John D. Chodera

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 1%percentile

5.5Author DataRank

Indexed papers

9in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 9 indexed papers attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

SPICE, A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials

Scientific Data(2023)10.1038/s41597-022-01882-6

Top 7%

3.3DataRank

Top 7%171 citations

Pavan Kumar Behara, David Dotson, Raimondas Galvelis, John E. Herr, Joshua T. Horton +7 more

Papers

Driven by 63 papers — median percentile 53. Top paper: “INK4 Tumor Suppressor Proteins Mediate Resistance to CDK4/6 Kinase Inhibitors”.

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

Cancer Discovery(2021)10.1158/2159-8290.cd-20-1726

N/A

3.8DataRank · unranked

168 citations

Baishan Jiang, Jiaye Guo, Hong Shao, Isabella Del Priore, Qing Chang +20 more

SPICE, A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials

Scientific Data(2023)10.1038/s41597-022-01882-6

Top 7%

3.3DataRank

Top 7%171 citations

Pavan Kumar Behara, David Dotson, Raimondas Galvelis, John E. Herr, Joshua T. Horton +7 more

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

Cell(2021)10.1016/j.cell.2021.01.037

N/A

0.974DataRank · unranked

660 citations

Laura E. Rosen, James G. Shepherd, Roberto Spreafico, Ana da Silva Filipe, Jason A. Wojcechowskyj +61 more

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

Nature(2021)10.1038/s41586-021-03807-6

N/A

0.959DataRank · unranked

595 citations

Nadine Czudnochowski, Zhuoming Liu, Fabrizia Zatta, Young‐Jun Park, Amin Addetia +52 more

Nutmeg and SPICE: Models and Data for Biomolecular Machine Learning

Journal of Chemical Theory and Computation(2024)10.1021/acs.jctc.4c00794

Top 21%

0.955DataRank

Top 21%37 citations

Benjamin P. Pritchard, John D. Chodera, Thomas E. Markland, Peter Eastman

SAMPL7 protein-ligand challenge: A community-wide evaluation of computational methods against fragment screening and pose-prediction

Journal of Computer-Aided Molecular Design(2022)10.1007/s10822-022-00452-7

Top 22%

0.933DataRank

Top 22%26 citations

Mehtap Işık, A. Aimon, David L. Mobley, John D. Chodera, F. von Delft +2 more

MEN1 mutations mediate clinical resistance to menin inhibition

Nature(2023)10.1038/s41586-023-05755-9

N/A

0.829DataRank · unranked

251 citations

Eytan M. Stein, Daniela V. Wenge, Sukrit Singh, Jeonghyeon Kim, Athina Apazidis +24 more

Overview of the SAMPL6 pKa challenge: evaluating small molecule microscopic and macroscopic pKa predictions

Journal of Computer-Aided Molecular Design(2021)10.1007/s10822-020-00362-6

N/A

0.641DataRank · unranked

71 citations

Ariën S. Rustenburg, Andrea Rizzi, M. R. Gunner, David L. Mobley, John D. Chodera +1 more

Fitting quantum machine learning potentials to experimental free energy data: predicting tautomer ratios in solution

Chemical Science(2021)10.1039/d1sc01185e

N/A

0.561DataRank · unranked

41 citations

Josh Fass, John D. Chodera, Marcus Wieder

Standard state free energies, not pKas, are ideal for describing small molecule protonation and tautomeric states

Journal of Computer-Aided Molecular Design(2020)10.1007/s10822-020-00280-7

N/A

0.524DataRank · unranked

32 citations

Taichi Murakami, Ariën S. Rustenburg, Mehtap Işık, John D. Chodera, M. R. Gunner

OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials

arXiv (Cornell University)(2023)10.48550/arxiv.2310.03121

N/A

0.457DataRank · unranked

20 citations

Raimondas Galvelis, Raúl P. Peláez, Charlles R. A. Abreu, Stephen E. Farr, Emilio Gallicchio +20 more

Development and Benchmarking of Open Force Field v1.0.0, the Parsley Small Molecule Force Field

