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Chemistry

D-Index
116
Citations
116663
World Ranking
578
National Ranking
244

Overview

Alexander D. MacKerell is affiliated with the University of Maryland, Baltimore in the United States. Their research primarily falls within the broad field of Biochemistry, Genetics and Molecular Biology, with a particular emphasis on Molecular Biology, Computational Theory and Mathematics, Atomic and Molecular Physics and Optics, Spectroscopy, and Materials Chemistry.

The scientist's work covers several key topics, including:

  • Protein Structure and Dynamics
  • Computational Drug Discovery Methods
  • RNA and protein synthesis mechanisms
  • Spectroscopy and Quantum Chemical Studies
  • Monoclonal and Polyclonal Antibodies Research
  • DNA and Nucleic Acid Chemistry
  • Receptor Mechanisms and Signaling

Alexander D. MacKerell has published extensively, with recent papers that include:

  • "Additive CHARMM36 Force Field for Nonstandard Amino Acids" (2021), published in Journal of Chemical Theory and Computation
  • "Further Optimization and Validation of the Classical Drude Polarizable Protein Force Field" (2020), published in Journal of Chemical Theory and Computation
  • "Statistical mechanics of polarizable force fields based on classical Drude oscillators with dynamical propagation by the dual-thermostat extended Lagrangian" (2020), published in The Journal of Chemical Physics
  • "Semi-automated Optimization of the CHARMM36 Lipid Force Field to Include Explicit Treatment of Long-Range Dispersion" (2021), published in Journal of Chemical Theory and Computation
  • "CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed" (2024), published in The Journal of Physical Chemistry B

The scientist frequently collaborates with several researchers, including Wenbo Yu, Anmol Kumar, Abhishek A. Kognole, Sunhwan Jo, and Benoît Roux. Their scholarly output has been published in a variety of journals, with a notable concentration in:

  • Biophysical Journal
  • Journal of Chemical Theory and Computation
  • Faculty Opinions - Post-Publication Peer Review of the Biomedical Literature
  • The Journal of Physical Chemistry B
  • Journal of Chemical Information and Modeling

Best Publications

  • All-atom empirical potential for molecular modeling and dynamics studies of proteins.

    A. D. MacKerell;D. Bashford;M. Bellott;R. L. Dunbrack

  • CHARMM: the biomolecular simulation program.

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

  • CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields.

    Kenno Vanommeslaeghe;Elizabeth Hatcher;Chayan Acharya;Sibsankar Kundu

  • CHARMM36m: An improved force field for folded and intrinsically disordered proteins

    Jing Huang;Sarah Rauscher;Grzegorz Nawrocki;Ting Ran

  • Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles.

    Robert B. Best;Xiao Zhu;Jihyun Shim;Pedro E. M. Lopes

  • Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types

    Jeffery B. Klauda;Richard M. Venable;J. Alfredo Freites;Joseph W. O’Connor

  • CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data

    Jing Huang;Alexander D. MacKerell

  • CHARMM-GUI Input Generator for NAMD, Gromacs, Amber, Openmm, and CHARMM/OpenMM Simulations using the CHARMM36 Additive Force Field

    Jumin Lee;Xi Cheng;Jason M. Swails;Min Sun Yeom

  • Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations.

    Alexander D. Mackerell;Michael Feig;Charles L. Brooks

  • Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing.

    Kenno Vanommeslaeghe;Alexander D. MacKerell

  • All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data

    Nicolas Foloppe;Alexander D. MacKerell

  • Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges

    Kenno Vanommeslaeghe;E. Prabhu Raman;Alexander D. MacKerell

  • Empirical force fields for biological macromolecules: overview and issues.

    Alexander D. Mackerell

  • Development and current status of the CHARMM force field for nucleic acids

    Alexander D. MacKerell;Nilesh Banavali;Nicolas Foloppe

  • Improved treatment of the protein backbone in empirical force fields.

    Alexander D. MacKerell;Michael Feig;Charles L. Brooks

  • Extension of the CHARMM General Force Field to sulfonyl-containing compounds and its utility in biomolecular simulations.

    Wenbo Yu;Xibing He;Kenno Vanommeslaeghe;Alexander D. MacKerell

  • All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution

    Alexander D. MacKerell;Nilesh K. Banavali

  • An all-atom empirical energy function for the simulation of nucleic acids

    Alexander D. MacKerell;Joanna Wiorkiewicz-Kuczera;Martin Karplus

  • A simple polarizable model of water based on classical Drude oscillators

    Guillaume Lamoureux;Alexander D. MacKerell;Benoı̂t Roux

  • CHARMM: The Energy Function and Its Parameterization

    Alexander D. MacKerell;Bernard Brooks;Charles L. Brooks;Lennart Nilsson

Frequent Co-Authors

Benoît Roux
Benoît Roux University of Chicago
David J. Weber
David J. Weber University of Maryland, Baltimore
Richard W. Pastor
Richard W. Pastor National Institutes of Health
Lennart Nilsson
Lennart Nilsson Karolinska Institute
Jeffery B. Klauda
Jeffery B. Klauda University of Maryland, College Park
Wonpil Im
Wonpil Im Lehigh University
Michael Feig
Michael Feig Michigan State University
Ari Melnick
Ari Melnick Cornell University
Richard M. Venable
Richard M. Venable National Institutes of Health
Jeffrey R. Deschamps
Jeffrey R. Deschamps United States Naval Research Laboratory

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