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D-Index & Metrics

Chemistry

D-Index
63
Citations
57623
World Ranking
8254
National Ranking
2384

Overview

Darrin M. York is affiliated with Rutgers, The State University of New Jersey in the United States. Their research spans multiple fields with significant contributions to biochemistry, genetics, and molecular biology as well as materials science. Within these broad areas, their work delves into key subfields including molecular biology, materials chemistry, computational theory and mathematics, spectroscopy, and atomic and molecular physics and optics.

The main topics of York's research include protein structure and dynamics, machine learning in materials science, computational drug discovery methods, RNA and protein synthesis mechanisms, DNA and nucleic acid chemistry, X-ray diffraction in crystallography, and enzyme structure and function.

York has published extensively in a variety of scientific journals. Frequent venues for their work include:

  • Journal of Chemical Theory and Computation
  • Journal of Chemical Information and Modeling
  • The Journal of Physical Chemistry B
  • Journal of Chemical Education
  • The Journal of Chemical Physics

The scientist's recent notable publications include:

  • AmberTools, 2023, Journal of Chemical Information and Modeling
  • DeePMD-kit v2: A software package for deep potential models, 2023, The Journal of Chemical Physics
  • Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery, 2020, Journal of Chemical Information and Modeling
  • Fast, Accurate, and Reliable Protocols for Routine Calculations of Protein-Ligand Binding Affinities in Drug Design Projects Using AMBER GPU-TI with ff14SB/GAFF, 2020, ACS Omega
  • Development of Range-Corrected Deep Learning Potentials for Fast, Accurate Quantum Mechanical/Molecular Mechanical Simulations of Chemical Reactions in Solution, 2021, Journal of Chemical Theory and Computation

York frequently collaborates with other researchers, including Timothy J. Giese, Jinzhe Zeng, Tai-Sung Lee, Şölen Ekesan, and Duo Zhang.

Best Publications

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

    Tom Darden;Darrin York;Lee Pedersen

  • CHARMM: the biomolecular simulation program.

    B. R. Brooks;C. L. Brooks;A. D. Mackerell;L. Nilsson

  • AmberTools

    Unknown

  • The effect of long‐range electrostatic interactions in simulations of macromolecular crystals: A comparison of the Ewald and truncated list methods

    Darrin M. York;Tom A. Darden;Lee G. Pedersen

  • GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features.

    Tai-Sung Lee;David S. Cerutti;Dan Mermelstein;Charles Lin

  • Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method: Third-Order Expansion of the Density Functional Theory Total Energy and Introduction of a Modified Effective Coulomb Interaction

    Yang Yang;Haibo Yu;Darrin York;Qiang Cui

  • An Efficient Linear-Scaling Ewald Method for Long-Range Electrostatic Interactions in Combined QM/MM Calculations.

    Kwangho Nam;Jiali Gao;Darrin M. York

  • Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery.

    Tai Sung Lee;Bryce K. Allen;Timothy J. Giese;Zhenyu Guo

  • Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation

    Jason M. Swails;Darrin M. York;Adrian E. Roitberg

  • A chemical potential equalization method for molecular simulations

    Darrin M. York;Weitao Yang

  • Atomic-level accuracy in simulations of large protein crystals

    Darrin M. York;Alexander Wlodawer;Lee G. Pedersen;Tom A. Darden

  • Toward the Accurate Modeling of DNA: The Importance of Long-Range Electrostatics

    Darrin M. York;Weitao Yang;Hsing Lee;Tom Darden

  • Linear‐scaling semiempirical quantum calculations for macromolecules

    Tai‐Sung Lee;Darrin M. York;Weitao Yang

  • Using AMBER18 for Relative Free Energy Calculations.

    Lin Frank Song;Tai Sung Lee;Chun Zhu;Darrin M. York

  • Specific Reaction Parametrization of the AM1/d Hamiltonian for Phosphoryl Transfer Reactions: H, O, and P Atoms

    Kwangho Nam;Qiang Cui;Jiali Gao;Darrin M. York

  • Accurate proton affinity and gas-phase basicity values for molecules important in biocatalysis.

    Adam Moser;Kevin Range;Darrin M. York

  • The fast Fourier Poisson method for calculating Ewald sums

    Darrin York;Weitao Yang

  • Solvent Structure and Hammerhead Ribozyme Catalysis

    Monika Martick;Tai-Sung Lee;Darrin M. York;William G. Scott;William G. Scott

  • Role of Mg2+ in Hammerhead Ribozyme Catalysis from Molecular Simulation

    Tai-Sung Lee;Carlos Silva López;George M Giambasu;Monika Martick

  • Theoretical methods that help understanding the structure and reactivity of gas phase ions

    J.M. Mercero;J.M. Matxain;X. Lopez;D.M. York

  • Threshold Occupancy and Specific Cation Binding Modes in the Hammerhead Ribozyme Active Site are Required for Active Conformation

    Tai-Sung Lee;George M. Giambaşu;Carlos P. Sosa;Carlos P. Sosa;Monika Martick

Frequent Co-Authors

Joseph A. Piccirilli
Joseph A. Piccirilli University of Chicago
Lee G. Pedersen
Lee G. Pedersen University of North Carolina at Chapel Hill
Weitao Yang
Weitao Yang Duke University
Jiali Gao
Jiali Gao University of Minnesota
David A. Case
David A. Case Rutgers, The State University of New Jersey
Qiang Cui
Qiang Cui Boston University
Angel R. de Lera
Angel R. de Lera Universidade de Vigo
Shantenu Jha
Shantenu Jha Rutgers, The State University of New Jersey
Walter Thiel
Walter Thiel Max Planck Society
Marcus Elstner
Marcus Elstner Karlsruhe Institute of Technology

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