John D. Chodera

26.2k citations

125 papers · 15.2k indexed · 12 hit papers · h-index 50

Impact in

Computational Theory and Mathematics top 0.05%
- Computational Drug Discovery Methods
Molecular Biology top 0.2%
- Protein Structure and Dynamics
- RNA and protein synthesis mechanisms

Papers in

Computational Theory and Mathematics 36
- Computational Drug Discovery Methods 36
Physical and Theoretical Chemistry 12

Co-authors: Michael R. Shirts David L. Mobley Vijay S. Pande Ken A. Dill Frank Noé William C. Swope Peter Eastman Lee‐Ping Wang
Journals: Journal of Chemical Theory and Computation (17 papers)Journal of Computer-Aided Molecular Design (12 papers)The Journal of Physical Chemistry B (10 papers)The Journal of Chemical Physics (9 papers)Journal of Chemical Information and Modeling (7 papers)
Partner nations: United States Germany United Kingdom

In The Last Decade

John D. Chodera

121 papers receiving 15.0k citations

Hit Papers

12 papers align trajectories log scale

Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field 2023 · 111 citations

What are hit papers?

Hit papers significantly outperform the citation benchmark for their cohort. A paper qualifies if any of the following hold:

it has ≥500 total citations;
it reaches ≥1.5× the top-1% citation threshold for papers in the same subfield and year (the threshold is the minimum needed to enter the top 1%, not the average within it);
it reaches the top citation threshold in at least one of its specific research topics.

2023 Journal of Chemical Theory and Computation
2023 Scientific Data
2018 Biophysical Journal
2017 PLoS Computational Biology
2014 Current Opinion in Structural Biology
2013 Annual Review of Biophysics
2012 Journal of Chemical Theory and Computation
2011 The Journal of Chemical Physics
2011 Current Opinion in Structural Biology
2010 The Journal of Physical Chemistry B
2008 The Journal of Chemical Physics
2007 The Journal of Chemical Physics

Peers

Countries citing papers authored by John D. Chodera

Since Specialization

Citations

This map shows the geographic impact of John D. Chodera's research. It shows the number of citations coming from papers published by authors working in each country. You can also color the map by specialization and compare the number of citations received by John D. Chodera with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites John D. Chodera more than expected).

Fields of papers citing papers by John D. Chodera

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by John D. Chodera. Nodes represent research fields, and links connect fields that are likely to share authors. Colored nodes show fields that tend to cite the papers produced by John D. Chodera. The network helps show where John D. Chodera may publish in the future.

Co-authors

The 25 scholars most cited alongside John D. Chodera, linked wherever they have co-authored with each other. Click a name or a connecting line to browse the papers they share.

Border = papers with John D. Chodera Line = papers co-authored together John D. Chodera links everyone, so they are left out of the graph.

All Works

Sort: Min cites: Since: Top N: Style:

