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. 2012 Jan;10(1):e1001244.
doi: 10.1371/journal.pbio.1001244. Epub 2012 Jan 17.

Putting the Pieces Together: Integrative Modeling Platform Software for Structure Determination of Macromolecular Assemblies

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Free PMC article

Putting the Pieces Together: Integrative Modeling Platform Software for Structure Determination of Macromolecular Assemblies

Daniel Russel et al. PLoS Biol. .
Free PMC article

Abstract

A set of software tools for building and distributing models of macromolecular assemblies uses an integrative structure modeling approach, which casts the building of models as a computational optimization problem where information is encoded into a scoring function used to evaluate candidate models.

Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Integrative structure modeling of the human RNA Polymerase II .
The first round of modeling was performed using only the 2nm EM density map of the assembly from EMDB and subunit comparative models from ModBase , on the basis of the crystallographic structures of the yeast RNAPII proteins. The data were found to be insufficient to uniquely resolve the structure. To overcome this challenge, protein interaction networks extracted from BioGrid were added. The addition of these data resulted in a single structure. The scripts are available as part of IMP.

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References

    1. Lasker K, Förster F, Bohn S, Walzthoeni T, Villa E, et al. Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach. Proc Natl Acad Sci U S A. - PMC - PubMed
    1. Simon B, Madl T, Mackereth C. D, Nilges M, Sattler M. An efficient protocol for NMR-spectroscopy-based structure determination of protein complexes in solution. Angewandte Chemie (International ed in English) 2010;49:1967–1970. - PubMed
    1. Baù D, Sanyal A, Lajoie B. R, Capriotti E, Byron M, et al. The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules. Nature Struct Biol. 2010;18:107–114. - PMC - PubMed
    1. Alber F, Dokudovskaya S, Veenhoff L. M, Zhang W, Kipper J, et al. The molecular architecture of the nuclear pore complex. Nature. 2007;450:695–701. - PubMed
    1. Alber F, Dokudovskaya S, Veenhoff L. M, Zhang W, Kipper J, et al. Determining the architectures of macromolecular assemblies. Nature. 2007;450:683–694. - PubMed

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