News, page updates and bug fixes


When we make changes to the model, fix bugs, or we just want to share something cool with everyone, you'll see it here. If you are going to present work with these models at a conference, or if you publish a paper, send us an email and we'll be happy to add it as an announcement.

NEWS

October 18th, 2022 Hassan and Whitford used SMOG 2 and SMOG models to identify novel single-molecule strategies for monitoring collective rearrangements in the ribosome during tRNA translocation. By comparing different single-molecule labeling sites, they showed how future experiments may be able to simultaneously measrure two large-scale motions in the ribosome. See the results in J Phys Chem B.

October 17th, 2022 Wang et al. used SMOG 2 and SMOG models to isolate the precise steric interactions that govern a large-scale conformational rearrangement in the ribosome. Using an perturbative approach, they found that a single residue can control tRNA motion on the ribosome. See the results in J Phys Chem B.

July 22th, 2022 Ahn et al. used SMOG 2 and SMOG models to study protein folding on the ribosome. They showed how perturbations to the ribosome can impact folding properties. See the results in Nature Communications

May 20th, 2022 Wang et al. used SMOG 2 to develop SMOG-ion, a model that allows for SMOG models to be used with electrostatics and explicit ions. To demonstrate the utility of this approach, free-energy barriers were calculated for the ribosome. This revealed a strong ion-concentration dependence of tRNA motion on the ribosome. The model may be used with OpenMM or Gromacs, and the templates are freely available through the SMOG 2 force field repo. For a full description of the model, see the manuscript in JACS.

April 14th, 2022 Paul Whitford gave a Protein Society webinar today that described SMOG 2 and OpenSMOG. Check out the talk here.

October 16th, 2021 The OpenSMOG manuscript appeared online today. As described in the manuscript, with SMOG 2.4 it is possible to use all-atom SMOG models to study a broad range of systems, including extremely large assemblies. Simulations were reported that described multi-million atom systems, such as crystallographic lattices of ribosomes, chromosomes and the HIV capsid with explicit electrostatics and ions. In addition, the OpenSMOG module allows for the utilization of high-performance GPU accelerators. See these example applications and performance statistics in the manuscript.

October 14th, 2021 Cassaignau et al. used SMOG 2 to study co-translational folding on the ribosome. In this study, the authors demonstrated how a delicate balance between folding energetics and binding can facilate nascent chain dynamics. The study appeared in Nature Chemistry.

August 31st, 2021 Dodero-Rojas et al. used all-atom structure based models and SMOG 2 to simulate the complete conformational rearrangement of the SARS-CoV-2 Spike protein. These provide the first mechanistic description of this large-scale (hundreds of Angstroms) rearrangement. The results appeared in eLife. The study was selected for a press release by eLife, which can be found here. This was accompanied by a press release by Rice University. If you would like to download one of the simulated trajectories, you may find it here.

May 24th, 2021 Freitas et al. used all-atom structure based models and SMOG 2 to simulate subunit rotation in a eukaryotic ribosome. These are the first simulations with an all-atom in which spontaneous subunit subunit rotation has been observed in a ribosome (for any organism) and they are the first simulations of a spontaneous large-scale rearrangement in a eukaryotic ribosome. The results appeared in Biophysica.

November 11th, 2020 Levi et al. used all-atom structure based models and SMOG 2 to study P/E hybrid formation on the ribosome. The results appeared in Nature Communications.

November 7th, 2020 Whitford, Jiang and Serwer used all-atom structure based models and SMOG 2 to simulate maturation of a complete viral capsid (1.1 million atoms). The results appeared in a special issue of Viruses that was in memory of Michael Rossmann.

October 29th, 2020 Javitt et al. used the C-alpha structure-based model, and SMOG 2, to study assembly of mucin and von Willibrand factor polymers. The results appeared in Cell.

August 4th, 2020 Roy et al. used the C-alpha structure-based model, and SMOG 2, to study the receptor binding domain in the SARS-CoV-2 spike protein. These simulations show how the structure of the spike protein has evolved to allow for efficient receptor binding. The results appeared in J Phys Chem Letters.

