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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.

No MeSH data available.


Related in: MedlinePlus

Schematic diagram of flexible fitting with Situs 2.5. The modeling of distance constraints for the MCN is shown in dark blue. Standard volumetric map formats are converted with the map2map utility and the data can be prepared for coarse graining by vector quantization using a variety of map visualization and analysis tools. Atomic coordinates in PDB format can be transformed to low-resolution maps, if necessary, and vice versa. During vector quantization of the high-resolution structure, distances can be learnt that are sent to the vector quantizer of the low-resolution structure to enable MCN-based fitting. After the vector quantization, the high-resolution structure is flexibly docked by the qplasty tool (Rusu et al. 2008). As an alternative to spatial interpolation with qplasty, a molecular dynamics refinement is also supported
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Fig5: Schematic diagram of flexible fitting with Situs 2.5. The modeling of distance constraints for the MCN is shown in dark blue. Standard volumetric map formats are converted with the map2map utility and the data can be prepared for coarse graining by vector quantization using a variety of map visualization and analysis tools. Atomic coordinates in PDB format can be transformed to low-resolution maps, if necessary, and vice versa. During vector quantization of the high-resolution structure, distances can be learnt that are sent to the vector quantizer of the low-resolution structure to enable MCN-based fitting. After the vector quantization, the high-resolution structure is flexibly docked by the qplasty tool (Rusu et al. 2008). As an alternative to spatial interpolation with qplasty, a molecular dynamics refinement is also supported

Mentions: Rigid-body docking, as described above, laid the groundwork for the development of a flexible docking technique that brings deviating features of multi-resolution structures into register. In such situations, the atomic structure is moved towards the target density by systematically reducing the rms deviation between coarse-grained control points in a refinement of the atomic structure. One of the open questions in flexible docking is how to maintain the stereochemical quality of a fitted structure, since any over-fitting to noisy experimental data would compromise the quality of the atomic model. In an earlier review article (Wriggers et al. 2004), we described the details of a significant improvement to our flexible fitting algorithm, the Motion Capture Network (MCN). The basic idea of the workflow, depicted in Fig. 5, is that lateral connections (distance constraints) are formed between control points that reflect the connectivity of the biological polypeptide chain. This approximation of the movement can be justified by the statistics of biomolecular domain motions documented in the Protein Data Bank (PDB). In the following, a (previously unpublished) modeling of the actomyosin complex illustrates MCN-based flexible fitting.Fig. 5


Using Situs for the integration of multi-resolution structures.

Wriggers W - Biophys Rev (2010)

Schematic diagram of flexible fitting with Situs 2.5. The modeling of distance constraints for the MCN is shown in dark blue. Standard volumetric map formats are converted with the map2map utility and the data can be prepared for coarse graining by vector quantization using a variety of map visualization and analysis tools. Atomic coordinates in PDB format can be transformed to low-resolution maps, if necessary, and vice versa. During vector quantization of the high-resolution structure, distances can be learnt that are sent to the vector quantizer of the low-resolution structure to enable MCN-based fitting. After the vector quantization, the high-resolution structure is flexibly docked by the qplasty tool (Rusu et al. 2008). As an alternative to spatial interpolation with qplasty, a molecular dynamics refinement is also supported
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2821521&req=5

Fig5: Schematic diagram of flexible fitting with Situs 2.5. The modeling of distance constraints for the MCN is shown in dark blue. Standard volumetric map formats are converted with the map2map utility and the data can be prepared for coarse graining by vector quantization using a variety of map visualization and analysis tools. Atomic coordinates in PDB format can be transformed to low-resolution maps, if necessary, and vice versa. During vector quantization of the high-resolution structure, distances can be learnt that are sent to the vector quantizer of the low-resolution structure to enable MCN-based fitting. After the vector quantization, the high-resolution structure is flexibly docked by the qplasty tool (Rusu et al. 2008). As an alternative to spatial interpolation with qplasty, a molecular dynamics refinement is also supported
Mentions: Rigid-body docking, as described above, laid the groundwork for the development of a flexible docking technique that brings deviating features of multi-resolution structures into register. In such situations, the atomic structure is moved towards the target density by systematically reducing the rms deviation between coarse-grained control points in a refinement of the atomic structure. One of the open questions in flexible docking is how to maintain the stereochemical quality of a fitted structure, since any over-fitting to noisy experimental data would compromise the quality of the atomic model. In an earlier review article (Wriggers et al. 2004), we described the details of a significant improvement to our flexible fitting algorithm, the Motion Capture Network (MCN). The basic idea of the workflow, depicted in Fig. 5, is that lateral connections (distance constraints) are formed between control points that reflect the connectivity of the biological polypeptide chain. This approximation of the movement can be justified by the statistics of biomolecular domain motions documented in the Protein Data Bank (PDB). In the following, a (previously unpublished) modeling of the actomyosin complex illustrates MCN-based flexible fitting.Fig. 5

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