Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing.

doi:10.1016/S0006-3495(99)77443-6

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Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing.

Journal Article•DOI•

Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing.

Dmitri I. Svergun¹•Institutions (1)

Russian Academy of Sciences¹

01 Jun 1999-Biophysical Journal (Cell Press)-Vol. 76, Iss: 6, pp 2879-2886

TL;DR: Application of the method is illustrated by the restoration of a ribosome-like model structure and more realistically by the determination of the shape of several proteins from experimental x-ray scattering data.

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About: This article is published in Biophysical Journal.The article was published on 1999-06-01 and is currently open access. It has received 2105 citations till now. The article focuses on the topics: Biological small-angle scattering & Small-angle X-ray scattering.

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Journal Article•DOI•

Reduction and analysis of SANS and USANS data using IGOR Pro

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Steven R. Kline¹•Institutions (1)

National Institute of Standards and Technology¹

01 Dec 2006-Journal of Applied Crystallography

TL;DR: A graphical interface has been developed to visualize and quickly reduce raw SANS and USANS data into one- or two-dimensional formats for interpretation, allowing users to contribute code and models for distribution to all users.

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Abstract: A software package is presented for performing reduction and analysis of small-angle neutron scattering (SANS) and ultra-small-angle neutron scattering (USANS) data. A graphical interface has been developed to visualize and quickly reduce raw SANS and USANS data into one- or two-dimensional formats for interpretation. The resulting reduced data can then be analyzed using model-independent methods or non-linear fitting to one of a large and growing catalog of included structural models. The different instrumental smearing effects for slit-smeared USANS and pinhole-smeared SANS data are handled automatically during analysis. In addition, any number of SANS and USANS data sets can be analyzed simultaneously. The reduction operations and analysis models are written in a modular format for extensibility, allowing users to contribute code and models for distribution to all users. The software package is based on Igor Pro, providing freely distributable and modifiable code that runs on Macintosh and Windows operating systems.

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1,738 citations

Cites methods from "Restoring low resolution structure ..."

...This package does not duplicate any indirect Fourier transform techniques or ab initio methods, such as those developed by Moore (1980), Brunner-Popela & Glatter (1997), Svergun (1999) and Chacon et al. (1998)....
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Journal Article•DOI•

New developments in the ATSAS program package for small-angle scattering data analysis

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Maxim V. Petoukhov¹, Daniel Franke¹, Alexander V. Shkumatov¹, Giancarlo Tria¹, Alexey Kikhney¹, Michal J. Gajda¹, Christian Gorba¹, Haydyn D. T. Mertens¹, Petr V. Konarev¹, Dmitri I. Svergun¹ - Show less +6 more•Institutions (1)

European Bioinformatics Institute¹

01 Apr 2012-Journal of Applied Crystallography

TL;DR: The paper presents new developments and amendments to the ATSAS package (version 2.4) for processing and analysis of isotropic small-angle scattering data.

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Abstract: New developments in the program package ATSAS (version 2.4) for the processing and analysis of isotropic small-angle X-ray and neutron scattering data are described. They include (i) multiplatform data manipulation and display tools, (ii) programs for automated data processing and calculation of overall parameters, (iii) improved usage of high- and low-resolution models from other structural methods, (iv) new algorithms to build three-dimensional models from weakly interacting oligomeric systems and complexes, and (v) enhanced tools to analyse data from mixtures and flexible systems. The new ATSAS release includes installers for current major platforms (Windows, Linux and Mac OSX) and provides improved indexed user documentation. The web-related developments, including a user discussion forum and a widened online access to run ATSAS programs, are also presented.

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1,634 citations

Cites methods from "Restoring low resolution structure ..."

...The online access was recently opened also to the optimized shape determination algorithm DAMMIF (Franke & Svergun, 2009), the multiphase bead modelling program MONSA (Svergun, 1999; Svergun & Nierhaus, 2000) and the EOM method (Bernadó et al., 2007)....
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...45, 342–350 Maxim V. Petoukhov et al. New developments in ATSAS 345 from particle to solvent during DAMMIN refinement while the core beads remain fixed....
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...Originally (Petoukhov et al., 2007), the interfaces to the ab initio programs DAMMIN (Svergun, 1999) and GASBOR (Svergun et al., 2001) and atomic structure-based programs CRYSOL (Svergun et al., 1995) and SASREF (Petoukhov & Svergun, 2005) were provided....
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...If the ‘--damform’ option is selected, the resulting model can be used as an initial search volume in DAMMIN (Svergun, 1999), whereby the surface beads (within a user-specified cutoff) can change their phase J. Appl....
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Journal Article•DOI•

DAMMIF, a program for rapid ab-initio shape determination in small-angle scattering

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Daniel Franke, Dmitri I. Svergun

01 Apr 2009-Journal of Applied Crystallography

TL;DR: DAMMIF, an enhanced and significantly faster implementation of the ab-initio shape-determination program DAMMIN for small-angle scattering data, is presented.

