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Libraries

  • MMTK:
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  • ProDy: ProDy is a Python package for analyzing protein dynamics and sequence co-evolution, offering tools for comparative modeling and analysis of protein structural dynamics.
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    Publication JIF

  • QUIP:

Analysis

  • MDAnalysis: MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations
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    Publication

  • MDTraj: MDTraj is a Python library for analyzing molecular dynamics trajectories, offering a wide range of functionalities for trajectory manipulation and analysis.
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    Publication JIF

Preparation

  • Packmol: Packmol creates initial configurations for molecular dynamics simulations by packing molecules to meet specified conditions, aiding in the setup of simulation boxes.

    Publication JIF

Refinement

  • MDRefine: package for refining Molecular Dynamics trajectories with experimental data
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