Using Situs for the integration of multi-resolution structures

被引：185

作者：

Wriggers W. ^{[1
,2
]}

机构：

[1] Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, NY, 10065

[2] D.E. Shaw Research, New York, NY, 10036

来源：

Biophysical Reviews | 2010年 / 2卷 / 1期

基金：

美国国家卫生研究院;

关键词：

3D data sets; Modeling; Multi-platform; Structural models;

D O I：

10.1007/s12551-009-0026-3

中图分类号：

学科分类号：

摘要：

Situs is a modular and widely used software package for the integration of biophysical data across the spatial resolution scales. It has been developed over the last decade with a focus on bridging the resolution gap between atomic structures, coarse-grained models, and volumetric data from low-resolution biophysical origins, such as electron microscopy, tomography, or small-angle scattering. Structural models can be created and refined with various flexible and rigid body docking strategies. The software consists of multiple, stand-alone programs for the format conversion, analysis, visualization, manipulation, and assembly of 3D data sets. The programs have been ported to numerous platforms in both serial and shared memory parallel architectures and can be combined in various ways for specific modeling applications. The modular design facilitates the updating of individual programs and the development of novel application workflows. This review provides an overview of the Situs package as it exists today with an emphasis on functionality and workflows supported by version 2. 5. © 2009 The Author(s).

引用

页码：21 / 27

页数：6

共 24 条

[1]

Alamo L., Wriggers W., Pinto A., Bartoli F., Salazar L., Zhao F.-Q., Craig R., Padron R., Three-dimensional reconstruction of tarantula myosin filaments suggests how phosphorylation may regulate myosin activity, J Mol Biol, 384, pp. 780-797, (2008)

[2]

Alvarado D., Klein D.E., Lemmon M.A., ErbB2 resembles an autoinhibited invertebrate epidermal growth factor receptor, Nature, 461, pp. 287-291, (2009)

[3]

Baker T.S., Johnson J.E., Low resolution meets high: towards a resolution continuum from cells to atoms, Curr Opin Struct Biol, 6, pp. 585-594, (1996)

[4]

Chacon P., Wriggers W., Multi-resolution contour-based fitting of macromolecular structures, J Mol Biol, 317, pp. 375-384, (2002)

[5]

Chacon P., Diaz J.F., Moran F., Andreu J.M., Reconstruction of protein form with X-ray solution scattering and a genetic algorithm, J Mol Biol, 299, pp. 1289-1302, (2000)

[6]

Coloma R., Valpuesta J.M., Arranz R., Carrascosa J.L., Ortin J., Martin-Benito J., The structure of a biologically active influenza virus ribonucleoprotein complex, PLoS Pathog, 5, (2009)

[7]

Coureux P.D., Wells A.L., Menetrey J., Yengo C.M., Morris C.A., Sweeney H.L., Houdusse A., A structural state of the myosin V motor without bound nucleotide, Nature, 425, pp. 419-423, (2003)

[8]

Fagan R.P., Albesa-Jove D., Qazi O., Svergun D.I., Brown K.A., Fairweather N.F., Structural insights into the molecular organization of the S-layer from Clostridium difficile, Mol Microbiol, 71, pp. 1308-1322, (2009)

[9]

Gerstein M., Krebs W., A database of macromolecular motions, Nucl Acids Res, 26, pp. 4280-4290, (1998)

[10]

Holmes K.C., Angert I., Kull F.J., Jahn W., Schroer R.R., Electron cryo- microscopy shows how strong binding of myosin to actin releases nucleotide, Nature, 425, pp. 423-427, (2003)

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