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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 Post-Doc Ph.D. Computational Chemistry, IIT Kanpur, India
Dr. Mingtian Zhao zhaomt@outerbanks.umaryland.edu Post-Doc Ph.D. Condensed Matter Physics, Nankai University
Dr. Asuka Orr asukaorr@outerbanks.umaryland.edu Post-Doc Ph.D. Chemical Engineering, Texas A & M 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

Our Lab:

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

    2

  2. Open-Source-Data-Template Open-Source-Data-Template Public

    A template for open sourcing your data a long with your paper.

    2 2

  3. silcs-protac silcs-protac Public

    Data and code for SILCS-PROTAC workflow

    Python 1

Repositories

Showing 10 of 27 repositories
  • pyGCMC Public
    mackerell-lab/pyGCMC’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Dec 27, 2024
  • silcs-pathway Public
    mackerell-lab/silcs-pathway’s past year of commit activity
    0 BSD-3-Clause 0 0 0 Updated Dec 20, 2024
  • silcs-protac Public

    Data and code for SILCS-PROTAC workflow

    mackerell-lab/silcs-protac’s past year of commit activity
    Python 1 MIT 0 0 0 Updated Dec 10, 2024
  • mackerell-lab/NBFIX_NBTHOLE_test’s past year of commit activity
    Python 0 0 0 0 Updated Nov 23, 2024
  • polli-solubility Public

    Drug solubility differential equation solvers

    mackerell-lab/polli-solubility’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Nov 22, 2024
  • mackerell-lab/Paper_Ion_Protein_Nucleic-Acids’s past year of commit activity
    C 0 0 0 0 Updated Nov 16, 2024
  • Coordinate-Conversion-Tool-For-Alex Public

    A coordinate tool app for alex

    mackerell-lab/Coordinate-Conversion-Tool-For-Alex’s past year of commit activity
    Python 2 MIT 0 0 0 Updated Aug 28, 2024
  • FDA-compounds-SILCS-Hotspots-SI Public

    SI data repository for the SILCS-Hotspots / druggable sites paper

    mackerell-lab/FDA-compounds-SILCS-Hotspots-SI’s past year of commit activity
    2 0 0 0 Updated Aug 6, 2024
  • silcs-water Public

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

    mackerell-lab/silcs-water’s past year of commit activity
    0 0 0 0 Updated Aug 2, 2024
  • silcsmc-gpu-example Public

    Input example for SILCS-MC simulations using the GPU version of the SILCS-MC program

    mackerell-lab/silcsmc-gpu-example’s past year of commit activity
    Batchfile 0 0 0 0 Updated Jul 1, 2024

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