SBGrid Consortium - Supported Software

SAXS

SBGrid supports 5 saxs software titles. The following software packages are supported by SBGrid; availability of a specific software package may be limited based on license requirements.

Software Title	Description	Linux 32-bit	Linux 64-bit	OS X Intel	Links	HiddenDetail
ATSAS	- a program suite for small-angle scattering (SAXS) data analysis from biological macromolecules. This suite of programs was ...	check	check	check		a program suite for small-angle scattering (SAXS) data analysis from biological macromolecules. This suite of programs was developed in Dmitri Svergun's group at EMBL Hamburg. Authorship by program is as follows: PRIMUS - P.V. Konarev, A.G. Kikhney, A.V. Sokolova, D.I. Svergun & V.V. Volkov GNOM - D.I. Svergun & A. Semenyuk DAMMIN - D.I. Svergun with M. Kozin, M. Petoukhov, V. Volkov DAMMIF - D. Franke MONSA, GASBOR, SASREF, BUNCH, CORAL, GLOBSYMM, DAMAVER - M.V. Petoukhov & D.I. Svergun MASSHA - P.V. Konarev, M.V. Petoukhov, D.I. Svergun & V.V. Volkov OLIGOMER - D.I. Svergun with A.V. Sokolova, P.V. Konarev, V.V. Volkov MIXTURE - P.V. Konarev, D.I. Svergun1 & V.V. Volkov EOM - P. BernadÃ³, E. Mylonas, M.V. Petoukhov & D.I. Svergun CRYSOL - D. Svergun, C. Barberato, M. Malfois, V. Volkov, P. Konarev, M. Petoukhov & A. Shkumatov CRYSON - D. Svergun, M. Malfois, M. Petoukhov & A. Shkumatov SUPCOMB - M.B. Kozin, M.V. Petoukhov & D.I. Svergun DARA - A. V. Sokolova, V. V. Volkov & D. I. Svergun SASHA - D.I. Svergun & V.V. Volkov ASSA - M.B. Kozin & D.I. Svergun CREDO - M.V. Petoukhov & D.I. Svergun Developers Maxim Petoukhov Dmitri Svergun Martin Raditsch Categories SAXS Versions Linux 32: 2.4.2-1 Linux 64: 2.4.2-1 OSX Intel: 2.4.2-3 OSX PPC: 2.2 Citations PRIMUS, MIXTURE: Konarev. PRIMUS - a Windows-PC based system for small-angle scattering data analysis. J Appl Cryst. 2003. 36:1277-1282. GNOM: Svergun. Determination of the regularization parameter in indirect-transform methods using perceptual criteria. J. Appl. Crystallogr. 1992. 25:495-503. DAMMIN, MONSA: Svergun. Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys J. 1999. 2879-2886. DAMMIF: Franke and Svergun.DAMMIF, a program for rapid ab-initio shape determination in small-angle scattering. J. Appl. Cryst. 2009. 42:342-346. SASREF, BUNCH, CORAL, GLOBSYMM: Petoukhov and Svergun. Global rigid body modelling of macromolecular complexes against small-angle scattering data. Biophys. J. 2005. 89:1237-1250. MASSHA: Konarev et al. MASSHA - a graphic system for rigid body modelling of macromolecular complexes against solution scattering data. J Appl Cryst. 2001. 34:527-532. EOM: Bernado et al. Structural Characterization of Flexible Proteins Using Small-Angle X-ray Scattering. J. Am. Chem. Soc. 2007. 129(17):5656-5664. CRYSOL, CRYSON, : Svergun et al. CRYSOL - a Program to Evaluate X-ray Solution Scattering of Biological Macromolecules from Atomic Coordinates J. Appl. Cryst. 1995. 28:768-773. SUPCOMB: Kozin & Svergun. Automated matching of high- and low-resolution structural models J Appl Cryst. 2000. 34:33-41. DAMAVER: Volkov and Svergun. Uniqueness of ab-initio shape determination in small-angle scattering. J. Appl. Cryst. 2003. 36:860-864. DARA: Sokolova et al. Prototype of a database for rapid protein classification based on solution scattering data. J. Appl. Cryst. 2003. 36:865-868. License Type This software is distributed under a Non-Profit license.
