DOI: 10.1146/annurev-biophys-062215-011113. Computational Methodologies for Real-Space Structural Refinement of Large Macromolecular Complexes

Computational Methodologies for Real-Space Structural Refinement of Large Macromolecular Complexes

10.1146/annurev-biophys-062215-011113

Crossref journal-article

Annual Reviews

Annual Review of Biophysics (22)

Abstract

The rise of the computer as a powerful tool for model building and refinement has revolutionized the field of structure determination for large biomolecular systems. Despite the wide availability of robust experimental methods capable of resolving structural details across a range of spatiotemporal resolutions, computational hybrid methods have the unique ability to integrate the diverse data from multimodal techniques such as X-ray crystallography and electron microscopy into consistent, fully atomistic structures. Here, commonly employed strategies for computational real-space structural refinement are reviewed, and their specific applications are illustrated for several large macromolecular complexes: ribosome, virus capsids, chemosensory array, and photosynthetic chromatophore. The increasingly important role of computational methods in large-scale structural refinement, along with current and future challenges, is discussed.

Bibliography

Goh, B. C., Hadden, J. A., Bernardi, R. C., Singharoy, A., McGreevy, R., Rudack, T., Cassidy, C. K., & Schulten, K. (2016). Computational Methodologies for Real-Space Structural Refinement of Large Macromolecular Complexes. Annual Review of Biophysics, 45(1), 253â278.

Authors 8

Boon Chong Goh (first)
Jodi A. Hadden (additional)
Rafael C. Bernardi (additional)
Abhishek Singharoy (additional)
Ryan McGreevy (additional)
Till Rudack (additional)
C. Keith Cassidy (additional)
Klaus Schulten (additional)

References 157 Referenced 68

Dates

Type	When
Created	9 years, 3 months ago (May 4, 2016, 8:34 p.m.)
Deposited	3 years, 10 months ago (Oct. 6, 2021, 2:58 p.m.)
Indexed	20 hours, 7 minutes ago (Aug. 21, 2025, 1:17 p.m.)
Issued	9 years, 1 month ago (July 5, 2016)
Published	9 years, 1 month ago (July 5, 2016)
Published Print	9 years, 1 month ago (July 5, 2016)

Funders 0

None

BibTeX

@article{Goh_2016, title={Computational Methodologies for Real-Space Structural Refinement of Large Macromolecular Complexes}, volume={45}, ISSN={1936-1238}, url={http://dx.doi.org/10.1146/annurev-biophys-062215-011113}, DOI={10.1146/annurev-biophys-062215-011113}, number={1}, journal={Annual Review of Biophysics}, publisher={Annual Reviews}, author={Goh, Boon Chong and Hadden, Jodi A. and Bernardi, Rafael C. and Singharoy, Abhishek and McGreevy, Ryan and Rudack, Till and Cassidy, C. Keith and Schulten, Klaus}, year={2016}, month=jul, pages={253–278} }

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  "abstract": "<jats:p> The rise of the computer as a powerful tool for model building and refinement has revolutionized the field of structure determination for large biomolecular systems. Despite the wide availability of robust experimental methods capable of resolving structural details across a range of spatiotemporal resolutions, computational hybrid methods have the unique ability to integrate the diverse data from multimodal techniques such as X-ray crystallography and electron microscopy into consistent, fully atomistic structures. Here, commonly employed strategies for computational real-space structural refinement are reviewed, and their specific applications are illustrated for several large macromolecular complexes: ribosome, virus capsids, chemosensory array, and photosynthetic chromatophore. The increasingly important role of computational methods in large-scale structural refinement, along with current and future challenges, is discussed. </jats:p>",
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