10.5281/zenodo.820724
https://zenodo.org/records/820724
oai:zenodo.org:820724
Shi, Yi
Yi
Shi
Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York 10065
Fernandez-Martinez, Javier
Javier
Fernandez-Martinez
Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York 10065
Tjioe, Elina
Elina
Tjioe
Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall, 1700 4th Street, Suite 503B, University of California, San Francisco, San Francisco, California 94158
Pellarin, Riccardo
Riccardo
Pellarin
Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall, 1700 4th Street, Suite 503B, University of California, San Francisco, San Francisco, California 94158
Kim, Seung Joong
Seung Joong
Kim
Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall, 1700 4th Street, Suite 503B, University of California, San Francisco, San Francisco, California 94158
Williams, Rosemary
Rosemary
Williams
Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York 10065
Schneidman-Duhovny, Dina
Dina
Schneidman-Duhovny
Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall, 1700 4th Street, Suite 503B, University of California, San Francisco, San Francisco, California 94158
Rout, Michael
Michael
Rout
Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York 10065
Sali, Andrej
Andrej
Sali
Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall, 1700 4th Street, Suite 503B, University of California, San Francisco, San Francisco, California 94158
Chait, Brian
Brian
Chait
Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York 10065
Modeling of the Nup84 subcomplex of the Nuclear Pore Complex
Zenodo
2014
Integrative Modeling Platform (IMP)
Chemical crosslinks
Electron microscopy class average
MODELLER
PMI
Webb, Benjamin
Benjamin
Webb
University of California, San Francisco, United States.
2014-08-26
https://github.com/integrativemodeling/nup84/tree/v1.0
10.1074/mcp.M114.041673
10.5281/zenodo.580803
https://salilab.org/nup84
10.5281/zenodo.596089
https://zenodo.org/communities/integrativemodeling
https://zenodo.org/communities/salilab
GNU Lesser General Public License v2.1 only
These scripts demonstrate the use of IMP, MODELLER, and PMI in the modeling of the Nup84 complex using 286 DSS/EDC chemical cross-links and an electron microscopy (EM) 2D class average.
First, MODELLER is used to generate initial structures for the individual components in the Nup84 complex. Then, IMP is used to model these components using DSS/EDC crosslinks and the electron microscopy 2D class average for the entire Nup84 complex.
For more information about how to reproduce this modeling, see the Sali lab website or the README file.