a program suite for small-angle scattering (SAXS) data analysis from biological macromolecules. This suite of programs was developed in Dmitri Svergun's group at EMBL Hamburg. Authorship by program is as follows: PRIMUS - P.V. Konarev, A.G. Kikhney, A.V. Sokolova, D.I. Svergun & V.V. Volkov GNOM - D.I. Svergun & A. Semenyuk DAMMIN - D.I. Svergun with M. Kozin, M. Petoukhov, V. Volkov DAMMIF - D. Franke MONSA, GASBOR, SASREF, BUNCH, CORAL, GLOBSYMM, DAMAVER - M.V. Petoukhov & D.I. Svergun MASSHA - P.V. Konarev, M.V. Petoukhov, D.I. Svergun & V.V. Volkov OLIGOMER - D.I. Svergun with A.V. Sokolova, P.V. Konarev, V.V. Volkov MIXTURE - P.V. Konarev, D.I. Svergun1 & V.V. Volkov EOM - P. BernadÃ³, E. Mylonas, M.V. Petoukhov & D.I. Svergun CRYSOL - D. Svergun, C. Barberato, M. Malfois, V. Volkov, P. Konarev, M. Petoukhov & A. Shkumatov CRYSON - D. Svergun, M. Malfois, M. Petoukhov & A. Shkumatov SUPCOMB - M.B. Kozin, M.V. Petoukhov & D.I. Svergun DARA - A. V. Sokolova, V. V. Volkov & D. I. Svergun SASHA - D.I. Svergun & V.V. Volkov ASSA - M.B. Kozin & D.I. Svergun CREDO - M.V. Petoukhov & D.I. Svergun Developers Maxim Petoukhov Dmitri Svergun Martin Raditsch Categories SAXS Versions Linux 32: 2.4.2-1 Linux 64: 2.4.2-1 OSX Intel: 2.4.2-3 OSX PPC: 2.2 Citations PRIMUS, MIXTURE: Konarev. PRIMUS - a Windows-PC based system for small-angle scattering data analysis. J Appl Cryst. 2003. 36:1277-1282. GNOM: Svergun. Determination of the regularization parameter in indirect-transform methods using perceptual criteria. J. Appl. Crystallogr. 1992. 25:495-503. DAMMIN, MONSA: Svergun. Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys J. 1999. 2879-2886. DAMMIF: Franke and Svergun.DAMMIF, a program for rapid ab-initio shape determination in small-angle scattering. J. Appl. Cryst. 2009. 42:342-346. SASREF, BUNCH, CORAL, GLOBSYMM: Petoukhov and Svergun. Global rigid body modelling of macromolecular complexes against small-angle scattering data. Biophys. J. 2005. 89:1237-1250. MASSHA: Konarev et al. MASSHA - a graphic system for rigid body modelling of macromolecular complexes against solution scattering data. J Appl Cryst. 2001. 34:527-532. EOM: Bernado et al. Structural Characterization of Flexible Proteins Using Small-Angle X-ray Scattering. J. Am. Chem. Soc. 2007. 129(17):5656-5664. CRYSOL, CRYSON, : Svergun et al. CRYSOL - a Program to Evaluate X-ray Solution Scattering of Biological Macromolecules from Atomic Coordinates J. Appl. Cryst. 1995. 28:768-773. SUPCOMB: Kozin & Svergun. Automated matching of high- and low-resolution structural models J Appl Cryst. 2000. 34:33-41. DAMAVER: Volkov and Svergun. Uniqueness of ab-initio shape determination in small-angle scattering. J. Appl. Cryst. 2003. 36:860-864. DARA: Sokolova et al. Prototype of a database for rapid protein classification based on solution scattering data. J. Appl. Cryst. 2003. 36:865-868. License Type This software is distributed under a Non-Profit license. Static link to the SBGrid ATSAS page.
MES	- (Minimal Ensemble Search) a genetic algorithm used to identify the minimal ensemble required to best ï¬t experimental ...	check	check	check		(Minimal Ensemble Search) a genetic algorithm used to identify the minimal ensemble required to best ï¬t experimental data. The simulations provide an ensemble of molecular models from which a SAXS curve is calculated and compared to the experimental curve. Written by Martin Pelikan and Michal Hammel at Lawrence Berkeley Laboratory. Developers Michal Hammel Categories SAXS Versions Linux 32: 20101116 Linux 64: 20101116 OSX Intel: 20101116 OSX PPC: 20101116 Citations BernadÃ³ et al. Structural characterization of flexible proteins using small-angle X-ray scattering. Journal of the American Chemical Society (2007) vol. 129 (17) pp. 5656-64 Pelikan et al. Structure and flexibility within proteins as identified through small angle X-ray scattering. General physiology and biophysics (2009) vol. 28 (2) pp. 174-89 License Type This software is distributed under an Academic license.
