Molecular dynamics simulation for new force calculations - Proteogram v2#4
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Molecular dynamics simulation for new force calculations - Proteogram v2#4
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This is the v2 of the Proteogram project, a big evolution where we pull in molecular dynamics simulations to calculate non-bonded potential energies between residues. Here, the main update is the use of MD simulation to robustly optimize a protein structure and add the following calculations to the generation of the Proteogram data structure (in addition to the distogram and hydrophobicity deltas). Interaction potential energies are calculated for:
This library may also be used separately to run simulations. See the MD guide in the
docsfolder for more information on the update and how the simulations work in the context of this project.A big thank you to @swapnilashtekar for his contributions around reproducibility, with a Docker setup, to this PR!