ATSAS 2.1, a program package for small‐angle scattering data analysis

The program package ATSAS 2.1 for small-angle X-ray and neutron scattering data analysis is presented. The programs included in the package cover the major processing and interpretation steps from primary data reduction to three-dimensional modelling. This system is primarily oriented towards the analysis of biological macromolecules, but could also be used for non-biological isotropic and partially ordered objects (nanoparticle systems, colloidal solutions, polymers in solution and bulk). Recent developments in the programs included in ATSAS 2.1 are highlighted. The main programs run on multiple hardware platforms, including Windows PC, Linux RedHat and Suse, DEC Alpha, SGI IRIX and Mac OSX.

[1]  Peter V. Konarev,et al.  MASSHA – a graphics system for rigid-body modelling of macromolecular complexes against solution scattering data , 2001 .

[2]  R. Huber,et al.  Crystal structure of the tricorn protease reveals a protein disassembly line , 2001, Nature.

[3]  Dmitri I. Svergun,et al.  New developments in direct shape determination from small-angle scattering. 2. Uniqueness , 1996 .

[4]  Charles L. Lawson,et al.  Solving least squares problems , 1976, Classics in applied mathematics.

[5]  Dmitri I. Svergun,et al.  Automated matching of high- and low-resolution structural models , 2001 .

[6]  G. G. Stokes.  "J." , 1890, The New Yale Book of Quotations.

[7]  Sebastian Doniach,et al.  Reconstruction of low-resolution three-dimensional density maps from one-dimensional small-angle X-ray solution scattering data for biomolecules , 2000 .

[8]  Dmitri I. Svergun,et al.  PRIMUS: a Windows PC-based system for small-angle scattering data analysis , 2003 .

[9]  D. Svergun,et al.  A small angle x-ray scattering study of the droplet–cylinder transition in oil-rich sodium bis(2-ethylhexyl) sulfosuccinate microemulsions , 2000 .

[10]  D. Svergun,et al.  Mathematical methods in small-angle scattering data analysis , 1991 .

[11]  A. V. Semenyuk,et al.  Small-angle-scattering-data treatment by the regularization method , 1988 .

[12]  D. Svergun,et al.  CRYSOL : a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates , 1995 .

[13]  Maxim V. Petoukhov,et al.  New methods for domain structure determination of proteins from solution scattering data , 2003 .

[14]  C. Boulin,et al.  Data appraisal, evaluation and display for synchrotron radiation experiments: Hardware and software , 1986 .

[15]  Dmitri I Svergun,et al.  Global rigid body modeling of macromolecular complexes against small-angle scattering data. , 2005, Biophysical journal.

[16]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[17]  Sang Joon Kim,et al.  A Mathematical Theory of Communication , 2006 .

[18]  良二 上田.  J. Appl. Cryst.の発刊に際して , 1970 .

[19]  P. Rosevear,et al.  The solution structure of a cardiac troponin C-troponin I-troponin T complex shows a somewhat compact troponin C interacting with an extended troponin I-troponin T component. , 2002, Biochemistry.

[20]  A. V. Semenyuk,et al.  GNOM – a program package for small-angle scattering data processing , 1991 .

[21]  T. Earnest,et al.  From words to literature in structural proteomics , 2003, Nature.

[22]  M. Wall,et al.  Large-scale shape changes in proteins and macromolecular complexes. , 2000, Annual review of physical chemistry.

[23]  Dmitri I. Svergun,et al.  Determination of the regularization parameter in indirect-transform methods using perceptual criteria , 1992 .

[24]  William H. Press,et al.  Numerical recipes , 1990 .

[25]  Otto Dykstra.  Statistics: An Introduction , 1975 .

[26]  P Chacón,et al.  Reconstruction of protein form with X-ray solution scattering and a genetic algorithm. , 2000, Journal of molecular biology.

[27]  W. Ehrenberg,et al.  Small-Angle X-Ray Scattering , 1952, Nature.

