SMOG Literature

SMOG Primary References

We kindly request that you cite the appropriate primary references when using the SMOG models and webtool.

SMOG2 or Webtool: Noel JK, Levi M, Raghunathan M, Lammert H, Hayes RL, Onuchic JN, Whitford PC. (2016) PLOS Comp. Bio.
DOI: 10.1371/journal.pcbi.1004794
OpenSMOG: Oliveira AB, Contessoto VG, Hassan A, Byju S, Wang A, Wang Y, Dodero-Rojas E, Mohanty U, Noel JK, Onuchic JN, Whitford PC. (2022) Protein Science, DOI:10.1002/pro.4209.
SMOG Models
All-Atom: Whitford PC, et al. (2009) Proteins: Structure, Function, Bioinformatics 75, 430-441. DOI: 10.1002/prot.22253.
C-alpha: Clementi C, et al. (2000) Journal of Molecular Biology 298, 937-953. DOI:10.1006/jmbi.2000.3693
Contact Potential Options
Shadow Algorithm: Noel JK, et al. (2012) Journal of Physical Chemistry DOI:10.1021/jp300852d
All-Atom Gaussian Interactions: Noel JK, et al. (2012) Journal of Physical Chemistry DOI:10.1021/jp300852d
C-alpha Gaussian Interactions: Lammert H, et al. (2009) Proteins: Structure, Function, Bioinformatics 77, 881-891. DOI: 10.1002/prot.22511.

Relevant Literature on SMOG Modeling

Overview of SMOG Modeling and Introduction to Structure-based Models
Noel JK and Onuchic JN. (2012) "The Many Faces of Structure-Based Potentials: From Protein Folding Landscapes to Structural Characterization of Complex Biomolecules" in Computational Modeling of Biological Systems, Part 1, pg 31-54, DOI: 10.1007/978-1-4614-2146-7_2.
Introduction to using SMOG 2
Levi M, Bandarkar P, Yang H, Wang A, Mohanty U, Noel JK, Whitford PC. (2019) "Using SMOG 2 to simulate complex biomolecular assemblies" in Biomolecular Simulations. DOI:10.1007/978-1-4939-9608-7_6

Software Registry Information

SMOG 2- RRID:SCR_021536
OpenSMOG- RRID:SCR_022551

This resource is provided by the Center for Theoretical Biological Physics.
Please direct questions and comments to
Page created and maintained by Jeff Noel and Paul Whitford