Darrin M. York

Rutgers Sexual and Reproductive Health and Rights

Also affiliated with Quantitative BioSciences

Biochemistry, Genetics and Molecular BiologyPhysics and Astronomy

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 6%percentile

0.298Author DataRank

Indexed papers

1in 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 1 indexed paper 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.

The QDπ dataset, training data for drug-like molecules and biopolymer fragments and their interactions

Scientific Data(2025)10.1038/s41597-025-04972-3

Top 55%

0.298DataRank

Top 55%5 citations

Timothy J. Giese, Andreas Goetz, Darrin M. York, Jinzhe Zeng

Papers

Driven by 49 papers — median percentile 45. Top paper: “Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems”.

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

The Journal of Chemical Physics(1993)10.1063/1.464397

N/A

1.5DataRank · unranked

30282 citations

Darrin York, Darrin M. York, Lee G. Pedersen, Tom Darden

The QDπ dataset, training data for drug-like molecules and biopolymer fragments and their interactions

Scientific Data(2025)10.1038/s41597-025-04972-3

Top 55%

0.298DataRank

Top 55%5 citations

Timothy J. Giese, Andreas Goetz, Darrin M. York, Jinzhe Zeng

Confluence of theory and experiment reveals the catalytic mechanism of the Varkud satellite ribozyme

Nature Chemistry(2020)10.1038/s41557-019-0391-x

N/A

0DataRank · unranked

58 citations

Benjamin P. Weissman, Timothy J. Giese, Nan‐Sheng Li, Shuichi Hoshika, Saieesh A. Rao +4 more

Beneath the Surface: An Investigation of General Chemistry Students’ Study Skills to Predict Course Outcomes

Journal of Chemical Education(2020)10.1021/acs.jchemed.0c01074

N/A

0DataRank · unranked

22 citations

Darrin M. York, Marc N. Muñiz, Emily L. Atieh

Validation of Free Energy Methods in AMBER

Journal of Chemical Information and Modeling(2020)10.1021/acs.jcim.0c00285

N/A

0DataRank · unranked

27 citations

Yujun Tao, Tai‐Sung Lee, Kenneth M. Merz, Darrin M. York, Hsu‐Chun Tsai

Molecular modeling studies suggest that zinc ions inhibit HIV-1 protease by binding at catalytic aspartates

UNC Libraries(2020)10.17615/93jn-1j40

N/A

0DataRank · unranked

0 citations

Darrin M. York, M W Anderson, L G Pedersen, T A Darden

Development of Range-Corrected Deep Learning Potentials for Fast, Accurate Quantum Mechanical/Molecular Mechanical Simulations of Chemical Reactions in Solution

Journal of Chemical Theory and Computation(2021)10.1021/acs.jctc.1c00201

N/A

0DataRank · unranked

106 citations

Timothy J. Giese, Şölen Ekesan, Darrin M. York, Jinzhe Zeng

Variational Method for Networkwide Analysis of Relative Ligand Binding Free Energies with Loop Closure and Experimental Constraints

Journal of Chemical Theory and Computation(2021)10.1021/acs.jctc.0c01219

N/A

0DataRank · unranked

37 citations

Darrin M. York, Timothy J. Giese

Extension of the Variational Free Energy Profile and Multistate Bennett Acceptance Ratio Methods for High-Dimensional Potential of Mean Force Profile Analysis

The Journal of Physical Chemistry A(2021)10.1021/acs.jpca.1c00736

N/A

0DataRank · unranked

27 citations

Şölen Ekesan, Darrin M. York, Timothy J. Giese

Peripheral Methionine Residues Impact Flavin Photoreduction and Protonation in an Engineered LOV Domain Light Sensor

Biochemistry(2021)10.1021/acs.biochem.1c00064

N/A

0DataRank · unranked

10 citations

Sabine Oldemeyer, Elena Böhm, Abir Ganguly, Darrin M. York, Tilman Kottke +2 more

Development of Range-Corrected Deep Learning Potentials for Fast, Accurate Quantum Mechanical/molecular Mechanical Simulations of Chemical Reactions in Solution