(2021)10.33774/chemrxiv-2021-l070l-v3

N/A

0.442DataRank · unranked

18 citations

Daniel Smith, Simon Boothroyd, Hyesu Jang, Jeffrey Wagner, Caitlin C. Bannan +13 more

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

UCL Discovery (University College London)(2021)10.33774/chemrxiv-2021-rzq4n

N/A

0.396DataRank · unranked

13 citations

Rima Al‐awar, Rommie E. Amaro, C.H. Arrowsmith, Hátylas Azevedo, Robert A. Batey +34 more

Prospective Evaluation of Structure-Based Simulations Reveal Their Ability to Predict the Impact of Kinase Mutations on Inhibitor Binding

The Journal of Physical Chemistry B(2025)10.1021/acs.jpcb.4c07794

N/A

0.373DataRank · unranked

11 citations

Vytautas Gapsys, Matteo Aldeghi, David Schaller, Aziz M. Rangwala, Jessica White +11 more

Development and Benchmarking of Open Force Field 2.0.0 — the Sage Small Molecule Force Field

ChemRxiv(2022)10.26434/chemrxiv-2022-n2z1c

N/A

0.345DataRank · unranked

9 citations

Pavan Kumar Behara, Owen Madin, David F. Hahn, Hyesu Jang, Vytautas Gapsys +14 more

A Computational Community Blind Challenge on Pan-Coronavirus Drug Discovery Data

Journal of Chemical Information and Modeling(2026)10.1021/acs.jcim.5c02106

N/A

0.330DataRank · unranked

8 citations

Jenke Scheen, Cas Wognum, Joshua T. Horton, Devany West, Alexander Matthew Payne +121 more

Benchmarking Cross-Docking Strategies in Kinase Drug Discovery

Journal of Chemical Information and Modeling(2024)10.1021/acs.jcim.4c00905

N/A

0.330DataRank · unranked

8 citations

Clara D. Christ, John D. Chodera, Andrea Volkamer, David Schaller

Improving force field accuracy by training against condensed phase mixture properties

ChemRxiv(2022)10.26434/chemrxiv-2021-gsgr4-v3

N/A

0.312DataRank · unranked

7 citations

Owen Madin, David L. Mobley, Lee‐Ping Wang, John D. Chodera, Michael R. Shirts +1 more

Development and Benchmarking of Open Force Field v1.0.0, the Parsley Small Molecule Force Field

(2021)10.33774/chemrxiv-2021-l070l-v4

N/A

0.292DataRank · unranked

6 citations

Daniel Smith, Simon Boothroyd, Hyesu Jang, Jeffrey Wagner, Caitlin C. Bannan +13 more

Identifying and overcoming the sampling challenges in relative binding free energy calculations of a model protein:protein complex

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.03.07.530278

N/A

0.208DataRank · unranked

3 citations

Dominic A. Rufa, Iván Pulido, Michael M. Henry, Laura E. Rosen, Kevin Hauser +3 more

Nutmeg and SPICE: Models and Data for Biomolecular Machine Learning

arXiv (Cornell University)(2024)10.48550/arxiv.2406.13112

Top 72%

0.115DataRank

Top 72%1 citations

Benjamin P. Pritchard, John D. Chodera, Thomas E. Markland, Peter Eastman

How many crystal structures do you need to trust your docking results?

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.09.19.677428

N/A

0.104DataRank · unranked

1 citations

Benjamin Kaminow, Hugo MacDermott-Opeskin, Iván Pulido, Jenke Scheen, Maria A. Castellanos +4 more

Automated High Throughput pKa and Distribution Coefficient Measurements of Pharmaceutical Compounds for the SAMPL8 Blind Prediction Challenge

(2021)10.33774/chemrxiv-2021-8gd90

Top 78%

0.104DataRank

Top 78%1 citations

Aakankschit Nandkeolyar, John K. Kenna, Luigi DaVia, Neysa Nevins, Mehtap Işık +3 more

