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

@article{Hsieh2017APG,
  title={A Practical Guide to iSPOT Modeling: An Integrative Structural Biology Platform.},
  author={An Hsieh and Lanyuan Lu and Mark R. Chance and Sichun Yang},
  journal={Advances in experimental medicine and biology},
  year={2017},
  volume={1009},
  pages={
          229-238
        }
}
Integrative structure modeling is an emerging method for structural determination of protein-protein complexes that are challenging for conventional structural techniques. Here, we provide a practical protocol for implementing our integrated iSPOT platform by integrating three different biophysical techniques: small-angle X-ray scattering (SAXS), hydroxyl radical footprinting, and computational docking simulations. Specifically, individual techniques are described from experimental and/or… 
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References

SHOWING 1-10 OF 28 REFERENCES
HADDOCK: a protein-protein docking approach based on biochemical or biophysical information.
TLDR
An approach called HADDOCK (High Ambiguity Driven protein-protein Docking) that makes use of biochemical and/or biophysical interaction data such as chemical shift perturbation data resulting from NMR titration experiments or mutagenesis data to drive the docking process.
Methods for SAXS‐Based Structure Determination of Biomolecular Complexes
TLDR
Current and recent SAXS-driven developments are described, with an emphasis on computational modeling, and accurate methods to computing one theoretical scattering profile from a given structure model are discussed, with a key focus on structure factor coarse-graining and hydration contribution.
ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers
TLDR
This paper presents a user-friendly protein docking server, based on the rigid-body docking programs ZDOCK and M-ZDOCK, to predict structures of protein-protein complexes and symmetric multimers, and provides options for users to guide the scoring and the selection of output models.
Quantitative Protein Topography Analysis and High-Resolution Structure Prediction Using Hydroxyl Radical Labeling and Tandem-Ion Mass Spectrometry (MS)*
TLDR
Tandem ion based hydroxyl radical footprinting-MS provides quantitative high-resolution protein topology information in solution that can fill existing gaps in structure determination for large proteins and macromolecular complexes.
RNA structure determination using SAXS data.
TLDR
The method developed here makes use of a coarse-grained representation of RNA that offers a powerful strategy for recognizing native RNA conformations as well as multimeric assemblies and alternative secondary structures, thus enabling high-throughput RNA structure determination using SAXS data.
ClusPro: a fully automated algorithm for protein-protein docking
TLDR
ClusPro (http://nrc.bu.edu/cluster) represents the first fully automated, web-based program for the computational docking of protein structures and produces a short list of putative complexes ranked according to their clustering properties, which is automatically sent back to the user via email.
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