ChemRxiv(2021)10.26434/chemrxiv.14120447.v1

N/A

0DataRank · unranked

6 citations

Timothy J. Giese, Şölen Ekesan, Darrin M. York, Jinzhe Zeng

Development of Range-Corrected Deep Learning Potentials for Fast, Accurate Quantum Mechanical/molecular Mechanical Simulations of Chemical Reactions in Solution

ChemRxiv(2021)10.26434/chemrxiv.14120447

N/A

0DataRank · unranked

3 citations

Timothy J. Giese, Şölen Ekesan, Darrin M. York, Jinzhe Zeng

Introducing a New Bond-Forming Activity in an Archaeal DNA Polymerase by Structure-Guided Enzyme Redesign

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.12.28.474375

N/A

0DataRank · unranked

1 citations

William A. Hansen, Jonathan Hong, Abir Ganguly, Darrin M. York, Sagar D. Khare +2 more

Robust, Efficient and Automated Methods for Accurate Prediction of Protein-Ligand Binding Affinities in AMBER Drug Discovery Boost

ChemRxiv(2021)10.26434/chemrxiv.14727573.v1

N/A

0DataRank · unranked

0 citations

Hsu‐Chun Tsai, Abir Ganguly, Timothy J. Giese, Darrin M. York, Tai‐Sung Lee

Robust, Efficient and Automated Methods for Accurate Prediction of Protein-Ligand Binding Affinities in AMBER Drug Discovery Boost

ChemRxiv(2021)10.26434/chemrxiv.14727573

N/A

0DataRank · unranked

0 citations

Hsu‐Chun Tsai, Abir Ganguly, Timothy J. Giese, Darrin M. York, Tai‐Sung Lee

Combined QM/MM, Machine Learning Path Integral Approach to Compute Free Energy Profiles and Kinetic Isotope Effects in RNA Cleavage Reactions

Journal of Chemical Theory and Computation(2022)10.1021/acs.jctc.2c00151

N/A

0DataRank · unranked

42 citations

Jinzhe Zeng, Şölen Ekesan, Darrin M. York, Timothy J. Giese

AMBER Drug Discovery Boost Tools: Automated Workflow for Production Free-Energy Simulation Setup and Analysis (ProFESSA)

Journal of Chemical Information and Modeling(2022)10.1021/acs.jcim.2c00879

N/A

0DataRank · unranked

38 citations

Hsu‐Chun Tsai, Mario Fernández-Pendás, Tai‐Sung Lee, Timothy J. Giese, Darrin M. York +1 more

Multireference Generalization of the Weighted Thermodynamic Perturbation Method

The Journal of Physical Chemistry A(2022)10.1021/acs.jpca.2c06201

N/A

0DataRank · unranked

23 citations

Jinzhe Zeng, Darrin M. York, Timothy J. Giese

Online Orbital Explorer and BingOrbital Game for Inquiry-Based Activities

Journal of Chemical Education(2022)10.1021/acs.jchemed.1c01277

N/A

0DataRank · unranked

13 citations

Marc N. Muñiz, Karlun Chun, Jonathan Tai, Francesca Guerra, Darrin M. York +1 more

Give and Take: Narrowing the Gap between Theory and Practice of Peer Instructors over Time

Journal of Chemical Education(2022)10.1021/acs.jchemed.2c00170

N/A

0DataRank · unranked

1 citations

Darrin M. York, Emily L. Atieh

Growth of Polycyclic Aromatic Hydrocarbon and Soot Inception by in silico Simulation

ChemRxiv(2022)10.26434/chemrxiv-2022-qp8fc

N/A

0DataRank · unranked

3 citations

Jinzhe Zeng, Liqun Cao, Chih‐Hao Chin, Darrin M. York, Tong Zhu +2 more

AmberTools

Journal of Chemical Information and Modeling(2023)10.1021/acs.jcim.3c01153

N/A

0DataRank · unranked

1916 citations

Hasan Metin Aktulga, Kellon Belfon, David S. Cerutti, G. Andrés Cisneros, Vinícius Wilian D. Cruzeiro +42 more