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

Chemical Science(2022)10.1039/d2sc02739a

N/A

0DataRank · unranked

92 citations

Josh Fass, Benjamin Kaminow, John E. Herr, Dominic A. Rufa, Ivy Zhang +6 more

Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization at Scale

Journal of Chemical Information and Modeling(2022)10.1021/acs.jcim.2c01153

N/A

0DataRank · unranked

61 citations

Simon Boothroyd, Jeffrey Wagner, Joshua A. Mitchell, Trevor Gokey, David Dotson +8 more

Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization At Scale

ChemRxiv(2022)10.26434/chemrxiv-2022-6h628

N/A

0DataRank · unranked

8 citations

Simon Boothroyd, Jeffrey Wagner, Joshua Mitchell, Trevor Gokey, David Dotson +8 more

The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations

Journal of Computer-Aided Molecular Design(2020)10.1007/s10822-020-00290-5

N/A

0DataRank · unranked

136 citations

Travis Jensen, David R. Slochower, Matteo Aldeghi, Vytautas Gapsys, Dimitris Ntekoumes +12 more

Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field

Journal of Chemical Theory and Computation(2023)10.1021/acs.jctc.3c00039

N/A

0DataRank · unranked

193 citations

Pavan Kumar Behara, Owen Madin, David F. Hahn, Hyesu Jang, Vytautas Gapsys +14 more

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

Journal of Chemical Information and Modeling(2023)10.1021/acs.jcim.3c00773

N/A

0DataRank · unranked

92 citations

Alejandro Varela‐Rial, Stefan Doerr, Roberto Fino, Peter Eastman, Thomas E. Markland +3 more

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)10.1021/acs.jctc.3c00333

N/A

0DataRank · unranked

22 citations

Dominic A. Rufa, Iván Pulido, Michael M. Henry, Laura E. Rosen, Kevin Hauser +3 more

Death by a thousand cuts through kinase inhibitor combinations that maximize selectivity and enable rational multitargeting

eLife(2023)10.7554/elife.86189

N/A

0DataRank · unranked

10 citations

Sukrit Singh, Benedict‐Tilman Berger, Stefan Knapp, John D. Chodera, Markus A. Seeliger +1 more

Development and Benchmarking of Open Force Field 2.0.0 — the Sage Small Molecule Force Field

ChemRxiv(2023)10.26434/chemrxiv-2022-n2z1c-v2

N/A

0DataRank · unranked

21 citations

Pavan Kumar Behara, Owen Madin, David F. Hahn, Hyesu Jang, Vytautas Gapsys +14 more

Benchmarking Cross-Docking Strategies for Structure-Informed Machine Learning in Kinase Drug Discovery

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.09.11.557138

N/A

0DataRank · unranked

6 citations

Clara D. Christ, John D. Chodera, Andrea Volkamer, David Schaller

Death by a Thousand Cuts – Combining Kinase Inhibitors for Selective Target Inhibition and Rational Polypharmacology

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.01.13.523972

N/A

0DataRank · unranked

1 citations

Sukrit Singh, Benedict‐Tilman Berger, Stefan Knapp, John D. Chodera, Markus A. Seeliger +1 more

Enhancing Protein–Ligand Binding Affinity Predictions Using Neural Network Potentials

Journal of Chemical Information and Modeling(2024)10.1021/acs.jcim.3c02031

N/A

0DataRank · unranked

52 citations

Raimondas Galvelis, Emilio Gallicchio, John D. Chodera, Thomas E. Markland, Gianni De Fabritiis +1 more

Machine-learned molecular mechanics force fields from large-scale quantum chemical data

Chemical Science(2024)10.1039/d4sc00690a

N/A

0DataRank · unranked

40 citations

Anika J. Friedman, Chapin E. Cavender, Pavan Kumar Behara, Iván Pulido, Michael M. Henry +9 more

Lessons learned during the journey of data: from experiment to model for predicting kinase affinity, selectivity, polypharmacology, and resistance

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.09.10.612176

N/A

0DataRank · unranked

2 citations

Jaime Rodrı́guez-Guerra, David Schaller, Talia B. Kimber, Corey Taylor, Jessica White +10 more

