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csbrasnett committed Oct 21, 2024
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Expand Up @@ -4,11 +4,11 @@ Gō models

The MartiniGō model is a method of maintaining secondary and tertiary structure using native contacts of proteins
to create a `Gō-like model <https://pubs.acs.org/doi/full/10.1021/acs.jctc.6b00986>`_ between beads.
In contrast to an elastic network, the Go model applies non-bonded interactions between pairs of
In contrast to an elastic network, the model applies non-bonded interactions between pairs of
beads within a protein based on residue overlap and restricted chemical structural unit criteria.

The latest version of Martinize2 (version ≥ 0.10.0) implements the newest version of the
`Gō model <https://www.biorxiv.org/content/10.1101/2024.04.15.589479v1>`_. In this version of the Go model, interactions
`Gō model <https://www.biorxiv.org/content/10.1101/2024.04.15.589479v1>`_. In this version of the model, interactions
are mediated through the addition of extra virtual sites on top of backbone beads in the protein. Interactions are in
the form of Lennard-Jones interactions, which are written as an extra file to be included in the protein topology.

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