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Publications

Research using PRISM and related publications.

PRISM Software

Primary Citation

If you use PRISM in your research, please cite:

@software{prism2024,
  author = {Shi, Zhaoqi},
  title = {PRISM: Protein Receptor Interaction Simulation Modeler},
  year = {2024},
  version = {1.2.0},
  institution = {Institute of Quantitative Biology, Zhejiang University},
  url = {https://github.com/AIB001/PRISM}
}

Publications describing PRISM methodology and applications (in preparation):

  1. PRISM: An Automated Toolkit for Protein-Ligand Molecular Dynamics Simulations
    Shi, Z. et al.
    Manuscript in preparation, 2024

  2. Force Field Comparison for Protein-Ligand Binding: Insights from PRISM
    Shi, Z. et al.
    Manuscript in preparation, 2024

Research Using PRISM

2024

  1. Application Study 1
    Authors et al.
    Journal Name, 2024
    DOI: [link]

  2. Application Study 2
    Authors et al.
    Journal Name, 2024
    DOI: [link]

Methodology Papers

Force Fields

GAFF (General AMBER Force Field) - Wang, J., et al. (2004). Development and testing of a general amber force field. J. Comput. Chem., 25(9), 1157-1174. - DOI: 10.1002/jcc.20035

GAFF2 - He, X., et al. (2020). A fast and high-quality charge model for the next generation general AMBER force field. J. Chem. Phys., 153(11), 114502.

OpenFF (Open Force Field) - Mobley, D. L., et al. (2020). Open Force Field Initiative. Living J. Comp. Mol. Sci., 2(1), 18378.

OPLS-AA - Jorgensen, W. L., et al. (1996). Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids. J. Am. Chem. Soc., 118(45), 11225-11236.

Free Energy Methods

Umbrella Sampling - Torrie, G. M., & Valleau, J. P. (1977). Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling. J. Comput. Phys., 23(2), 187-199.

WHAM - Kumar, S., et al. (1992). The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method. J. Comput. Chem., 13(8), 1011-1021. - Hub, J. S., et al. (2010). g_wham—A Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation Estimates. J. Chem. Theory Comput., 6(12), 3713-3720.

PMF Calculations - Lemkul, J. A. (2019). From Proteins to Perturbed Hamiltonians: A Suite of Tutorials for the GROMACS-2018 Molecular Simulation Package. Living J. Comp. Mol. Sci., 1(1), 5068.

MD Simulations

GROMACS - Abraham, M. J., et al. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1-2, 19-25. - Van Der Spoel, D., et al. (2005). GROMACS: fast, flexible, and free. J. Comput. Chem., 26(16), 1701-1718.

Presentations and Talks

2024

  • PRISM: Automated MD System Building
    ACS National Meeting, Spring 2024
    Presenter: Zhaoqi Shi

  • Force Field Comparison Using PRISM
    Computational Chemistry Symposium, 2024

2023

  • PRISM Development and Applications
    Zhejiang University IQB Seminar Series

Theses and Dissertations

PhD Dissertation - Shi, Z. (Expected 2025). Development and Application of PRISM for Protein-Ligand Simulations. Zhejiang University.

Review Articles

Computational Drug Discovery

  • Relevant reviews that cite or relate to PRISM methodology

Molecular Dynamics Methods

  • Recent advances in MD simulation methods

Force Field Development

  • Current state of force field research

Submit Your Publication

Have you used PRISM in your research? Let us know!

Submit your publication information: - Email: zshi268@wisc.edu - Subject: "PRISM Publication" - Include: Title, Authors, Journal, DOI, Brief description

We'll add it to this page and may feature it on our website.

Citation Guidelines

In Methods Section

Example text for methods section:

"Protein-ligand systems were built using PRISM (Protein Receptor Interaction Simulation Modeler) version 1.2.0 [citation]. Ligand force field parameters were generated using [GAFF/OpenFF/etc], and the protein was modeled with the AMBER99SB force field. The system was solvated in a TIP3P water box with 0.15 M NaCl. Molecular dynamics simulations were performed using GROMACS 2024.3."

In Acknowledgments

"We thank Zhaoqi Shi for developing PRISM and providing support."

Dependencies

Complementary Tools

  • VMD: Visualization
  • PyMOL: Molecular graphics
  • ProDy: Protein dynamics analysis
  • MDAnalysis: Trajectory analysis

Last Updated: October 2024

Add Your Publication: zshi268@wisc.edu