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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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Low-resolution molecular envelopes from SAXS studies of s-dEGFRΔV (left) and s-dEGFR (right). The envelopes (blue), created after kernel convolution with pdb2vol, readily accommodate the Situs-docked crystallographic models (see text). The graphic, kindly provided by Diego Alvarado and Mark Lemmon, emphasizes interior domain details; see also Fig. 2b in Alvarado et al. (2009)
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Fig4: Low-resolution molecular envelopes from SAXS studies of s-dEGFRΔV (left) and s-dEGFR (right). The envelopes (blue), created after kernel convolution with pdb2vol, readily accommodate the Situs-docked crystallographic models (see text). The graphic, kindly provided by Diego Alvarado and Mark Lemmon, emphasizes interior domain details; see also Fig. 2b in Alvarado et al. (2009)

Mentions: Our approach to rendering and interpretation of SAXS data has been adopted by other groups (Lipfert et al. 2007; Fagan et al. 2009). Here, we highlight a recent Nature article on structural studies of the single epidermal growth factor receptor family member (dEGFR) in Drosophila melanogaster. Alvarado et al. (2009) determined the 2.7 Å X-ray crystal structure of the unliganded dEGFR extracellular region, encompassing domains I to IV (s-dEGFRΔV). A structural overlay of an active, extended, receptor tyrosine kinase sErbB2 and s-dEGFRΔV showed them to be remarkably similar, with important functional implications. One key question was whether crystal packing causes s-dEGFRΔV to be extended. This hypothesis was ruled out by SAXS studies of s-dEGFRΔV and complete s-dEGFR (Fig. 4). The Situs-derived models, shown in Fig. 4, indicate that s-dEGFRΔV is extended in solution (the envelope readily encompasses the crystal structure), and that domain V (orange) simply projects from the end of domain IV (red) to extend the structure further.Fig. 4


Using Situs for the integration of multi-resolution structures.

Wriggers W - Biophys Rev (2010)

Low-resolution molecular envelopes from SAXS studies of s-dEGFRΔV (left) and s-dEGFR (right). The envelopes (blue), created after kernel convolution with pdb2vol, readily accommodate the Situs-docked crystallographic models (see text). The graphic, kindly provided by Diego Alvarado and Mark Lemmon, emphasizes interior domain details; see also Fig. 2b in Alvarado et al. (2009)
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2821521&req=5

Fig4: Low-resolution molecular envelopes from SAXS studies of s-dEGFRΔV (left) and s-dEGFR (right). The envelopes (blue), created after kernel convolution with pdb2vol, readily accommodate the Situs-docked crystallographic models (see text). The graphic, kindly provided by Diego Alvarado and Mark Lemmon, emphasizes interior domain details; see also Fig. 2b in Alvarado et al. (2009)
Mentions: Our approach to rendering and interpretation of SAXS data has been adopted by other groups (Lipfert et al. 2007; Fagan et al. 2009). Here, we highlight a recent Nature article on structural studies of the single epidermal growth factor receptor family member (dEGFR) in Drosophila melanogaster. Alvarado et al. (2009) determined the 2.7 Å X-ray crystal structure of the unliganded dEGFR extracellular region, encompassing domains I to IV (s-dEGFRΔV). A structural overlay of an active, extended, receptor tyrosine kinase sErbB2 and s-dEGFRΔV showed them to be remarkably similar, with important functional implications. One key question was whether crystal packing causes s-dEGFRΔV to be extended. This hypothesis was ruled out by SAXS studies of s-dEGFRΔV and complete s-dEGFR (Fig. 4). The Situs-derived models, shown in Fig. 4, indicate that s-dEGFRΔV is extended in solution (the envelope readily encompasses the crystal structure), and that domain V (orange) simply projects from the end of domain IV (red) to extend the structure further.Fig. 4

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