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Abstract: DAMMIF, a revised implementation of the ab-initio shape-determination program DAMMIN for small-angle scattering data, is presented. The program was fully rewritten, and its algorithm was optimized for speed of execution and modified to avoid limitations due to the finite search volume. Symmetry and anisometry constraints can be imposed on the particle shape, similar to DAMMIN. In equivalent conditions, DAMMIF is 25–40 times faster than DAMMIN on a single CPU. The possibility to utilize multiple CPUs is added to DAMMIF. The application is available in binary form for major platforms.

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1,482 citations

Cites background or methods from "Restoring low resolution structure ..."

...Starting from a random assignment, a Monte Carlo search, for example a genetic algorithm in DALAI_GA or simulated annealing (SA) in DAMMIN (Svergun, 1999), is employed to find a model that fits the data....
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...Extensive tests on simulated and experimental data showed that the models provided by DAMMIF are comparable to those of DAMMIN and the quality of reconstruction is compatible with that presented by Svergun (1999) and Volkov & Svergun (2003)....
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...This paper describes a new implementation of DAMMIN (Svergun, 1999), one of the most popular shape determination programs publicly available....
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...The reader is referred to the original publication (Svergun, 1999) for further details....
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...Here we present DAMMIF, an advanced implementation of the popular ab-initio modelling program DAMMIN (Svergun, 1999)....
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Journal Article•DOI•

Determination of domain structure of proteins from X-ray solution scattering.

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Dmitri I. Svergun, Maxim V. Petoukhov¹, Maxim V. Petoukhov², Michel H. J. Koch•Institutions (2)

Moscow State University¹, Russian Academy of Sciences²

01 Jun 2001-Biophysical Journal

TL;DR: The new method substantially improves the resolution and reliability of models derived from scattering data and makes solution scattering a useful technique in large-scale structural characterization of proteins.

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1,363 citations

Cites background or methods from "Restoring low resolution structure ..."

...tween the DR models are substantially smaller than those observed for the low resolution shape determination using densely packed beads (Svergun, 1999)....
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...This is not surprising given that the DR models use fewer independent parameters to fit much larger portions of the scattering pattern than do the bead modeling programs (Chacon et al., 1998; Svergun, 1999; Walther et al., 1999)....
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...…been developed representing the shape either by an angular envelope function (Svergun and Stuhrmann, 1991; Svergun et al., 1996), or as an ensemble of densely packed beads (Chacon et al., 1998; Svergun, 1999; Walther et al., 1999), and employing nonlinear minimization to fit the scattering data....
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...For lysozyme, a low resolution shape obtained by DAMMIN (Svergun; 1999) is displayed in green (left column)....
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..., 1996), or as an ensemble of densely packed beads (Chacon et al., 1998; Svergun, 1999; Walther et al., 1999), and employing nonlinear minimization to fit the scattering data....
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Journal Article•DOI•

Automated matching of high‐ and low‐resolution structural models

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M. B. Kozin¹, M. B. Kozin², Dmitri I. Svergun¹, Dmitri I. Svergun²•Institutions (2)

European Bioinformatics Institute¹, Russian Academy of Sciences²

01 Feb 2001-Journal of Applied Crystallography

TL;DR: A normalized spatial discrepancy (NSD) is introduced as a proximity measure between three-dimensional objects so as to provide a quantitative estimate of similarity between the objects.

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Abstract: A method is presented for automated best-matching alignment of three-dimensional models represented by ensembles of points. A normalized spatial discrepancy (NSD) is introduced as a proximity measure between three-dimensional objects. Starting from an inertia-axes alignment, the algorithm minimizes the NSD; the final value of the NSD provides a quantitative estimate of similarity between the objects. The method is implemented in a computer program. Simulations have been performed to test its performance on model structures with specified numbers of points ranging from a few to a few thousand. The method can be used for comparative analysis of structural models obtained by different methods, e.g. of high-resolution crystallographic atomic structures and low-resolution models from solution scattering or electron microscopy.

