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Using Situs for the integration of multi-resolution structures.

Wriggers W - Biophys Rev (2010)

Bottom Line: 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.ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s12551-009-0026-3) contains supplementary material, which is available to authorized users.

View Article: PubMed Central - PubMed

ABSTRACT
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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s12551-009-0026-3) contains supplementary material, which is available to authorized users.

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Flexible fitting of myosin 2 subfragment 1. a MCN (see text) and Voronoi tessellation of the atomic structure. b MCN fitted to the segmented EM density. c Before flexing. d Displacements sampled at the control points. e After flexing
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Fig6: Flexible fitting of myosin 2 subfragment 1. a MCN (see text) and Voronoi tessellation of the atomic structure. b MCN fitted to the segmented EM density. c Before flexing. d Displacements sampled at the control points. e After flexing

Mentions: We first attempted rigid-body fitting of the atomic model, taken from the supplementary structure “motor domain.pdb” (Holmes et al. 2003), into the 3D map with colores, as described above. Rigid-body docking was not satisfactory with respect to the position of the upper 50K domain and the lever arm, even when performed independently for each structural subunit. Therefore, we subjected the predicted atomic model to flexible docking (Fig. 6) to characterize the observed changes. The flexible docking procedure was based on a connected MCN of identified features within the atomic model (Wriggers et al. 2004). The atomic model was allowed to move according to displacements tracked by 10 control points defined by the network, to find the best match to the cryo-EM map. The number of control points was judged to be sufficient for capturing the shape details of the single S1 map that occupies a volume of 185,000 Å3 at the isocontour level shown (Fig. 6). The number of independent pieces of information contained in the 14 Å resolution map is then 185,000/143 ≈ 67. This number comprises an upper bound for the number of recognizable features in this particular volume. The conservative choice of 10 points (corresponding to a spatial resolution of 26 Å in the reduced network) was significantly below this upper bound to avoid an over-fitting of the data (Wriggers and Chacón 2001b). This level of detail, however, was quite sufficient for the flexing.Fig. 6


Using Situs for the integration of multi-resolution structures.

Wriggers W - Biophys Rev (2010)

Flexible fitting of myosin 2 subfragment 1. a MCN (see text) and Voronoi tessellation of the atomic structure. b MCN fitted to the segmented EM density. c Before flexing. d Displacements sampled at the control points. e After flexing
© Copyright Policy
Related In: Results  -  Collection

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Fig6: Flexible fitting of myosin 2 subfragment 1. a MCN (see text) and Voronoi tessellation of the atomic structure. b MCN fitted to the segmented EM density. c Before flexing. d Displacements sampled at the control points. e After flexing
Mentions: We first attempted rigid-body fitting of the atomic model, taken from the supplementary structure “motor domain.pdb” (Holmes et al. 2003), into the 3D map with colores, as described above. Rigid-body docking was not satisfactory with respect to the position of the upper 50K domain and the lever arm, even when performed independently for each structural subunit. Therefore, we subjected the predicted atomic model to flexible docking (Fig. 6) to characterize the observed changes. The flexible docking procedure was based on a connected MCN of identified features within the atomic model (Wriggers et al. 2004). The atomic model was allowed to move according to displacements tracked by 10 control points defined by the network, to find the best match to the cryo-EM map. The number of control points was judged to be sufficient for capturing the shape details of the single S1 map that occupies a volume of 185,000 Å3 at the isocontour level shown (Fig. 6). The number of independent pieces of information contained in the 14 Å resolution map is then 185,000/143 ≈ 67. This number comprises an upper bound for the number of recognizable features in this particular volume. The conservative choice of 10 points (corresponding to a spatial resolution of 26 Å in the reduced network) was significantly below this upper bound to avoid an over-fitting of the data (Wriggers and Chacón 2001b). This level of detail, however, was quite sufficient for the flexing.Fig. 6

Bottom Line: 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.ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s12551-009-0026-3) contains supplementary material, which is available to authorized users.

View Article: PubMed Central - PubMed

ABSTRACT
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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s12551-009-0026-3) contains supplementary material, which is available to authorized users.

No MeSH data available.


Related in: MedlinePlus