July 27th, 2020 Suma et al. used the all-atom SMOG model to undestand how xrRNAs are able to exhibit asymmetric nanopore translocation properties. The study was published in Nature Communications.

February 2020 Bandarkar et al. used all-atom structure-based models to interpret the dynamics of tRNA in nanopore experiments. The results appeared in Biophysical Journal.

August 2019 Yang et al. compared the diffusive properties of tRNA inside the ribosome when using all-atom structure-based models and all-atom explicit-solvent simulations. Through this, they showed how electrostatic and solvation effects can lead to position-dependent diffusion of tRNA during elongation. The article was selected as a 2019 Editor's Choice for J Chem Phys.

July 2019 Faelber et al. investigated the structure of the mitochondrial membrane remodeling protein Mgm1/Opa1. Structure-based models of the filament formed by Mgm1 were used to predict how the filament will adjust to varying membrane tube radii. The results appeared in Nature.

October 2018 Yang, Perrier and Whitford used C-alpha SMOG models to identify a disordered intermediate during large-scale conformational rearrangments in EF-Tu. The results appeared on the cover of Proteins.

September 18th, 2018 Gatsogiannis et al. used SMOG2 to generate SMOG models to study conformational changes in Tc toxin. The results were published in Nature.

August 2018 Liu et al. used structure-based models determine if distal domains within a crystal structure were geometrically able to dimerize. The results appeared in Nature Communications.

Dec 19th, 2017 Levi et al used SMOG 2 to develop a new coarse-grained model for ribonucleoprotein assemblies. Using their model they explored how observations in single-molecule experiments can be influenced by the choice of probe location. The results appeared in Biophysical Journal.

Nov 30th, 2017 Yang, Noel and Whitford used all-atom SMOG models to explore the relationship between structural fluctuations in the ribosome and large-scale rearrangements of tRNA molecules. The study appeared on the cover of J Phys Chem B.

May 8th, 2017 Today, the SMOG webtool has generated its 20,000th force field! Excellent work everybody!

May 4th, 2017 SMOG models were used to interpret measurements of proteins in nanopores. The results appeared in ACS Nano.

March 9th, 2017 Nguyen, Yang and Whitford used SMOG models to show how differences in the tRNA variable loop can lead to species-specific dynamics during hybrid-state formation on the ribosome. The results appeared in J Phys Chem B.

Dec 2016 An updated version 1.07 of WHAM.jar is available on the tools page. If you use this tool, make sure you use the updated version as it fixes an issue that often prolongs the convergence time for parallel runs.

October 31st, 2016 Noel and Whitford used SMOG models to show how EF-Tu can reduce the free-energy barrier of tRNA accommodation on the ribosome. The results appeared today in Nature Communications.

August 1st, 2016 Nguyen and Whitford used SMOG models to identify appropriate single-molecule labeling sites for measuring tRNA hybrid-state formation in the ribosome. The manuscript appeared in J. Phys. Chem. B.

March 10th, 2016 Our paper describing SMOG 2 appeared today in PLOS Computational Biology.

February 3rd, 2016 Nguyen and Whitford used SMOG models to identify a new collective tilting motion in the ribosome. The results appeared today in Nature Communications.

July 31st, 2015 Ramirez-Sarmiento et al uses SMOG to show how interdomain contacts control native state switching of RfaH on a dual-funneled landscape. The results were reported in PLOS Comp Bio.

July 20th, 2015 SMOG 2 is now available! This is a downloadable version of the software, which has been designed to provide a robust platform for the flexible design of new SMOG models. Check out the SMOG 2 page here.

May 2015 A user forum for smog users is now available. This is for discussion/questions regarding structure-based models, as well as the SMOG and SMOG 2 software. To sign up, go to the forum page.

December 2014 Noel et al use SMOG models to identify optimal coordinates for describing the large-scale accommodation process in the ribosome. The results were reported in Biophysical Journal.

Aug 1st, 2014 Lin et al. use dual-basin SMOG models to present the first dynamical picture of the massive functional rearrangment of the influenza virus glycoprotein hemagglutinin. The results were reported in PNAS.

May 22nd-23rd, 2014 Many members of the SMOG team and others who use SMOG models presented work at the 1st Symposium on Current Topics in Molecular Biophysics at the University of São Paulo, Brazil.