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)10.1021/acs.jctc.3c01298

N/A

0DataRank · unranked

1 citations

Dominic A. Rufa, Iván Pulido, Michael M. Henry, Laura E. Rosen, Kevin Hauser +3 more

Trastuzumab Deruxtecan Resistance via Loss of HER2 Expression and Binding

Cancer Discovery(2025)10.1158/2159-8290.cd-25-0647

N/A

0DataRank · unranked

21 citations

Avantika Gupta, Nicholas Mai, Sharanya Nag, Joshua Lau, Sukrit Singh +12 more

Data from INK4 Tumor Suppressor Proteins Mediate Resistance to CDK4/6 Kinase Inhibitors

10.1158/2159-8290.c.6549415.v1

N/A

0DataRank · unranked

0 citations

Baishan Jiang, Jiaye Guo, Hong Shao, Isabella Del Priore, Qing Chang +20 more

OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials

The Journal of Physical Chemistry B(2023)10.1021/acs.jpcb.3c06662

N/A

0DataRank · unranked

495 citations

Raimondas Galvelis, Raúl P. Peláez, Charlles R. A. Abreu, Stephen E. Farr, Emilio Gallicchio +20 more

Towards chemical accuracy for alchemical free energy calculations with hybrid physics-based machine learning / molecular mechanics potentials

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.07.29.227959

N/A

0DataRank · unranked

108 citations

Hannah E. Bruce Macdonald, Josh Fass, Marcus Wieder, Patrick Grinaway, Adrián E. Roitberg +3 more

SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.06.27.175430

N/A

0DataRank · unranked

61 citations

Justin R. Porter, Michael D. Ward, Sukrit Singh, Neha Vithani, Artur Meller +13 more

Development and Benchmarking of Open Force Field v1.0.0, the Parsley Small Molecule Force Field

ChemRxiv(2020)10.26434/chemrxiv.13082561.v2

N/A

0DataRank · unranked

31 citations

Daniel G. A. Smith, Simon Boothroyd, Hyesu Jang, Jeffrey Wagner, Caitlin C. Bannan +13 more

Capturing non-local through-bond effects in molecular mechanics force fields I: Fragmenting molecules for quantum chemical torsion scans [Article v1.1]

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.08.27.270934

N/A

0DataRank · unranked

15 citations

Christopher I. Bayly, Daniel G. A. Smith, Josh Fass, Lee‐Ping Wang, David L. Mobley +2 more

Fitting quantum machine learning potentials to experimental free energy data: Predicting tautomer ratios in solution

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.10.24.353318

N/A

0DataRank · unranked

15 citations

Josh Fass, John D. Chodera, Marcus Wieder

What Markov state models can and cannot do: Correlation versus path-based observables in protein folding models

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.11.09.374496

N/A

0DataRank · unranked

7 citations

Rafal Wiewiora, Chris Wehmeyer, Frank Noé, John D. Chodera, Daniel Zuckerman +1 more

Is structure based drug design ready for selectivity optimization?

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.07.02.185132

N/A

0DataRank · unranked

3 citations

John D. Chodera, Andrea Volkamer, Simon Keng, Robert Abel, Lingle Wang +1 more

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

Nature Chemistry(2021)10.1038/s41557-021-00707-0

N/A

0DataRank · unranked

304 citations

Justin R. Porter, Michael D. Ward, Sukrit Singh, Neha Vithani, Artur Meller +13 more

Mutation in Abl kinase with altered drug-binding kinetics indicates a novel mechanism of imatinib resistance

Proceedings of the National Academy of Sciences(2021)10.1073/pnas.2111451118

N/A

0DataRank · unranked

73 citations

Benedict‐Tilman Berger, Aziz M. Rangwala, YiTing Paung, Jessica Tom, Hannah Philipose +7 more

What Markov State Models Can and Cannot Do: Correlation versus Path-Based Observables in Protein-Folding Models

