Literature DB >> 22707386

A hierarchical algorithm for fast Debye summation with applications to small angle scattering.

Nail A Gumerov1, Konstantin Berlin, David Fushman, Ramani Duraiswami.   

Abstract

Debye summation, which involves the summation of sinc functions of distances between all pair of atoms in three-dimensional space, arises in computations performed in crystallography, small/wide angle X-ray scattering (SAXS/WAXS), and small angle neutron scattering (SANS). Direct evaluation of Debye summation has quadratic complexity, which results in computational bottleneck when determining crystal properties, or running structure refinement protocols that involve SAXS or SANS, even for moderately sized molecules. We present a fast approximation algorithm that efficiently computes the summation to any prescribed accuracy ε in linear time. The algorithm is similar to the fast multipole method (FMM), and is based on a hierarchical spatial decomposition of the molecule coupled with local harmonic expansions and translation of these expansions. An even more efficient implementation is possible when the scattering profile is all that is required, as in small angle scattering reconstruction (SAS) of macromolecules. We examine the relationship of the proposed algorithm to existing approximate methods for profile computations, and show that these methods may result in inaccurate profile computations, unless an error-bound derived in this article is used. Our theoretical and computational results show orders of magnitude improvement in computation complexity over existing methods, while maintaining prescribed accuracy.
Copyright © 2012 Wiley Periodicals, Inc.

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Year:  2012        PMID: 22707386      PMCID: PMC3425727          DOI: 10.1002/jcc.23025

Source DB:  PubMed          Journal:  J Comput Chem        ISSN: 0192-8651            Impact factor:   3.376


  22 in total

1.  An efficient ab initio calculation of powder diffraction intensity using Debye's equation.

Authors:  R F Grover; D R McKenzie
Journal:  Acta Crystallogr A       Date:  2001-10-26       Impact factor: 2.290

2.  Refinement of multidomain protein structures by combination of solution small-angle X-ray scattering and NMR data.

Authors:  Alexander Grishaev; Justin Wu; Jill Trewhella; Ad Bax
Journal:  J Am Chem Soc       Date:  2005-11-30       Impact factor: 15.419

3.  Small-angle X-ray scattering from RNA, proteins, and protein complexes.

Authors:  Jan Lipfert; Sebastian Doniach
Journal:  Annu Rev Biophys Biomol Struct       Date:  2007

4.  Structural characterization of flexible proteins using small-angle X-ray scattering.

Authors:  Pau Bernadó; Efstratios Mylonas; Maxim V Petoukhov; Martin Blackledge; Dmitri I Svergun
Journal:  J Am Chem Soc       Date:  2007-04-06       Impact factor: 15.419

5.  A rapid coarse residue-based computational method for x-ray solution scattering characterization of protein folds and multiple conformational states of large protein complexes.

Authors:  Sichun Yang; Sanghyun Park; Lee Makowski; Benoît Roux
Journal:  Biophys J       Date:  2009-06-03       Impact factor: 4.033

6.  Integration of small-angle X-ray scattering data into structural modeling of proteins and their assemblies.

Authors:  Friedrich Förster; Benjamin Webb; Kristin A Krukenberg; Hiro Tsuruta; David A Agard; Andrej Sali
Journal:  J Mol Biol       Date:  2008-07-31       Impact factor: 5.469

7.  A broadband fast multipole accelerated boundary element method for the three dimensional Helmholtz equation.

Authors:  Nail A Gumerov; Ramani Duraiswami
Journal:  J Acoust Soc Am       Date:  2009-01       Impact factor: 1.840

8.  SoftWAXS: a computational tool for modeling wide-angle X-ray solution scattering from biomolecules.

Authors:  Jaydeep Bardhan; Sanghyun Park; Lee Makowski
Journal:  J Appl Crystallogr       Date:  2009-09-08       Impact factor: 3.304

9.  Rapid calculation of the solution scattering profile from a macromolecule of known structure.

Authors:  E E Lattman
Journal:  Proteins       Date:  1989

10.  The structure and conformation of Lys63-linked tetraubiquitin.

Authors:  Ajit B Datta; Greg L Hura; Cynthia Wolberger
Journal:  J Mol Biol       Date:  2009-08-04       Impact factor: 5.469

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  9 in total

1.  Accurate SAXS profile computation and its assessment by contrast variation experiments.

Authors:  Dina Schneidman-Duhovny; Michal Hammel; John A Tainer; Andrej Sali
Journal:  Biophys J       Date:  2013-08-20       Impact factor: 4.033

2.  Interpretation of solution x-ray scattering by explicit-solvent molecular dynamics.

Authors:  Po-Chia Chen; Jochen S Hub
Journal:  Biophys J       Date:  2015-05-19       Impact factor: 4.033

3.  D+: software for high-resolution hierarchical modeling of solution X-ray scattering from complex structures.

Authors:  Avi Ginsburg; Tal Ben-Nun; Roi Asor; Asaf Shemesh; Lea Fink; Roee Tekoah; Yehonatan Levartovsky; Daniel Khaykelson; Raviv Dharan; Amos Fellig; Uri Raviv
Journal:  J Appl Crystallogr       Date:  2019-02-01       Impact factor: 3.304

4.  Validating solution ensembles from molecular dynamics simulation by wide-angle X-ray scattering data.

Authors:  Po-Chia Chen; Jochen S Hub
Journal:  Biophys J       Date:  2014-07-15       Impact factor: 4.033

5.  Hierarchical O(N) computation of small-angle scattering profiles and their associated derivatives.

Authors:  Konstantin Berlin; Nail A Gumerov; David Fushman; Ramani Duraiswami
Journal:  J Appl Crystallogr       Date:  2014-03-28       Impact factor: 3.304

6.  WAXSiS: a web server for the calculation of SAXS/WAXS curves based on explicit-solvent molecular dynamics.

Authors:  Christopher J Knight; Jochen S Hub
Journal:  Nucleic Acids Res       Date:  2015-04-08       Impact factor: 16.971

Review 7.  Using small angle solution scattering data in Xplor-NIH structure calculations.

Authors:  Charles D Schwieters; G Marius Clore
Journal:  Prog Nucl Magn Reson Spectrosc       Date:  2014-04-03       Impact factor: 9.795

8.  Recovering a representative conformational ensemble from underdetermined macromolecular structural data.

Authors:  Konstantin Berlin; Carlos A Castañeda; Dina Schneidman-Duhovny; Andrej Sali; Alfredo Nava-Tudela; David Fushman
Journal:  J Am Chem Soc       Date:  2013-11-06       Impact factor: 15.419

Review 9.  Reconstruction of SAXS Profiles from Protein Structures.

Authors:  Daniel K Putnam; Edward W Lowe; Jens Meiler
Journal:  Comput Struct Biotechnol J       Date:  2013-11-26       Impact factor: 7.271

  9 in total

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