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

Author

Listed:
  • Daniel Russel
  • Keren Lasker
  • Ben Webb
  • Javier Velázquez-Muriel
  • Elina Tjioe
  • Dina Schneidman-Duhovny
  • Bret Peterson
  • Andrej Sali

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.

Suggested Citation

  • Daniel Russel & Keren Lasker & Ben Webb & Javier Velázquez-Muriel & Elina Tjioe & Dina Schneidman-Duhovny & Bret Peterson & Andrej Sali, 2012. "Putting the Pieces Together: Integrative Modeling Platform Software for Structure Determination of Macromolecular Assemblies," PLOS Biology, Public Library of Science, vol. 10(1), pages 1-5, January.
    • Handle: RePEc:plo:pbio00:1001244
    DOI: 10.1371/journal.pbio.1001244
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    References listed on IDEAS

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    1. Frank Alber & Svetlana Dokudovskaya & Liesbeth M. Veenhoff & Wenzhu Zhang & Julia Kipper & Damien Devos & Adisetyantari Suprapto & Orit Karni-Schmidt & Rosemary Williams & Brian T. Chait & Andrej Sali, 2007. "The molecular architecture of the nuclear pore complex," Nature, Nature, vol. 450(7170), pages 695-701, November.
    2. Nick Barnes, 2010. "Publish your computer code: it is good enough," Nature, Nature, vol. 467(7317), pages 753-753, October.
    3. Frank Alber & Svetlana Dokudovskaya & Liesbeth M. Veenhoff & Wenzhu Zhang & Julia Kipper & Damien Devos & Adisetyantari Suprapto & Orit Karni-Schmidt & Rosemary Williams & Brian T. Chait & Michael P. , 2007. "Determining the architectures of macromolecular assemblies," Nature, Nature, vol. 450(7170), pages 683-694, November.
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    Cited by:

    1. Avrin Ghanaeian & Sumita Majhi & Caitlyn L. McCafferty & Babak Nami & Corbin S. Black & Shun Kai Yang & Thibault Legal & Ophelia Papoulas & Martyna Janowska & Melissa Valente-Paterno & Edward M. Marco, 2023. "Integrated modeling of the Nexin-dynein regulatory complex reveals its regulatory mechanism," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    2. Simeon Carstens & Michael Nilges & Michael Habeck, 2016. "Inferential Structure Determination of Chromosomes from Single-Cell Hi-C Data," PLOS Computational Biology, Public Library of Science, vol. 12(12), pages 1-33, December.
    3. Patrick Bryant & Gabriele Pozzati & Wensi Zhu & Aditi Shenoy & Petras Kundrotas & Arne Elofsson, 2022. "Predicting the structure of large protein complexes using AlphaFold and Monte Carlo tree search," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    4. Eric A Yen & Aaron Tsay & Jerome Waldispuhl & Jackie Vogel, 2014. "Exploration of the Dynamic Properties of Protein Complexes Predicted from Spatially Constrained Protein-Protein Interaction Networks," PLOS Computational Biology, Public Library of Science, vol. 10(5), pages 1-12, May.
    5. Jonas Paulsen & Odin Gramstad & Philippe Collas, 2015. "Manifold Based Optimization for Single-Cell 3D Genome Reconstruction," PLOS Computational Biology, Public Library of Science, vol. 11(8), pages 1-19, August.
    6. Yana Valasatava & Anthony R Bradley & Alexander S Rose & Jose M Duarte & Andreas Prlić & Peter W Rose, 2017. "Towards an efficient compression of 3D coordinates of macromolecular structures," PLOS ONE, Public Library of Science, vol. 12(3), pages 1-15, March.

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