Journal of Chemical Theory and Computation(2021)10.1021/acs.jctc.0c01154

N/A

0DataRank · unranked

69 citations

Rafal Wiewiora, Chris Wehmeyer, Frank Noé, John D. Chodera, Daniel Zuckerman +1 more

Quantum Chemistry Common Driver and Databases (QCDB) and Quantum Chemistry Engine (QCEngine): Automation and interoperability among computational chemistry programs

The Journal of Chemical Physics(2021)10.1063/5.0059356

N/A

0DataRank · unranked

45 citations

Annabelle Lolinco, Zachary L. Glick, Jiyoung Lee, Asem Alenaizan, Taylor Barnes +43 more

Discovery of SARS-CoV-2 main protease inhibitors using a synthesis-directed de novo design model

Chemical Communications(2021)10.1039/d1cc00050k

N/A

0DataRank · unranked

38 citations

William McCorkindale, The COVID Moonshot Consortium, Nir Drayman, John D. Chodera, Savaş Tay +3 more

Antibodies to the SARS-CoV-2 receptor-binding domain that maximize breadth and resistance to viral escape

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.04.06.438709

N/A

0DataRank · unranked

21 citations

Nadine Czudnochowski, Fabrizia Zatta, Young‐Jun Park, Zhuoming Liu, Amin Addetia +41 more

Teaching free energy calculations to learn from experimental data

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.08.24.457513

N/A

0DataRank · unranked

15 citations

Josh Fass, John D. Chodera, Marcus Wieder

Mutation in Abl kinase with altered drug binding kinetics indicates a novel mechanism of imatinib resistance

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.06.28.449968

N/A

0DataRank · unranked

4 citations

Benedict‐Tilman Berger, Aziz M. Rangwala, YiTing Paung, Jessica Tom, Hannah Philipose +7 more

Turning high-throughput structural biology into predictive inhibitor design

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.10.15.464568

N/A

0DataRank · unranked

4 citations

D. Fearon, F. von Delft, John D. Chodera, Alpha A. Lee, Kadi L. Saar

Improving force field accuracy by training against condensed phase mixture properties

ChemRxiv(2021)10.26434/chemrxiv-2021-gsgr4-v2

N/A

0DataRank · unranked

3 citations

Owen Madin, David L. Mobley, Lee‐Ping Wang, John D. Chodera, Michael R. Shirts +1 more

Improving force field accuracy by training against condensed phase mixture properties

ChemRxiv(2021)10.26434/chemrxiv-2021-gsgr4

N/A

0DataRank · unranked

2 citations

Owen Madin, David L. Mobley, Lee‐Ping Wang, John D. Chodera, Michael R. Shirts +1 more

Development and Benchmarking of Open Force Field v1.0.0, the Parsley Small Molecule Force Field

ChemRxiv(2021)10.26434/chemrxiv-2021-l070l-v4

N/A

0DataRank · unranked

1 citations

Daniel Smith, Simon Boothroyd, Hyesu Jang, Jeffrey Wagner, Caitlin C. Bannan +13 more

Automated High Throughput pKa and Distribution Coefficient Measurements of Pharmaceutical Compounds for the SAMPL8 Blind Prediction Challenge

ChemRxiv(2021)10.26434/chemrxiv-2021-8gd90

Top 100%

0DataRank

Top 100%0 citations

Aakankschit Nandkeolyar, John K. Kenna, Luigi DaVia, Neysa Nevins, Mehtap Işık +3 more

Development and Benchmarking of Open Force Field v1.0.0, the Parsley Small Molecule Force Field

ChemRxiv(2021)10.26434/chemrxiv-2021-l070l-v3

N/A

0DataRank · unranked

0 citations

Daniel Smith, Simon Boothroyd, Hyesu Jang, Jeffrey Wagner, Caitlin C. Bannan +13 more

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

ChemRxiv(2021)10.26434/chemrxiv-2021-rzq4n

N/A

0DataRank · unranked

0 citations

Rima Al‐awar, Rommie E. Amaro, C.H. Arrowsmith, Hátylas Azevedo, Robert A. Batey +34 more

John D. Chodera

Indexed papers

Top data-sharing exemplar

Papers