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Morphoscanner2.0: A new python module for analysis of molecular dynamics simulations

Author

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  • Federico Fontana
  • Calogero Carlino
  • Ashish Malik
  • Fabrizio Gelain

Abstract

Molecular dynamics simulations, at different scales, have been exploited for investigating complex mechanisms ruling biologically inspired systems. Nonetheless, with recent advances and unprecedented achievements, the analysis of molecular dynamics simulations requires customized workflows. In 2018, we developed Morphoscanner to retrieve structural relations within self-assembling peptide systems. In particular, we conceived Morphoscanner for tracking the emergence of β-structured domains in self-assembling peptide systems. Here, we introduce Morphoscanner2.0. Morphoscanner2.0 is an object-oriented library for structural and temporal analysis of atomistic and coarse-grained molecular dynamics (CG-MD) simulations written in Python. The library leverages MDAnalysis, PyTorch and NetworkX to perform the pattern recognition of secondary structure patterns, and interfaces with Pandas, Numpy and Matplotlib to make the results accessible to the user. We used Morphoscanner2.0 on both simulation trajectories and protein structures. Because of its dependencies on the MDAnalysis package, Morphoscanner2.0 can read several file formats generated by widely-used molecular simulation packages such as NAMD, Gromacs, OpenMM. Morphoscanner2.0 also includes a routine for tracking the alpha-helix domain formation.

Suggested Citation

  • Federico Fontana & Calogero Carlino & Ashish Malik & Fabrizio Gelain, 2023. "Morphoscanner2.0: A new python module for analysis of molecular dynamics simulations," PLOS ONE, Public Library of Science, vol. 18(4), pages 1-19, April.
    • Handle: RePEc:plo:pone00:0284307
    DOI: 10.1371/journal.pone.0284307
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