DeePMD-kit v2: A software package for deep potential models

The Journal of Chemical Physics(2023)10.1063/5.0155600

N/A

0DataRank · unranked

552 citations

Duo Zhang, Denghui Lu, Pinghui Mo, Zeyu Li, Yixiao Chen +42 more

Modern Alchemical Free Energy Methods for Drug Discovery Explained

ACS Physical Chemistry Au(2023)10.1021/acsphyschemau.3c00033

N/A

0DataRank · unranked

95 citations

Darrin M. York

ACES: Optimized Alchemically Enhanced Sampling

Journal of Chemical Theory and Computation(2023)10.1021/acs.jctc.2c00697

N/A

0DataRank · unranked

55 citations

Hsu‐Chun Tsai, Abir Ganguly, Darrin M. York, Tai‐Sung Lee

QDπ: A Quantum Deep Potential Interaction Model for Drug Discovery

Journal of Chemical Theory and Computation(2023)10.1021/acs.jctc.2c01172

N/A

0DataRank · unranked

46 citations

Yujun Tao, Timothy J. Giese, Darrin M. York, Jinzhe Zeng

AMBER Free Energy Tools: A New Framework for the Design of Optimized Alchemical Transformation Pathways

Journal of Chemical Theory and Computation(2023)10.1021/acs.jctc.2c00725

N/A

0DataRank · unranked

43 citations

Tai‐Sung Lee, Abir Ganguly, Timothy J. Giese, Maximilian CCJC Ebert, Paul Labute +3 more

Catalytic mechanism and pH dependence of a methyltransferase ribozyme (MTR1) from computational enzymology

Nucleic Acids Research(2023)10.1093/nar/gkad260

N/A

0DataRank · unranked

19 citations

Şölen Ekesan, Timothy J. Giese, Timothy J. Wilson, Jie Deng, Lin Huang +3 more

Modern semiempirical electronic structure methods and machine learning potentials for drug discovery: Conformers, tautomers, and protonation states

The Journal of Chemical Physics(2023)10.1063/5.0139281

N/A

0DataRank · unranked

24 citations

Yujun Tao, Timothy J. Giese, Darrin M. York, Jinzhe Zeng

Dissociative Transition State in Hepatitis Delta Virus Ribozyme Catalysis

Journal of the American Chemical Society(2023)10.1021/jacs.2c10079

N/A

0DataRank · unranked

12 citations

Şölen Ekesan, Hsuan-Chun Lin, Shahbaz Gardezi, Nan‐Sheng Li, Timothy J. Giese +5 more

Rapid Kinetics of Pistol Ribozyme: Insights into Limits to RNA Catalysis

Biochemistry(2023)10.1021/acs.biochem.3c00160

N/A

0DataRank · unranked

6 citations

Edward W. Ollie, Darrin M. York, Joseph A. Piccirilli, Michael E. Harris, Suhyun Yoon

Estimation of frequency factors for the calculation of kinetic isotope effects from classical and path integral free energy simulations

The Journal of Chemical Physics(2023)10.1063/5.0147218

N/A

0DataRank · unranked

4 citations

Darrin M. York, Timothy J. Giese

DeePMD-kit v2: A software package for Deep Potential models

arXiv (Cornell University)(2023)10.48550/arxiv.2304.09409

N/A

0DataRank · unranked

15 citations

Duo Zhang, Denghui Lu, Pinghui Mo, Zeyu Li, Yixiao Chen +42 more

DPA-2: a large atomic model as a multi-task learner

arXiv (Cornell University)(2023)10.48550/arxiv.2312.15492

N/A

0DataRank · unranked

8 citations

Xinzijian Liu, Xiangyu Zhang, Chengqian Zhang, Chun Cai, Hangrui Bi +38 more

Altered Mechanisms for Acid-Catalyzed RNA Cleavage and Isomerization Reactions Models

Journal of Chemical Theory and Computation(2023)10.1021/acs.jctc.2c01277

N/A

0DataRank · unranked

0 citations

Michael E. Harris, Darrin M. York, K. Y. Wong, Yuqing Xu

DPA-2: a large atomic model as a multi-task learner

npj Computational Materials(2024)10.1038/s41524-024-01493-2

N/A

0DataRank · unranked

124 citations

Xinzijian Liu, Xiangyu Zhang, Chengqian Zhang, Chun Cai, Hangrui Bi +37 more

Software Infrastructure for Next-Generation QM/MM−ΔMLP Force Fields

The Journal of Physical Chemistry B(2024)10.1021/acs.jpcb.4c01466

N/A

0DataRank · unranked

29 citations

Jinzhe Zeng, Lauren Lerew, Erika McCarthy, Yujun Tao, Şölen Ekesan +2 more

The Role of General Acid Catalysis in the Mechanism of an Alkyl Transferase Ribozyme

