A Practical Guide to iSPOT Modeling: An Integrative Structural Biology Platform

doi:10.1007/978-981-10-6038-0_14

Title: A Practical Guide to iSPOT Modeling: An Integrative Structural Biology Platform

Book · Mon Apr 09 00:00:00 EDT 2018

DOI:https://doi.org/10.1007/978-981-10-6038-0_14· OSTI ID:1432844

Nanyang) ^[1]; Case Western) ^[1]

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Research Organization:: Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Organization:: National Institutes of Health (NIH)

OSTI ID:: 1432844

Country of Publication:: United States

Language:: ENGLISH

References (26)

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A Newfound Cancer-Activating Mutation Reshapes the Energy Landscape of Estrogen-Binding Domain Huang, Wei; Ravikumar, Krishnakumar M.; Yang, Sichun Journal of Chemical Theory and Computation, Vol. 10, Issue 8 https://doi.org/10.1021/ct500313e	journal	June 2014
Coarse-Grained Simulations of Protein-Protein Association: An Energy Landscape Perspective Ravikumar, Krishnakumar M.; Huang, Wei; Yang, Sichun Biophysical Journal, Vol. 103, Issue 4 https://doi.org/10.1016/j.bpj.2012.07.013	journal	August 2012
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Synchrotron-based small-angle X-ray scattering of proteins in solution Skou, Soren; Gillilan, Richard E.; Ando, Nozomi Nature Protocols, Vol. 9, Issue 7 https://doi.org/10.1038/nprot.2014.116	journal	June 2014
Theoretical modeling of multiprotein complexes by iSPOT: Integration of small-angle X-ray scattering, hydroxyl radical footprinting, and computational docking Huang, Wei; Ravikumar, Krishnakumar M.; Parisien, Marc Journal of Structural Biology, Vol. 196, Issue 3 https://doi.org/10.1016/j.jsb.2016.08.001	journal	December 2016
Proteins in dynamic equilibrium Bernadó, Pau; Blackledge, Martin Nature, Vol. 468, Issue 7327 https://doi.org/10.1038/4681046a	journal	December 2010
Fast-SAXS-pro : A unified approach to computing SAXS profiles of DNA, RNA, protein, and their complexes Ravikumar, Krishnakumar M.; Huang, Wei; Yang, Sichun The Journal of Chemical Physics, Vol. 138, Issue 2 https://doi.org/10.1063/1.4774148	journal	January 2013
Methods for SAXS-Based Structure Determination of Biomolecular Complexes Yang, Sichun Advanced Materials, Vol. 26, Issue 46 https://doi.org/10.1002/adma.201304475	journal	May 2014
RNA Structure Determination Using SAXS Data Yang, Sichun; Parisien, Marc; Major, François The Journal of Physical Chemistry B, Vol. 114, Issue 31 https://doi.org/10.1021/jp1057308	journal	August 2010
CAPRI: A Critical Assessment of PRedicted Interactions Janin, Jo�l; Henrick, Kim; Moult, John Proteins: Structure, Function, and Genetics, Vol. 52, Issue 1 https://doi.org/10.1002/prot.10381	journal	May 2003
Quantitative Protein Topography Analysis and High-Resolution Structure Prediction Using Hydroxyl Radical Labeling and Tandem-Ion Mass Spectrometry (MS) Kaur, Parminder; Kiselar, Janna; Yang, Sichun Molecular & Cellular Proteomics, Vol. 14, Issue 4 https://doi.org/10.1074/mcp.O114.044362	journal	February 2015
X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution Putnam, Christopher D.; Hammel, Michal; Hura, Greg L. Quarterly Reviews of Biophysics, Vol. 40, Issue 3 https://doi.org/10.1017/S0033583507004635	journal	August 2007
Modelling protein docking using shape complementarity, electrostatics and biochemical information 1 1Edited by J. Thornton Gabb, Henry A.; Jackson, Richard M.; Sternberg, Michael J. E. Journal of Molecular Biology, Vol. 272, Issue 1 https://doi.org/10.1006/jmbi.1997.1203	journal	September 1997
GRAMM-X public web server for protein-protein docking Tovchigrechko, A.; Vakser, I. A. Nucleic Acids Research, Vol. 34, Issue Web Server https://doi.org/10.1093/nar/gkl206	journal	July 2006
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Preparing monodisperse macromolecular samples for successful biological small-angle X-ray and neutron-scattering experiments Jeffries, Cy M.; Graewert, Melissa A.; Blanchet, Clément E. Nature Protocols, Vol. 11, Issue 11 https://doi.org/10.1038/nprot.2016.113	journal	October 2016
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Accurate optimization of amino acid form factors for computing small-angle X-ray scattering intensity of atomistic protein structures Tong, Dudu; Yang, Sichun; Lu, Lanyuan Journal of Applied Crystallography, Vol. 49, Issue 4 https://doi.org/10.1107/S1600576716007962	journal	June 2016

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