SMOG Literature

SMOG Primary References

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

SMOG Software and 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
.
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.
Additional Modeling Tools
MDfit: Whitford PC, et al. (2011) Proc Nat Acad Sci USA 108, 18943-18948. DOI:10.1073/pnas.1108363108.

Relevant Literature on SMOG Modeling

Overview of SMOG Modelng 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.
Historical Perspective on the Development of Structure-Based Models
Whitford PC, et al. (2012) "Biomolecular Dynamics: Order-disorder transitions and energy landscapes" Rep Prog Phys 75,076601. doi:10.1088/0034-4885/75/7/076601.

Please direct questions and comments to info@smog-server.org.
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