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SMOG: Structure-based Models for Biomolecules. A very brief introduction to structure-based modeling. Additionally, with the computational simplicity of the models, they are proving to be very useful for structural modeling purposes, including atomic modeling of cryo-EM (e.g. MDfit. And recent review articles. How to prepare and simulate a SMOG model for a specific biomolecule. To run a single-basin structure-based model, the following steps should be adhered to. Available on the Gromacs. Due to some tec...

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SMOG | smog-server.org Reviews

<META> DESCRIPTION

SMOG: Structure-based Models for Biomolecules. A very brief introduction to structure-based modeling. Additionally, with the computational simplicity of the models, they are proving to be very useful for structural modeling purposes, including atomic modeling of cryo-EM (e.g. MDfit. And recent review articles. How to prepare and simulate a SMOG model for a specific biomolecule. To run a single-basin structure-based model, the following steps should be adhered to. Available on the Gromacs. Due to some tec...

<META> KEYWORDS

1 Whitford

2 Noel

3 Onuchic

4 Rice University

5 Northeastern University

6 CTBP

7 SMOG force field

8 Protein Folding

9 Protein Function

10 Protein Kinetics

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jump to main,introduction,prepare a simulation,run a simulation,additional tools,the contact map,source code extensions,faqs,news,standalone smog2,citing smog,and saxs,data,step 0,install the gromacs,step 1,alternate step 1,step 2,run the simulation

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SMOG | smog-server.org Reviews

https://smog-server.org

SMOG: Structure-based Models for Biomolecules. A very brief introduction to structure-based modeling. Additionally, with the computational simplicity of the models, they are proving to be very useful for structural modeling purposes, including atomic modeling of cryo-EM (e.g. MDfit. And recent review articles. How to prepare and simulate a SMOG model for a specific biomolecule. To run a single-basin structure-based model, the following steps should be adhered to. Available on the Gromacs. Due to some tec...

INTERNAL PAGES

smog-server.org

1

SMOG

http://www.smog-server.org/noel

Max Delbruck Center, Berlin. BS 2005, University of Wisconsin-Madison. PhD 2012, University of California-San Diego. Postdoctoral Fellow, Rice University. Humboldt Foundation Fellow, Berlin. Structure-based models book chapter. Molecular biophysics of biomolecular folding and function. As a Humboldt Fellow in Berlin, I am collaborating with Oliver Daumke. In an effort to provide a structure-based understanding of the dynamics and power stroke of the dynamin molecular motor. Lin X, Eddy NR, Noel JK, Whitf...

2

SMOG

http://www.smog-server.org/sbm_faq.html

General SMOG model questions. When running grompp, why does Gromacs call RNA residues "DNA" and call DNA residues "other"? This does not mean anything is wrong with the simulation. Our software uses pdb naming for our residues. i.e. RNA is called U, A, C and G and DNA is called DT, DC, DG and DA. But, Gromacs expects DNA to use single-letter names. This can also happen when porting amber nucleic acid forcefields to Gromacs V 4.0.X. Why does the CA model use a 10-12 Lennard-Jones potential? 000831451, and...

3

SMOG

http://www.smog-server.org/updates.html

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 post it. August 1st, 2016. March 10th, 2016. Our paper describing SMOG 2 appeared today in PLOS Computational Biology. February 3rd, 2016. July 31st, 2015. July 20th, 2015. SMOG v2 is now available! A user forum for smog...

4

SMOG

http://www.smog-server.org/Shadow.html

Click here to make your own Shadow contact map. Shadow contact map (SCM). The SCM algorithm is described in the above figure. It is a cut-off contact map with a screening term. Introduced. All atoms are given a radius. To determine the atoms contacting atom. All atoms within a cutoff distance. Are considered possible contacts. Those contacts which have an intervening atom are considered screened out and are discarded. The algorithm is simply stated: a light source is located at the center of atom. 11: Ad...

5

SMOG

http://www.smog-server.org/SB_analysis.html

Step 3: Analyze your trajectory. Calculating quantities from your simulations:. Gromacs also includes a large number of analysis programs with their distribution. Many produce text files formatted for use with Grace. A very powerful 2-D plotting tool). Scripts for tasks not easily available through Gromacs and VMD will be posted here over time. Contributed tools are always appreciated. 11/1/2013) An implementation of weighted histogram analysis that is tailored for use with SMOG to compute thermodynamic ...

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SMOG

SMOG: Structure-based Models for Biomolecules. A very brief introduction to structure-based modeling. Additionally, with the computational simplicity of the models, they are proving to be very useful for structural modeling purposes, including atomic modeling of cryo-EM (e.g. MDfit. And recent review articles. How to prepare and simulate a SMOG model for a specific biomolecule. To run a single-basin structure-based model, the following steps should be adhered to. Available on the Gromacs. Due to some tec...

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