(Minimal Ensemble Search) a genetic algorithm used to identify the minimal ensemble required to best ï¬t experimental data. The simulations provide an ensemble of molecular models from which a SAXS curve is calculated and compared to the experimental curve. Written by Martin Pelikan and Michal Hammel at Lawrence Berkeley Laboratory. Developers Michal Hammel Categories SAXS Versions Linux 32: 20101116 Linux 64: 20101116 OSX Intel: 20101116 OSX PPC: 20101116 Citations BernadÃ³ et al. Structural characterization of flexible proteins using small-angle X-ray scattering. Journal of the American Chemical Society (2007) vol. 129 (17) pp. 5656-64 Pelikan et al. Structure and flexibility within proteins as identified through small angle X-ray scattering. General physiology and biophysics (2009) vol. 28 (2) pp. 174-89 License Type This software is distributed under an Academic license. Static link to the SBGrid MES page.
saxsview	- a plotting facility for SAXS-data, as well as a convenient tool to quickly generate plots for publication. ...	check		check		a plotting facility for SAXS-data, as well as a convenient tool to quickly generate plots for publication. saxsview shows 1D-data in .dat, .int, .fit and .fir formats of the ATSAS package, the cansas .xml format (v1.0), as well as .csv files. Categories SAXS Versions Linux 32: 0.2 OSX Intel: 0.2 License Type This software is distributed under an Open license.
a plotting facility for SAXS-data, as well as a convenient tool to quickly generate plots for publication. saxsview shows 1D-data in .dat, .int, .fit and .fir formats of the ATSAS package, the cansas .xml format (v1.0), as well as .csv files. Categories SAXS Versions Linux 32: 0.2 OSX Intel: 0.2 License Type This software is distributed under an Open license. Static link to the SBGrid saxsview page.
SITUS	- a program package for modeling of atomic resolution structures into low-resolution density maps. The software supports both ...	check	check	check		a program package for modeling of atomic resolution structures into low-resolution density maps. The software supports both rigid-body and flexible docking using a variety of fitting strategies. Developers Situs Developer Team Categories Electron Microscopy SAXS Versions Linux 32: 2.6.3 Linux 64: 2.6.3 OSX Intel: 2.6.3 OSX PPC: 2.6.1 SGI Irix: 2.1a3 Citations Wriggers. Using Situs for the Integration of Multi-Resolution Structures. Biophysical Reviews. 2010. 2: 21-27. License Type This software is distributed under an Open license.
a program package for modeling of atomic resolution structures into low-resolution density maps. The software supports both rigid-body and flexible docking using a variety of fitting strategies. Developers Situs Developer Team Categories Electron Microscopy SAXS Versions Linux 32: 2.6.3 Linux 64: 2.6.3 OSX Intel: 2.6.3 OSX PPC: 2.6.1 SGI Irix: 2.1a3 Citations Wriggers. Using Situs for the Integration of Multi-Resolution Structures. Biophysical Reviews. 2010. 2: 21-27. License Type This software is distributed under an Open license. Static link to the SBGrid SITUS page.
VOLSLICE3D	- a utility to display three dimensional electron density maps. It is an improved version of Volslice, a ...	check				a utility to display three dimensional electron density maps. It is an improved version of Volslice, a program that displays electron density maps using ASCII and is part of the SITUS package. Developers Stefan Birmanns Categories Electron Microscopy SAXS Versions Linux 32: 1.0 Citations Wriggers and Birmanns. Using situs for flexible and rigid-body fitting of multiresolution single-molecule data. J Struct Biol. 2001 133(2-3):193-202. License Type This software is distributed under an Open license.
a utility to display three dimensional electron density maps. It is an improved version of Volslice, a program that displays electron density maps using ASCII and is part of the SITUS package. Developers Stefan Birmanns Categories Electron Microscopy SAXS Versions Linux 32: 1.0 Citations Wriggers and Birmanns. Using situs for flexible and rigid-body fitting of multiresolution single-molecule data. J Struct Biol. 2001 133(2-3):193-202. License Type This software is distributed under an Open license. Static link to the SBGrid VOLSLICE3D page.