July 19th, 2013 Beta version of the downloadable local version of the webtool is available. It is based on Perl5 and XML. While we believe you will already find it useful, it is still an experimental version and we appreciate feedback.

June 11th, 2013 10,000th PDB converted to gro/top SBM. Keep up the great science!

January 17th, 2013 Walther et al. use SMOG models to help identify the structure and self-assembly properties of the TatA translocation pore. The results were reported in Cell.

November 2012 Lammert et al. show that backbone distortions decide the folding mechanism of SH3 in the Calpha model. The article appeared in PLoS Comp Bio

September 20th, 2012 Jamros et al. used SMOG models to characterize changes in the configurational distribution of Csk upon substrate binding. The results were published in PLoS Comp. Biol..

July 13th, 2012 Sulkowska et al. uses SBMs to explore the landscape of a designed trefoil knotted protein. The manuscript appeared in PNAS.

May 8th, 2012 Sutto and Camilloni used SBMs to study the engineered proteins GA98 and GB98, which provided insights into how protein folding motifs may evolve. The manuscript appeared in J. Chem. Phys..

April 2012 Wang et al. studied large-scale conformational rearrangements in Maltose Binding Protein. They used SBMs to built a triple-basin model to identify the extent to which induced-fit and population-shift mechanisms are used. The manuscript appeared in PLoS Computational Biology.

April 26th, 2012 Noel et al. characterizes the shadow map and shows how it is a general contact map definition for capturing the dynamics of biomolecular folding and function. The manuscript appeared in J. Phys. Chem. B.

April 12th, 2012 Noel et al. uses SBMs to more fully explore the competing folded conformations of three helix bundles found in explicit solvent REMD simulations. The manuscript appeared in J. Phys. Chem. B.

March, 2012 Gaye et al. used SBMs to study the effects of mutations in the protein TOP7. The results were published in EPL.

November 13th, 2011 Altman et al. used modified SBMs to characterize the properties of novel FRET dyes. The results were presented in Nature Methods.

November 12th, 2011 Lammert et al. used modified SBMs to investigate the detailed role of protein side-chain excluded volume during folding. The results were presented in Proteins: Structure, Function Bioinformatics.

November 11th, 2011 Whitford et al. used SBMs as the foundation for building atomic models from cryo-EM data for the ribosome. The results were reported in PNAS. The described atomic models can be found here.

October 13th, 2011 Aqeel et al. compared a variety of cryo-EM modeling techniques, including MDfit. The results were reported in J. Struct. Biol..

May 27th, 2011 Ferreira et al. used SBMs to interpret SAXS measurements, which demonstrated that PKD2 proteins likely form oligomeric assemblies in solution. The results were published in PNAS.

January 24th, 2011 Nechushtai et al. combined SBMs with x-ray crystallography, protein-film voltammetry and CD measurements to reveal hidden modes of long-range communication in a Ferredoxin protein domain. The results were published in PNAS.

August 26th, 2010 Jamros et al. used the all-atom SBM to model the ensemble of configurations of Csk that best accounts for measured Small Angle X-ray Scattering data. The results appeared in the Journal of Biological Chemistry, and can be accessed here.

August 11th, 2010 Noel et al. used the all-atom SBM to investigate the folding of complex topologies, namely a trefoil knotted protein. The paper can be accessed here.

December 29th, 2009 Using this webtool, Schug et al. utilized a structure-based force field to assist in modeling protein complexes. The results were published in PNAS and can be accessed here.

December 28th, 2009 With the use of this webtool and model, Camilloni and Sutto published results on the folding of Lymphotactin in J. Chem. Phys. Check it out here.

January 20th, 2009 Calpha model for proteins added to the webtool and tutorial.

November, 2008 "Shadow" contact analysis webtool for monomeric, and oligomeric, protein/RNA/DNA systems was released.

October, 2008 All-atom structure-based webtool for proteins, RNA and DNA is released.

September 2nd, 2008 Our initial all-atom paper on proteins is published online in Proteins: Structure, Function Bioinformatics.

Please direct questions and comments to info@smog-server.org.
Page created and maintained by Jeff Noel and Paul Whitford