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@mackerell-lab

mackerell-lab

Our lab's coding home for sharing and distributing scripts/projects.

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The MacKerell Group

Welcome to the MacKerell Group Github. If you are a collaborator, please browse through and feel free to reach out to Alex or Anmol for any access to repositories.

Important Links

Home Website: https://mackerell.umaryland.edu

Recent Papers: “Deep Neural Network Model to Predict the Electrostatic Parameters in the Polarizable Classical Drude Oscillator Force Field” https://pubs.acs.org/doi/10.1021/acs.jctc.1c01166

“SILCS-RNA: Toward a Structure-Based Drug Design Approach for Targeting RNAs with Small Molecules” https://pubs.acs.org/doi/10.1021/acs.jctc.2c00381

“In silico identification of a β2-adrenoceptor allosteric site that selectively augments canonical β2AR-Gs signaling and function” https://www.pnas.org/doi/10.1073/pnas.2214024119

Current Roster

Name Email Title Degree
Dr. Alexander MacKerell Jr. alex@outerbanks.umaryland.edu Professor Ph.D. Biochemistry, Rutgers University
Dr. Wenbo Yu wenbo@outerbanks.umaryland.edu Research Assistant Professor Ph.D. Condensed Matter Physics, Hefei National Laboratory for Physical Sciences at the Microscale
Dr. Anmol Kumar anmol@outerbanks.umaryland.edu Research Associate Faculty Ph.D. Theoretical and Computational Chemistry, IIT Kanpur, India
Dr. Mingtian Zhao zhaomt@outerbanks.umaryland.edu Post-Doc Ph.D. Condensed Matter Physics, Nankai University
Dr. Anastasia Croitoru anac@outerbanks.umaryland.edu Post-Doc Ph.D. Development of Force Field Methods, CNRS - Ecole Polytechnique
Dr. Yingling Nan ynan@outerbanks.umaryland.edu Post-Doc Ph.D. Civil and Environmental Engineering, University of Alberta
Dr. Prabin Baral pbaral@outerbanks.umaryland.edu Post-Doc Ph.D. Computational Biophysics, Florida International University
Dr. Erik Nordquist enord@outerbanks.umaryland.edu Post-Doc Ph.D. Computational Biophysics, University of Massachusetts Amherst
Suliman Sharif sulstice@outerbanks.umaryland.edu Graduate Student MSc. Organic Chemistry
Jihyeon Lee jihyeon.lee@outerbanks.umaryland.edu Graduate Student M.Sc. Chemistry

Our Lab:

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  1. SILCS-MC-Chem-Sci-2021 Public

    2

  2. charmm36-force-field Public

    CHARMM36 additive force field in a tarred gzipped file.

  3. silcs-water Public

    Data for article titled "Modeling Ligand Binding Site Water Networks with Site- Identification by Ligand Competitive Saturation"

Repositories

Showing 10 of 30 repositories
  • Python 1 0 0 1 Updated Mar 21, 2025
  • .github Public

    Our Github Organization Profile

    1 MIT 0 0 0 Updated Mar 16, 2025
  • charmm36-force-field Public

    CHARMM36 additive force field in a tarred gzipped file.

    0 MIT 0 0 0 Updated Feb 19, 2025
  • pyGCMC Public
    Jupyter Notebook 0 0 0 0 Updated Jan 26, 2025
  • 1 BSD-3-Clause 0 0 0 Updated Jan 19, 2025
  • cgenff5 Public

    Data and scripts for CGenFF 5.0 paper

    Rich Text Format 3 0 0 0 Updated Jan 7, 2025
  • silcs-pathway Public
    2 BSD-3-Clause 0 0 0 Updated Dec 20, 2024
  • Python 0 0 0 0 Updated Nov 23, 2024
  • polli-solubility Public

    Drug solubility differential equation solvers

    Python 0 MIT 0 0 0 Updated Nov 22, 2024
  • C 0 0 0 0 Updated Nov 16, 2024