[28]  A. Annila,et al.  Quaternary structure built from subunits combining NMR and small-angle x-ray scattering data. , 2002, Biophysical journal.

[29]  O. Glatter,et al.  19 – Small-Angle X-ray Scattering , 1973 .

[30]  D I Svergun,et al.  Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. , 1999, Biophysical journal.

[31]  M. Koch,et al.  [52] Neutron-scattering studies of ribosomes , 1979 .

[32]  Claudio Ferrero,et al.  The SAXS/WAXS software system of the DUBBLE CRG beamline at the ESRF , 2001 .

[33]  S. King,et al.  SANS at Pulsed Neutron Sources: Present and Future Prospects , 1997 .

[34]  D I Svergun,et al.  Determination of domain structure of proteins from X-ray solution scattering. , 2001, Biophysical journal.

[35]  Dmitri I Svergun,et al.  Addition of missing loops and domains to protein models by x-ray solution scattering. , 2002, Biophysical journal.

[36]  E Pantos,et al.  Low-resolution structures of proteins in solution retrieved from X-ray scattering with a genetic algorithm. , 1998, Biophysical journal.

[37]  D. Svergun,et al.  Small-angle scattering studies of biological macromolecules in solution , 2003 .

[38]  A. Garcia,et al.  Functional dynamics of the hydrophobic cleft in the N-domain of calmodulin. , 2001, Biophysical journal.

[39]  B. Vainshtein,et al.  Diffraction of X-rays by chain molecules , 1966 .

[40]  Dmitri I. Svergun,et al.  Uniqueness of ab initio shape determination in small-angle scattering , 2003 .

[41]  F. Young.  Biochemistry , 1955, The Indian Medical Gazette.

[42]  R A Sayle,et al.  RASMOL: biomolecular graphics for all. , 1995, Trends in biochemical sciences.

[43]  Tomoharu Matsumoto,et al.  SAXSANA: an interactive program for the analysis and monitoring of static and time-resolved small-angle X-ray solution scattering measurements. , 2003, Journal of synchrotron radiation.

[44]  D. Svergun,et al.  Prototype of a database for rapid protein classification based on solution scattering data , 2003 .

[45]  M. Brillouin,et al.  La diffraction des rayons X aux très petits angles: application a l'étude de phénomènes ultramicroscopiques , 1939 .

[46]  Pavel Strunz,et al.  General formula for determination of cross-section from measured SANS intensities , 2000 .

[47]  J H Prestegard,et al.  NMR structures of biomolecules using field oriented media and residual dipolar couplings , 2000, Quarterly Reviews of Biophysics.

[48]  C. D. Gelatt,et al.  Optimization by Simulated Annealing , 1983, Science.

[49]  P. Güntert.  Structure calculation of biological macromolecules from NMR data , 1998, Quarterly Reviews of Biophysics.

[50]  A. Hinde.  PRINSAS – a Windows-based computer program for the processing and interpretation of small-angle scattering data tailored to the analysis of sedimentary rocks , 2004 .

[51]  O. Glatter,et al.  A new method for the evaluation of small‐angle scattering data , 1977 .

[52]  S. Schor.  STATISTICS: AN INTRODUCTION. , 1965, The Journal of trauma.

[53]  D. I. Svergun,et al.  Structure Analysis by Small-Angle X-Ray and Neutron Scattering , 1987 .

[54]  Lester Ingber,et al.  Simulated annealing: Practice versus theory , 1993 .

[55]  D. I. Svergun,et al.  Solution scattering from biopolymers: advanced contrast‐variation data analysis , 1994 .

[56]  C. E. SHANNON,et al.  A mathematical theory of communication , 1948, MOCO.

[57]  J R Helliwell,et al.  Synchrotron and neutron techniques in biological crystallography. , 2004, Chemical Society reviews.

[58]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[59]  Gene H. Golub,et al.  Singular value decomposition and least squares solutions , 1970, Milestones in Matrix Computation.

[60]  D. I. Svergun,et al.  sasCIF: an extension of core Crystallographic Information File for SAS , 2000 .