US-SOMO Citations page
Please use the following citations
Please use the following citations for your publications:
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For the use of the US-SOMO program:
- Brookes, EH and Rocco, M., Recent advances in the UltraScan SOlution MOdeller (US-SOMO) hydrodynamic and small-angle scattering data analysis and simulation suite. Eur. Biophys. J. 47(7) 855-64 (2018) doi: 10.1007/s00249-018-1296-0
- 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
- For A to B usage:
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For BEST usage:
- S.R. Aragon, A precise boundary element method for macromolecular transport properties J. Comp.Chem., 25, 1191-1205 (2004).
- For CRYSOL usage
- For CRYSON usage
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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 HPLC-SAXS and SVD usage
- Brookes, E., Vachette, P., Rocco, M., Pérez, J. (2016) US-SOMO HPLC-SAXS Module: Dealing with Capillary Fouling, and Extraction of Pure Component Patterns from Poorly Resolved SEC-SAXS Data, J. Appl. Cryst. 49. Brookes, E, Pérez, J, Cardinali, B, Profumo, A, Vachette, P and Rocco, M (2013), Fibrinogen species as resolved by HPLC-SAXS data processing within the UltraScan SOlution MOdeler (US SOMO) enhanced SAS module, J. Appl. Cryst. 46, 1823-1833
- For IFT usage
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For Parsimonious models usage
- Brookes, E. Parsimonious modeling, (manuscript in preparation)
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For ZENO usage:
- Kang EH, Mansfield ML, Douglas JF (2004) Numerical path integration technique for the calculation of transport properties of proteins. Phys Rev E Stat Nonlinear Soft Matter Phys 69:031918.
- Mansfield ML, Douglas JF (2008) Improved path integration method for estimating the intrinsic viscosity of arbitrarily shaped particles. Phys Rev E Stat Nonlinear Soft Matter Phys 78:046712.
- Juba D, Audus DJ, Mascagni M, Douglas JF, Keyrouz W (2017) ZENO: Software for calculating hydrodynamic, electrical, and shape properties of polymer and particle suspensions. J Res Natl Inst Stand Technol 122:1-2.
And also please cite for specific utilities used within US-SOMO:
If you have any questions, please feel free to contact us directly.
|
Emre Brookes, Ph.D. |
Mattia Rocco, Ph.D. |