, John D Chodera, Antonia S J S Mey, David L Mobley, Laura Perez Benito, Christina E M Schindler, Gary John Tresadern, Gregory L Warren
Best practices for constructing, preparing, and evaluating protein-ligand binding affinity benchmarks [Article v0.1]. Living journal of computational molecular science 4 (1) (2022)
Simon Boothroyd, Owen C Madin, David L Mobley, Lee-Ping Wang, John D Chodera, Michael R Shirts
Improving Force Field Accuracy by Training against Condensed-Phase Mixture Properties. Journal of chemical theory and computation 18 (6) (2022)
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
End-to-end differentiable construction of molecular mechanics force fields. Chemical science 13 (41) (2022)
Ernesto Suárez, Rafal P Wiewiora, Chris Wehmeyer, Frank Noé, John D Chodera, Daniel M Zuckerman
What Markov State Models Can and Cannot Do: Correlation versus Path-Based Observables in Protein-Folding Models. Journal of chemical theory and computation 17 (5) (2021)
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 Agostini, Nicole Sprugasci, Katja Culap, Stefano Jaconi, Marcel Meury, Exequiel Dellota, Rana Abdelnabi, Shi-Yan Caroline 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 J Veesler, Davide Corti, Jesse D Bloom, Gyorgy Snell
SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape. Nature 597 (7874) (2021)
Mehtap Işık, Ariën S Rustenburg, Andrea Rizzi, M R Gunner, David L Mobley, John D Chodera
Overview of the SAMPL6 pKa challenge: evaluating small molecule microscopic and macroscopic pKa predictions. Journal of computer-aided molecular design 35 (2) (2021)
Daniel G A Smith, Annabelle T Lolinco, Zachary L Glick, Jiyoung Lee, Asem Alenaizan, Taylor A Barnes, Carlos H Borca, Roberto Di Remigio, David L Dotson, Sebastian Ehlert, Alexander G Heide, Michael F Herbst, Jan Hermann, Colton B Hicks, Joshua T Horton, Adrian G Hurtado, Peter Kraus, Holger Kruse, Sebastian J R Lee, Jonathon P Misiewicz, Levi N Naden, Farhad Ramezanghorbani, Maximilian Scheurer, Jeffrey B Schriber, Andrew C Simmonett, Johannes Steinmetzer, Jeffrey R Wagner, Logan Ward, Matthew Welborn, Doaa Altarawy, Jamshed Anwar, John D Chodera, Andreas Dreuw, Heather J Kulik, Fang Liu, Todd J Martinez, Devin A Matthews, Henry F Schaefer, Jiřı Šponer, Justin M Turney, Lee-Ping Wang, Nuwan De Silva, Rollin A King, John F Stanton, Mark S Gordon, Theresa L Windus, C David Sherrill, Lori A Burns
Quantum Chemistry Common Driver and Databases (QCDB) and Quantum Chemistry Engine (QCEngine): Automation and interoperability among computational chemistry programs. The Journal of chemical physics 155 (20) (2021)
Maxwell I Zimmerman, Justin R Porter, Michael D Ward, Sukrit Singh, Neha Vithani, Artur Meller, Upasana L Mallimadugula, Catherine E Kuhn, Jonathan H Borowsky, Rafal P 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
SARS-CoV-2 simulations go exascale to predict dramatic spike opening and cryptic pockets across the proteome. Nature chemistry 13 (7) (2021)
Marcus Wieder, Josh Fass, John D Chodera
Fitting quantum machine learning potentials to experimental free energy data: predicting tautomer ratios in solution. Chemical science 12 (34) (2021)
Yudong Qiu, Daniel G A Smith, Simon Boothroyd, Hyesu Jang, David F Hahn, Jeffrey Wagner, Caitlin C Bannan, Trevor Gokey, Victoria T Lim, Chaya D Stern, Andrea Rizzi, Bryon Tjanaka, Gary John Tresadern, Xavier Lucas, Michael R Shirts, Michael K Gilson, John D Chodera, Christopher I Bayly, David L Mobley, Lee-Ping Wang
Development and Benchmarking of Open Force Field v1.0.0-the Parsley Small-Molecule Force Field. Journal of chemical theory and computation 17 (10) (2021)
Qing Li, Baishan Jiang, Jiaye Guo, Hong Shao, Isabella S Del Priore, Qing Chang, Rei Kudo, Zhiqiang Li, Pedram Razavi, Bo Liu, Andrew S Boghossian, Matthew G Rees, Melissa A Ronan, Jennifer A Roth, Katherine Aleisha Donovan, Marta Palafox, Jorge S Reis-Filho, Elisa de Stanchina, Eric S Fischer, Neal X Rosen, Violeta Serra, Andrew Koff, John D Chodera, Nathanael S Gray, Sarat Chandarlapaty