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1,274 citations

Additional excerpts

...The two ®nal examples display superposition of crystallographic atomic models of proteins with low-resolution shapes restored ab initio from experimental solution-scattering data using the dummy-atoms method of Svergun (1999)....
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...Low-resolution models are represented, for example, as smooth surfaces de®ned by an angular envelope function (Svergun, 1994), as sets of densely packed dummy atoms (Chacon et al., 1998; Svergun, 1999) or as stacks of contoured layers (Frank et al., 1995)....
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References

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Journal Article•DOI•

Optimization by Simulated Annealing

[...]

Scott Kirkpatrick¹, C. D. Gelatt¹, Mario P. Vecchi²•Institutions (2)

IBM¹, Venezuelan Institute for Scientific Research²

13 May 1983-Science

TL;DR: There is a deep and useful connection between statistical mechanics and multivariate or combinatorial optimization (finding the minimum of a given function depending on many parameters), and a detailed analogy with annealing in solids provides a framework for optimization of very large and complex systems.

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Abstract: There is a deep and useful connection between statistical mechanics (the behavior of systems with many degrees of freedom in thermal equilibrium at a finite temperature) and multivariate or combinatorial optimization (finding the minimum of a given function depending on many parameters). A detailed analogy with annealing in solids provides a framework for optimization of the properties of very large and complex systems. This connection to statistical mechanics exposes new information and provides an unfamiliar perspective on traditional optimization problems and methods.

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41,772 citations

Journal Article•DOI•

Numerical recipes

[...]

William H. Press, Saul A. Teukolsky

01 Oct 1990-Computers in Physics

17,845 citations

"Restoring low resolution structure ..." refers methods in this paper

...The algorithm was implemented in its faster simulated quenching (Press et al., 1992; Ingber, 1993) version: 1....
[...]
...The algorithm was implemented in its faster simulated quenching (Press et al., 1992; Ingber, 1993) version: 1....
[...]

Journal Article•

The mathematical theory of communication

[...]

Claude E. Shannon, Warren Weaver

01 Jan 1949-IEEE Transactions on Instrumentation and Measurement

TL;DR: The Mathematical Theory of Communication (MTOC) as discussed by the authors was originally published as a paper on communication theory more than fifty years ago and has since gone through four hardcover and sixteen paperback printings.

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Abstract: Scientific knowledge grows at a phenomenal pace--but few books have had as lasting an impact or played as important a role in our modern world as The Mathematical Theory of Communication, published originally as a paper on communication theory more than fifty years ago. Republished in book form shortly thereafter, it has since gone through four hardcover and sixteen paperback printings. It is a revolutionary work, astounding in its foresight and contemporaneity. The University of Illinois Press is pleased and honored to issue this commemorative reprinting of a classic.

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15,525 citations

Journal Article•DOI•

The Mathematical Theory of Communication

[...]

Claude E. Shannon, Warren Weaver, Norbert Wiener

01 Sep 1950-Physics Today

TL;DR: The theory of communication is extended to include a number of new factors, in particular the effect of noise in the channel, and the savings possible due to the statistical structure of the original message anddue to the nature of the final destination of the information.

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Abstract: HE recent development of various methods of modulation such as PCM and PPM which exchange bandwidth for signal-to-noise ratio has intensified the interest in a general theory of communication. A basis for such a theory is contained in the important papers of Nyquist1 and Hartley2 on this subject. In the present paper we will extend the theory to include a number of new factors, in particular the effect of noise in the channel, and the savings possible due to the statistical structure of the original message and due to the nature of the final destination of the information. The fundamental problem of communication is that of reproducing at one point either exactly or approximately a message selected at another point. Frequently the messages have meaning; that is they refer to or are correlated according to some system with certain physical or conceptual entities. These semantic aspects of communication are irrelevant to the engineering problem. The significant aspect is that the actual message is one selected from a set of possible messages. The system must be designed to operate for each possible selection, not just the one which will actually be chosen since this is unknown at the time of design. If the number of messages in the set is finite then this number or any monotonic function of this number can be regarded as a measure of the information produced when one message is chosen from the set, all choices being equally likely. As was pointed out by Hartley the most natural choice is the logarithmic function. Although this definition must be generalized considerably when we consider the influence of the statistics of the message and when we have a continuous range of messages, we will in all cases use an essentially logarithmic measure. The logarithmic measure is more convenient for various reasons:

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10,281 citations

Book•

The Mathematical Theory of Communication

[...]

Claude E. Shannon

01 Jan 1948

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10,215 citations