ACS Catalysis(2024)10.1021/acscatal.4c04571

N/A

0DataRank · unranked

15 citations

Erika McCarthy, Şölen Ekesan, Timothy J. Giese, Nan‐Sheng Li, Lin Huang +4 more

Alchemical Enhanced Sampling with Optimized Phase Space Overlap

Journal of Chemical Theory and Computation(2024)10.1021/acs.jctc.4c00251

N/A

0DataRank · unranked

18 citations

Timothy J. Giese, Tai‐Sung Lee, Darrin M. York, Shi Zhang

Surface-Accelerated String Method for Locating Minimum Free Energy Paths

Journal of Chemical Theory and Computation(2024)10.1021/acs.jctc.3c01401

N/A

0DataRank · unranked

11 citations

Şölen Ekesan, Erika McCarthy, Yujun Tao, Darrin M. York, Timothy J. Giese

Improvements in Precision of Relative Binding Free Energy Calculations Afforded by the Alchemical Enhanced Sampling (ACES) Approach

Journal of Chemical Information and Modeling(2024)10.1021/acs.jcim.4c00464

N/A

0DataRank · unranked

9 citations

James Xu, Guo Zhenyu, Yinhui Yi, Chuan Tian, Xinyu Que +6 more

Electronic and Nuclear Quantum Effects on Proton Transfer Reactions of Guanine–Thymine (G-T) Mispairs Using Combined Quantum Mechanical/Molecular Mechanical and Machine Learning Potentials

Molecules(2024)10.3390/molecules29112703

N/A

0DataRank · unranked

6 citations

Timothy J. Giese, Darrin M. York, Yujun Tao

DPA-2: Towards a universal large atomic model for molecular and materials simulation

Research Square(2024)10.21203/rs.3.rs-4100052/v1

N/A

0DataRank · unranked

11 citations

Duo Zhang, Xinzijian Liu, Xiangyu Zhang, Chengqian Zhang, Chun Cai +37 more

Recent Developments in Amber Biomolecular Simulations

Journal of Chemical Information and Modeling(2025)10.1021/acs.jcim.5c01063

N/A

0DataRank · unranked

131 citations

David S. Cerutti, Vinícius Wilian D. Cruzeiro, Thomas A. Darden, Robert E. Duke, Mahdieh Ghazimirsaeed +26 more

DeePMD-GNN: A DeePMD-kit Plugin for External Graph Neural Network Potentials

Journal of Chemical Information and Modeling(2025)10.1021/acs.jcim.4c02441

N/A

0DataRank · unranked

21 citations

Timothy J. Giese, Duo Zhang, Han Wang, Darrin M. York, Jinzhe Zeng

Transferability of MACE Graph Neural Network for Range Corrected Δ-Machine Learning Potential QM/MM Applications

The Journal of Physical Chemistry B(2025)10.1021/acs.jpcb.5c02006

N/A

0DataRank · unranked

11 citations

Jinzhe Zeng, Darrin M. York, Timothy J. Giese

Mutation-driven RRE stem-loop II conformational change induces HIV-1 nuclear export dysfunction

Nucleic Acids Research(2025)10.1093/nar/gkaf583

N/A

0DataRank · unranked

1 citations

Lucia Hudson, Amanda Photenhauer, Trinity Zang, Lauren Lerew, Şölen Ekesan +9 more

Adsorption of Flavonoids in a Transcriptional Regulator TtgR: Relative Binding Free Energies and Intermolecular Interactions

The Journal of Physical Chemistry B(2024)10.1021/acs.jpcb.4c02303

N/A

0DataRank · unranked

2 citations

Shi Zhang, Darrin M. York, Lu Wang, Yuxuan Wu

Improved Alchemical Free Energy Calculations with Optimized Smoothstep Softcore Potentials

Journal of Chemical Theory and Computation(2020)10.1021/acs.jctc.0c00237

N/A

0DataRank · unranked

74 citations

Zhixiong Lin, Bryce K. Allen, Charles Lin, Brian K. Radak, Yujun Tao +4 more

Darrin M. York

Indexed papers

Top data-sharing exemplar

Papers