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Manuscript Title: SASSIE: A program to study intrinsically disordered biological molecules and macromolecular ensembles using experimental scattering restraints
Authors: Joseph E. Curtis, Sindhu Raghunandan, Hirsh Nanda, Susan Krueger
Program title: SASSIE
Catalogue identifier: AEKL_v1_0
Distribution format: tar.gz
Journal reference: Comput. Phys. Commun. 183(2012)382
Programming language: Python, C/C++, Fortran.
Computer: PC/Mac.
Operating system: 32- and 64-bit Linux (Ubuntu 10.04, Centos 5.6) and Mac OS X (10.6.6).
RAM: 1 GB
Keywords: Small-angle scattering, X-ray scattering, Neutron scattering, Intrinsically disordered proteins, Protein structure, Computer modeling.
PACS: 87.
Classification: 3.

External routines: Python 2.6.5, numpy 1.4.0, swig 1.3.40, scipy 0.8.0, Gnuplot-py-1.8, Tcl 8.5, Tk 8.5, Mac installation requires aquaterm 1.0 (or X window system) and Xcode 3 development tools.

Nature of problem:
Open source software to generate structures of disordered biological molecules that subsequently allow for the comparison of computational and experimental results is limiting the use of scattering resources.

Solution method:
Starting with an all atom model of a protein, for example, users can input regions to vary dihedral angles, ensembles of structures can be generated. Additionally, simple two-body rigid-body rotations are supported with and without disordered regions. Generated structures can then be used to calculate small-angle scattering profiles which can then be filtered against experimentally determined data. Filtered structures can be visualized individually or as an ensemble using density plots. In the modular and expandable program framework the user can easily access our subroutines and structural coordinates can be easily obtained for study using other computational physics methods.

Running time:
Varies depending on application. Typically 10 minutes to 24 hours depending on the number of generated structures.

References:
[1] M. S. Kent, J. K. Murton, S. Satija, B. Akgun, H. Nanda, J. E. Curtis, J. Majewski, J. R. Engen, and C. R. Morgan. Neutron reflectivity study of the conformation of hiv nef bound to lipid membranes. Biophys. J., 99(6), 1940-1948, 2010.
[2] H. Nanda, S. A. K. Datta, F. Heinrich, M. Losche, A. Rein, S. Krueger, and J. E. Curtis. Electrostatic interactions and binding orientation of hiv-1 matrix, studied by neutron reflectivity. Biophys. J., 99(7), 2516-2524, 2010.
[3] S.A. K. Datta, J. E. Curtis, W. Ratcli, P. K. Clark, R. M. Crist, J. Lebowitz, S. Krueger, and A. Rein. Conformation of the hiv-1 gag protein in solution. J. Mol. Biol., 365(3):812824, 2007.