SMOG 2 and OpenSMOG: Extending the limits of structure‐based models

  1. Antonio B. de Oliveira
  2. Vinícius G. Contessoto
  3. Asem Hassan
  4. Sandra Byju
  5. Ailun Wang
  6. Yang Wang
  7. Esteban Dodero‐Rojas
  8. Udayan Mohanty
  9. Jeffrey K. Noel
  10. Jose N. Onuchic
  11. Paul C. Whitford

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Abstract

Applying simulations with structure‐based models has proven to be an effective strategy for investigating the factors that control biomolecular dynamics. The common element of these models is that some (or all) of the intra/inter‐molecular interactions are explicitly defined to stabilize an experimentally determined structure. To facilitate the development and application of this broad class of models, we previously released the SMOG 2 software package. This suite allows one to easily customize and distribute structure‐based (i.e., SMOG) models for any type of polymer‐ligand system. The force fields generated by SMOG 2 may then be used to perform simulations in highly optimized MD packages, such as Gromacs, NAMD, LAMMPS, and OpenMM. Here, we describe extensions to the software and demonstrate the capabilities of the most recent version (SMOG v2.4.2). Changes include new tools that aid user‐defined customization of force fields, as well as an interface with the OpenMM simulation libraries (OpenSMOG v1.1.0). The OpenSMOG module allows for arbitrary user‐defined contact potentials and non‐bonded potentials to be employed in SMOG models, without source‐code modifications. To illustrate the utility of these advances, we present applications to systems with millions of atoms, long polymers and explicit ions, as well as models that include non‐structure‐based (e.g., AMBER‐based) energetic terms. Examples include large‐scale rearrangements of the SARS‐CoV‐2 Spike protein, the HIV‐1 capsid with explicit ions, and crystallographic lattices of ribosomes and proteins. In summary, SMOG 2 and OpenSMOG provide robust support for researchers who seek to develop and apply structure‐based models to large and/or intricate biomolecular systems.

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  1. Version published to 10.1002/pro.4209
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    SciScore for 10.1101/2021.08.15.456423: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    No key resources detected.

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    Results from scite Reference Check: We found no unreliable references.

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  3. Version published to 10.1101/2021.08.15.456423v1 on bioRxiv