INK4 tumor suppressor proteins mediate resistance to CDK4/6 kinase inhibitors. Cancer discovery (2021)
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
The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations. Journal of computer-aided molecular design 34 (5) (2020)
Mehtap Işık, Teresa Danielle Bergazin, Thomas Fox, Andrea Rizzi, John D Chodera, David L Mobley
Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II log P Challenge. Journal of computer-aided molecular design 34 (4) (2020)
Steven K Albanese, John D Chodera, Andrea Volkamer, Simon Keng, Robert Abel, Lingle Wang
Is Structure-Based Drug Design Ready for Selectivity Optimization? Journal of chemical information and modeling 60 (12) (2020)
Paraskevi Gkeka, Gabriel Stoltz, Amir Barati Farimani, Zineb Belkacemi, Michele Ceriotti, John D Chodera, Aaron R Dinner, Andrew L Ferguson, Jean-Bernard Maillet, Hervé Minoux, Christine Peter, Fabio Pietrucci, Ana Silveira, Alexandre Tkatchenko, Zofia Trstanova, Rafal Wiewiora, Tony Lelièvre
Machine Learning Force Fields and Coarse-Grained Variables in Molecular Dynamics: Application to Materials and Biological Systems. Journal of chemical theory and computation 16 (8) (2020)
Gerard Minuesa, Steven K Albanese, Wei Xie, Yaniv Kazansky, Daniel Worroll, Arthur Chow, Alexandra Schurer, Sun-Mi Park, Christina Z Rotsides, James Taggart, Andrea Rizzi, Levi N Naden, Timothy Chou, Saroj Gourkanti, Daniel Cappel, Maria C Passarelli, Lauren Fairchild, Carolina Adura, J Fraser Glickman, Jessica Schulman, Christopher Famulare, Minal Patel, Joseph K Eibl, Gregory M Ross, Shibani Bhattacharya, Derek S Tan, Christina S Leslie, Thijs Beuming, Dinshaw J Patel, Yehuda Goldgur, John D Chodera, Michael Gregory Kharas
Small-molecule targeting of MUSASHI RNA-binding activity in acute myeloid leukemia. Nature communications 10 (1) (2019)
Mehtap Işık, Dorothy Levorse, David L Mobley, Timothy Rhodes, John D Chodera
Octanol-water partition coefficient measurements for the SAMPL6 blind prediction challenge. Journal of computer-aided molecular design 34 (4) (2019)
David R Slochower, Niel M Henriksen, Lee-Ping Wang, John D Chodera, David L Mobley, Michael K Gilson
Binding Thermodynamics of Host-Guest Systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative. Journal of chemical theory and computation 15 (11) (2019)
Mark Abraham, Rossen Apostolov, Jonathan Barnoud, Paul Bauer, Christian Blau, Alexandre M J J Bonvin, Matthieu Chavent, John D Chodera, Karmen Čondić-Jurkić, Lucie Delemotte, Helmut Grubmüller, Rebecca J Howard, E Joseph Jordan, Erik Lindahl, O H Samuli Ollila, Jana Selent, Daniel G A Smith, Phillip J Stansfeld, Johanna K S Tiemann, Mikael Trellet, Christopher Woods, Artem Zhmurov
Sharing Data from Molecular Simulations. Journal of chemical information and modeling 59 (10) (2019)
Dajun Sang, Sudarshan Pinglay, Rafal P Wiewiora, Myvizhi E Selvan, Hua Jane Lou, John D Chodera, Benjamin E Turk, Zeynep Hülya Gümüş, Liam J Holt
Ancestral reconstruction reveals mechanisms of ERK regulatory evolution. eLife 8 (2019)
Gregory A Ross, Ariën S Rustenburg, Patrick B Grinaway, Josh Fass, John D Chodera
Biomolecular Simulations under Realistic Macroscopic Salt Conditions. The journal of physical chemistry. B 122 (21) (2019)
Shi Chen, Rafal P Wiewiora, Fan Wang Meng, Nicolas Babault, Anqi Ma, Wenyu Yu, Kun Qian, Hao Hu, Hua Zou, Junyi Wang, Shijie Fan, Gil Blum, Fabio Pittella-Silva, Kyle A Beauchamp, Wolfram Tempel, Hualiang Jiang, Kaixian Chen, Robert J Skene, Yujun George Zheng, Peter J Brown, Jian Jin, Cheng Luo, John D Chodera, Minkui Luo
The dynamic conformational landscape of the protein methyltransferase SETD8. eLife 8 (2019)
Camila Zanette, Caitlin C Bannan, Christopher I Bayly, Josh Fass, Michael K Gilson, Michael R Shirts, John D Chodera, David L Mobley
