Welcome to US-SOMO
Welcome to the US-SOMO website.
The current US-SOMO release version is 1919
To get started, you can look at the SOMO Manual
US-SOMO is bundled as part of the UltraScan software. For all Linux, Windows, and Macintosh (running OSX 10.5 or older version), we recommend downloading the US-II version here. For Macintosh users running OSX 10.6 or newer, we recommend downloading the US-III version here.
Intermediate Release Announcement
While a full new US-SOMO release is still in the making, we'd like to announce an "intermediate" release of US-SOMO for Linux, Windows and Mac systems. Besides several bug fixes, this version has many new features, additions and improvements, among which are:
- A revised somo.residue file in which the partial specific volumes of inorganic ions have been re-calculated from the molar volumes values present in Table III of Durchschlag and Zipper, Prog. Colloid Polym. Sci. 94:20-39,1994. Previously, and erroneously, these psv values were computed directly from the ions' radii. For some cations, like Ca++ and Mg++, the psv assumes relatively large negative values (which also required changes in the main program coding to handle them). We apologize for this mistake. While the effect on proteins is likely small, it is probably more relevant for peptides and nucleic acids.
- A revised Cluster access module. Access to some of the XSEDE (formerly TeraGrid) resources and the Alamo cluster at the UTHSCSA is now available. There are further improvements planned to this facility, but it is basically functional to compute SAXS curves on large numbers of structures and to perform discrete molecular dynamic simulations. Cluster usage can now be granted to users upon request. Hopefully, this will enable more users to take advantage of these resources.
- A functional PDB editor, which has some nice features like being able to split up a multi model PDB file and join individual files. You can also check your structure for errors with respect to the US-SOMO residue table and search for alternate matching residues. It is still under development, but is useable.
- In the SAXS/SANS module, there are now multiple methods for computing the scattering curve, including a full Debye (requiring explicitly hydrated structures), and interface with CRYSOL (which should be downloaded separately). There is also the ability to compute the distance distribution function p(r) vs. r from structures and a method to display a colored contribution of atoms to regions of the p(r) in the molecular viewer. Best fit and least squares methods of curves to experimental data are also included.
- A model classifier, functional to rank batches of results from hydrodynamic computations against experimental values is various ways.
- We also offer another hydrodynamic computation method, Zeno, based on the analogy between electrostatics and hydrodynamics (see the Zeno website, http://www.stevens.edu/zeno/). We have not yet completed a comparison of this method vs. our standard Garcia de la Torre-Bloomfield method, but we plan to do this shortly. A newer version will be available in the next release featuring faster processing times.
We will be starting our mailing list in a few days. If you wish to be added to the mailing list or would like a live tutorial over Skype or EVO, please send an email.
Please use the following citations for your publications:
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For the use of the US-SOMO program:
- Rai, N, Nollmann, M, Spotorno, B, Tassara, G, Byron, O, and Rocco, M. SOMO (SOlution MOdeler): Differences between X-Ray and NMR-Derived Bead Models Suggest a Role for Side Chain Flexibility in Protein Hydrodynamics. Structure 13, 723-734, 2005,
- Brookes, E., Demeler., B, and Rocco, M. The implementation of SOMO (SOlution MOdeller) in the UltraScan analytical ultracentrifugation data analysis suite: enhanced capabilities allow the reliable hydrodynamic modeling of virtually any kind of biomacromolecule. Eur. Biophys. J, 2010 DOI: 10.1007/s00249-009-0418-0
- Brookes, E., Demeler, B., Rosano, C., and Rocco, M. Developments in the US-SOMO Bead Modeling Suite: New Features in the Direct Residue-to-Bead Method, Improved Grid Routines, and Influence of Accessible Surface Area Screening, , Macromol. Biosci. 10:746-753, 2010 DOI: 10.1002/mabi.200900474
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For A to B usage:
- Byron, O. Construction of hydrodynamic bead models from high-resolution X-ray crystallographic or nuclear magnetic resonance data. Biophys. J. 72, 408-415, 1997.
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For BFNB usage
- Brookes, E. BFNB, (manuscript in preparation)
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For CRYSOL usage
- Svergun D.I., Barberato C. and Koch M.H.J. (1995) CRYSOL - a Program to Evaluate X-ray Solution Scattering of Biological Macromolecules from Atomic Coordinates J. Appl. Cryst. , 28, 768-773.
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For DAMMIF usage
- Franke, D. and Svergun, D.I. (2009) DAMMIF, a program for rapid ab-initio shape determination in small-angle scattering. J. Appl. Cryst., 42, 342-346.
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For DAMMIN usage
- D. I. Svergun (1999) Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys J. 2879-2886.
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For DMD usage:
- Dokholyan, NV,Buldyrev, SV, Stanley, HE, and EI Shaknovich. Discrete molecular dynamics studies of the folding of a protein-like model . (1998) Folding & Design 3:577-587
- Ding F, Dokholyan NV. Emergence of protein fold families through rational design. Public Library of ScienceComput Biol. (2006) 2(7):e85
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For GASBOR usage
- Svergun, D.I., Petoukhov, M.V. and Koch, M.H.J. (2001) Determination of domain structure of proteins from X-ray solution scattering. Biophys. J., 80, 2946-2953.
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For ZENO usage:
- Mansfield et al., Intrinsic Viscosity and the Electric Polarizability of Arbitrarily Shaped Objects, Phys. Rev. E, 64:61401-61416, 2001
And also please cite for specific utilities used within US-SOMO:
If you have any questions, please feel free to contact us directly.
We look forward to hearing from you!
|
Emre Brookes, Ph.D. |
Mattia Rocco, Ph.D. |