Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

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

Antonio B. de Oliveira Jr., View ORCID ProfileVinícius G. Contessoto, Asem Hassan, Sandra Byju, Ailun Wang, Yang Wang, View ORCID ProfileEsteban Dodero-Rojas, Udayan Mohanty, Jeffrey K. Noel, Jose N. Onuchic, View ORCID ProfilePaul C. Whitford
doi: https://doi.org/10.1101/2021.08.15.456423
Antonio B. de Oliveira Jr.
†Center for Theoretical Biological Physics, Rice University, BioScience Research Collaborative, 6566 Main St, Houston, TX 77030
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Vinícius G. Contessoto
†Center for Theoretical Biological Physics, Rice University, BioScience Research Collaborative, 6566 Main St, Houston, TX 77030
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Vinícius G. Contessoto
Asem Hassan
‡Department of Physics, Northeastern University, Dana Research Center 111, 360 Huntington Ave, Boston, MA 02115
¶Center for Theoretical Biological Physics, Northeastern University, 360 Huntington Ave, Boston, MA 02115
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Sandra Byju
‡Department of Physics, Northeastern University, Dana Research Center 111, 360 Huntington Ave, Boston, MA 02115
¶Center for Theoretical Biological Physics, Northeastern University, 360 Huntington Ave, Boston, MA 02115
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Ailun Wang
¶Center for Theoretical Biological Physics, Northeastern University, 360 Huntington Ave, Boston, MA 02115
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Yang Wang
§Department of Chemistry, Boston College, Chestnut Hill, MA 02467
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Esteban Dodero-Rojas
‖Center for Theoretical Biological Physics, Rice University, Houston, TX 77005
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Esteban Dodero-Rojas
Udayan Mohanty
§Department of Chemistry, Boston College, Chestnut Hill, MA 02467
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jeffrey K. Noel
⊥Crystallography, Max Delbrück Center for Molecular Medicine, Berlin, Germany
#Electric Ant Lab, Science Park 106, 1098 XG, Amsterdam, The Netherlands
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jose N. Onuchic
†Center for Theoretical Biological Physics, Rice University, BioScience Research Collaborative, 6566 Main St, Houston, TX 77030
@Department of Physics & Astronomy, Rice University, Houston, TX, USA
ΔDepartment of Chemistry, Rice University, Houston, TX, USA
ᐁDepartment of Biosciences, Rice University, Houston, TX, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Paul C. Whitford
‡Department of Physics, Northeastern University, Dana Research Center 111, 360 Huntington Ave, Boston, MA 02115
¶Center for Theoretical Biological Physics, Northeastern University, 360 Huntington Ave, Boston, MA 02115
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Paul C. Whitford
  • For correspondence: p.whitford@neu.edu
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Preview PDF
Loading

Abstract

Applying simulations with structure-based (Gō-like) 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 inter-actions 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. Since its original release, user feedback has driven the implementation of numerous enhancements. Here, we describe recent extensions to the software and demonstrate the capabilities of the most recent version, SMOG v2.4. Changes include new tools that aid user-defined customization of force fields, as well as an interface with the OpenMM simulation libraries (OpenSMOG v1.0). To illustrate the utility of these advances, we present several applications of SMOG2 and OpenSMOG, which include systems with millions of atoms, long polymers and explicit ions. We also highlight how one can incorporate non-structure-based (e.g. AMBER-based) energetics to define a hybrid class of models. The representative applications include large-scale rearrangements of the SARS-CoV-2 Spike protein, the HIV-1 capsid in the presence of explicit ions, and crystallographic lattices of ribosomes and proteins. In summary, SMOG 2 and OpenSMOG provide robust support for researchers who seek to apply structure-based models to large and/or intricate biomolecular systems.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • ↵* E-mail: jnoel{at}mdc-berlin.de; jonuchic{at}rice.edu; p.whitford{at}northeastern.edu

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted August 16, 2021.
Download PDF
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
SMOG 2 and OpenSMOG: Extending the limits of structure-based models
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
SMOG 2 and OpenSMOG: Extending the limits of structure-based models
Antonio B. de Oliveira Jr., Vinícius G. Contessoto, Asem Hassan, Sandra Byju, Ailun Wang, Yang Wang, Esteban Dodero-Rojas, Udayan Mohanty, Jeffrey K. Noel, Jose N. Onuchic, Paul C. Whitford
bioRxiv 2021.08.15.456423; doi: https://doi.org/10.1101/2021.08.15.456423
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
SMOG 2 and OpenSMOG: Extending the limits of structure-based models
Antonio B. de Oliveira Jr., Vinícius G. Contessoto, Asem Hassan, Sandra Byju, Ailun Wang, Yang Wang, Esteban Dodero-Rojas, Udayan Mohanty, Jeffrey K. Noel, Jose N. Onuchic, Paul C. Whitford
bioRxiv 2021.08.15.456423; doi: https://doi.org/10.1101/2021.08.15.456423

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Biophysics
Subject Areas
All Articles
  • Animal Behavior and Cognition (3704)
  • Biochemistry (7829)
  • Bioengineering (5706)
  • Bioinformatics (21364)
  • Biophysics (10613)
  • Cancer Biology (8217)
  • Cell Biology (11986)
  • Clinical Trials (138)
  • Developmental Biology (6792)
  • Ecology (10431)
  • Epidemiology (2065)
  • Evolutionary Biology (13918)
  • Genetics (9734)
  • Genomics (13118)
  • Immunology (8182)
  • Microbiology (20082)
  • Molecular Biology (7882)
  • Neuroscience (43204)
  • Paleontology (321)
  • Pathology (1285)
  • Pharmacology and Toxicology (2270)
  • Physiology (3367)
  • Plant Biology (7263)
  • Scientific Communication and Education (1317)
  • Synthetic Biology (2012)
  • Systems Biology (5552)
  • Zoology (1135)