Toward Learned Chemical Perception of Force Field Typing Rules. Journal of chemical theory and computation 15 (1) (2018)
Steven K Albanese, Daniel L Parton, Mehtap Işık, Lucelenie Rodríguez-Laureano, Sonya M Hanson, Julie M Behr, Scott Gradia, Chris Jeans, Nicholas M Levinson, Markus A Seeliger, John D Chodera
An Open Library of Human Kinase Domain Constructs for Automated Bacterial Expression. Biochemistry 57 (31) (2018)
Yosi Shamay, Janki Shah, Mehtap Işık, Aviram Mizrachi, Josef Leibold, Darjus F Tschaharganeh, Daniel Roxbury, Januka Budhathoki-Uprety, Karla Nawaly, James L Sugarman, Emily Baut, Michelle R Neiman, Megan Dacek, Kripa S Ganesh, Darren C Johnson, Ramya Sridharan, Karen L Chu, Vinagolu K Rajasekhar, Scott W Lowe, John D Chodera, Daniel A Heller
Quantitative self-assembly prediction yields targeted nanomedicines. Nature materials 17 (4) (2018)
David W H Swenson, Jan-Hendrik Prinz, Frank Noe, John D Chodera, Peter G Bolhuis
OpenPathSampling: A Python Framework for Path Sampling Simulations. 1. Basics. Journal of chemical theory and computation 15 (2) (2018)
Kevin Hauser, Christopher Negron, Steven K Albanese, Soumya Ray, Thomas Steinbrecher, Robert Abel, John D Chodera, Lingle Wang
Predicting resistance of clinical Abl mutations to targeted kinase inhibitors using alchemical free-energy calculations. Communications biology 1 (2018)
Emily F Ruff, Joseph M Muretta, Andrew R Thompson, Eric W Lake, Soreen Cyphers, Steven K Albanese, Sonya M Hanson, Julie M Behr, David D Thomas, John D Chodera, Nicholas M Levinson
A dynamic mechanism for allosteric activation of Aurora kinase A by activation loop phosphorylation. eLife 7 (2018)
Andrea Rizzi, Steven Murkli, J Nolan McNeill, Wei Yao, Matthew Sullivan, Michael K Gilson, Michael W Chiu, Lyle D Isaacs, Anthony Wishard, David L Mobley, John D Chodera
Overview of the SAMPL6 host-guest binding affinity prediction challenge. Journal of computer-aided molecular design 32 (10) (2018)
Samuel C Gill, Nathan M Lim, Patrick B Grinaway, Ariën S Rustenburg, Josh Fass, Gregory A Ross, John D Chodera, David L Mobley
Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo. The journal of physical chemistry. B 122 (21) (2018)
David L Mobley, Caitlin C Bannan, Andrea Rizzi, Christopher I Bayly, John D Chodera, Victoria T Lim, Nathan M Lim, Kyle A Beauchamp, David R Slochower, Michael R Shirts, Michael K Gilson, Peter K Eastman
Escaping Atom Types in Force Fields Using Direct Chemical Perception. Journal of chemical theory and computation 14 (11) (2018)
David W H Swenson, Jan-Hendrik Prinz, Frank Noe, John D Chodera, Peter G Bolhuis
OpenPathSampling: A Python Framework for Path Sampling Simulations. 2. Building and Customizing Path Ensembles and Sample Schemes. Journal of chemical theory and computation 15 (2) (2018)
Peter Eastman, Jason Swails, John D Chodera, Robert T McGibbon, Yutong Zhao, Kyle A Beauchamp, Lee-Ping Wang, Andrew C Simmonett, Matthew P Harrigan, Chaya D Stern, Rafal P Wiewiora, Bernard R Brooks, Vijay S Pande
OpenMM 7: Rapid development of high performance algorithms for molecular dynamics. PLoS computational biology 13 (7) (2017)
Soreen Cyphers, Emily F Ruff, Julie M Behr, John D Chodera, Nicholas M Levinson
A water-mediated allosteric network governs activation of Aurora kinase A. Nature chemical biology 13 (4) (2017)
Ariën S Rustenburg, Justin Dancer, Baiwei Lin, Jianwen A Feng, Daniel F Ortwine, David L Mobley, John D Chodera
Measuring experimental cyclohexane-water distribution coefficients for the SAMPL5 challenge. Journal of computer-aided molecular design 30 (11) (2016)
Sonya M Hanson, Sean Ekins, John D Chodera
Modeling error in experimental assays using the bootstrap principle: understanding discrepancies between assays using different dispensing technologies. Journal of computer-aided molecular design 29 (12) (2015)

John D Chodera.css-eqlu8i{font-size:small;padding-left:4px;} (John Chodera)

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John D Chodera (John Chodera)