20 of 20 papers shown

#	Work
1	The Need for Continuing Blinded Pose- and Activity Prediction Benchmarks Journal of Chemical Information and Modeling ·Christian Krämer, John D. Chodera, Kelly L. Damm‐Ganamet, Michael K. Gilson, Zheng Hong-ming, Uta Lessel, Richard A. Lewis, David L. Mobley, Eva Nittinger, Adam Pecina, Matthieu Schapira, W. Patrick Walters	2025	6
2	Trastuzumab Deruxtecan Resistance via Loss of HER2 Expression and Binding Cancer Discovery ·隆飯田, Linxuan Niu, Aihua Zhou, Jacqueline Colllett, M. Carter, Sukrit Singh, John D. Chodera, Bo Liu, Elisa de Stanchina, Fresia Pareja, Atif A Hashmi, M.R. Busetti, Shanu Modi, Jacqueline Bromberg, Pedram Razavi, Joshua Z. Drago, Sarat Chandarlapaty	2025	3
3	EspalomaCharge: Machine Learning-Enabled Ultrafast Partial Charge Assignment The Journal of Physical Chemistry A ·Yuanqing Wang, Hani Hatimatunnisani, 孝安柳屋, Benjamin Kaminow, J.S. Bouwens, Sheng-ze Lu, John D. Chodera	2024	19
4	Nutmeg and SPICE: Models and Data for Biomolecular Machine Learning Journal of Chemical Theory and Computation ·Peter Eastman, Benjamin P. Pritchard, John D. Chodera, Thomas E. Markland	2024	18
5	Benchmarking Cross-Docking Strategies in Kinase Drug Discovery Journal of Chemical Information and Modeling ·David Schaller, Clara D. Christ, John D. Chodera, Andrea Volkamer	2024	0
6	Death by a thousand cuts through kinase inhibitor combinations that maximize selectivity and enable rational multitargeting eLife ·Jason R. Birk, Sukrit Singh, Benedict‐Tilman Berger, Stefan Knapp, John D. Chodera, Markus A. Seeliger	2023	3
7	NNP/MM: Accelerating Molecular Dynamics Simulations with Machine Learning Potentials and Molecular Mechanics Journal of Chemical Information and Modeling ·Raimondas Galvelis, Alejandro Varela‐Rial, Stefan Doerr, 坂口謙吾, Peter Eastman, Thomas E. Markland, John D. Chodera, Gianni De Fabritiis	2023	49
8	SAMPL7 protein-ligand challenge: A community-wide evaluation of computational methods against fragment screening and pose-prediction Journal of Computer-Aided Molecular Design ·N. Schpak, Mehtap Işık, A. Aimon, David L. Mobley, John D. Chodera, F. von Delft, Philip C. Biggin	2022	16
9	Mutation in Abl kinase with altered drug-binding kinetics indicates a novel mechanism of imatinib resistance Proceedings of the National Academy of Sciences ·Agatha Lyczek, Benedict‐Tilman Berger, 杨敏福, Ping Li, 紳八郎鹿野, 敦山根, H. G. Munshi, Steven K. Albanese, Matthew B. Robers, Stefan Knapp, John D. Chodera, Markus A. Seeliger	2021	40
10	Overview of the SAMPL6 pKa challenge: evaluating small molecule microscopic and macroscopic pKa predictions Journal of Computer-Aided Molecular Design ·Mehtap Işık, Ariën S. Rustenburg, Andrea Rizzi, M. R. Gunner, David L. Mobley, John D. Chodera	2021	40
11	What Markov State Models Can and Cannot Do: Correlation versus Path-Based Observables in Protein-Folding Models Journal of Chemical Theory and Computation ·Ernesto Suárez, Rafal Wiewiora, Yutaka Kitani, Frank Noé, John D. Chodera, Daniel M. Zuckerman	2021	45
12	Machine learning force fields and coarse-grained variables in molecular\n dynamics: application to materials and biological systems arXiv (Cornell University) ·Paraskevi Gkeka, Gabriel Stoltz, Amir Barati Farimani, M. Latanision, Michele Ceriotti, John D. Chodera, Aaron R. Dinner, Andrew L. Ferguson, Jean‐Bernard Maillet, Hervé Minoux, Christine Peter, Fabio Pietrucci, E. Esparis, Alexandre Tkatchenko, Wayne Dennis Swift, Rafal Wiewiora, Tony Lelièvre	2020	138
13	Assessing the accuracy of octanol–water partition coefficient predictions in the SAMPL6 Part II log P Challenge Journal of Computer-Aided Molecular Design ·Mehtap Işık, Yanxin Zha, Thomas Fox, Andrea Rizzi, John D. Chodera, David L. Mobley	2020	50
14	Octanol–water partition coefficient measurements for the SAMPL6 blind prediction challenge Journal of Computer-Aided Molecular Design ·Mehtap Işık, Dorothy Levorse, David L. Mobley, Timothy Rhodes, John D. Chodera	2019	42
15	Quantifying Configuration-Sampling Error in Langevin Simulations of Complex Molecular Systems Entropy ·Josh Fass, David A. Sivak, Gavin E. Crooks, Kyle A. Beauchamp, Benedict Leimkuhler, John D. Chodera	2018	26
16	Biomolecular Simulations under Realistic Macroscopic Salt Conditions The Journal of Physical Chemistry B ·Gregory A. Ross, Ariën S. Rustenburg, Patrick Grinaway, Josh Fass, John D. Chodera	2018	79
17	Predicting resistance of clinical Abl mutations to targeted kinase inhibitors using alchemical free-energy calculations Communications Biology ·Kevin Hauser, Christopher Negron, Steven K. Albanese, Soumya S. Ray, Thomas Steinbrecher, Robert Abel, John D. Chodera, Lingle Wang	2018	64
18	OpenPathSampling: A Python Framework for Path Sampling Simulations. 2. Building and Customizing Path Ensembles and Sample Schemes Journal of Chemical Theory and Computation ·David W. Swenson, Jan-Hendrik Prinz, Frank Noé, John D. Chodera, Peter G. Bolhuis	2018	39
19	Microsecond molecular dynamics simulation of kinase domain of the human tyrosine kinase ABL1 Figshare ·John D. Chodera, Sonya M. Hanson	2016	1
20	The molten globule state is unusually deformable under mechanical force Proceedings of the National Academy of Sciences ·Carl, John D. Chodera, Carlos Bustamante, Susan Marqusee	2012	75

About John D. Chodera

John D. Chodera is a scholar working on Computational Theory and Mathematics, Physical and Theoretical Chemistry, Molecular Biology, Spectroscopy and Atomic and Molecular Physics, and Optics, having authored 125 papers that have together received 15.2k indexed citations. Recurring topics across this work include Protein Structure and Dynamics (67 papers), Computational Drug Discovery Methods (36 papers), Spectroscopy and Quantum Chemical Studies (22 papers), Machine Learning in Materials Science (20 papers), Enzyme Structure and Function (16 papers), Mass Spectrometry Techniques and Applications (13 papers), Advanced Thermodynamics and Statistical Mechanics (8 papers) and RNA and protein synthesis mechanisms (7 papers). The work is most often cited by research in Computational Theory and Mathematics (2.9k citations), Molecular Biology (10.5k citations), Spectroscopy (2.0k citations), Atomic and Molecular Physics, and Optics (3.6k citations) and Physical and Theoretical Chemistry (1.0k citations). John D. Chodera has collaborated with scholars based in United States, Germany and United Kingdom. Frequent co-authors include Michael R. Shirts, David L. Mobley, Vijay S. Pande, Ken A. Dill, Frank Noé, William C. Swope, Peter Eastman, Lee‐Ping Wang, Jed W. Pitera and Kyle A. Beauchamp. Their work appears in journals such as Journal of Chemical Theory and Computation, Journal of Computer-Aided Molecular Design, The Journal of Physical Chemistry B, The Journal of Chemical Physics and Journal of Chemical Information and Modeling.

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