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Integrative computational modeling of protein interactions

Authors: João P. G. L. M. Rodrigues; Alexandre M. J. J. Bonvin;

Integrative computational modeling of protein interactions

Abstract

Protein interactions define the homeostatic state of the cell. Our ability to understand these interactions and their role in both health and disease is tied to our knowledge of the 3D atomic structure of the interacting partners and their complexes. Despite advances in experimental method of structure determination, the majority of known protein interactions are still missing an atomic structure. High‐resolution methods such as X‐ray crystallography andNMRspectroscopy struggle with the high‐throughput demand, while low‐resolution techniques such as cryo‐electron microscopy or small‐angle X‐ray scattering provide data that are too coarse. Computational structure prediction of protein complexes, or docking, was first developed to complement experimental research and has since blossomed into an independent and lively field of research. Its most successful products are hybrid approaches that combine powerful algorithms with experimental data from various sources to generate high‐resolution models of protein complexes. This minireview introduces the concept of docking and docking with the help of experimental data, compares and contrasts the available integrative docking methods, and provides a guide for the experimental researcher for what types of data and which particular software can be used to model a protein complex.

Country
Netherlands
Related Organizations
Keywords

sampling, Magnetic Resonance Spectroscopy, Experimental data, restraints, 3D structure, Crystallography, X-Ray, Biochemistry, protein interactions, Computational biology, Docking (dog), interface prediction, Taverne, integrative modeling, Animals, Humans, Macromolecular docking, Biology, Molecular Biology, Protein–ligand docking, complexes, data-driven docking, Data type, scoring, Computational Biology, Proteins, Cell Biology, protein docking, Protein–protein interaction, Protein Binding

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    selected citations
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    This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    93
    popularity
    This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
    Top 1%
    influence
    This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    Top 10%
    impulse
    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
    Top 1%
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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
93
Top 1%
Top 10%
Top 1%
Green
bronze
Related to Research communities
EGI : advanced computing for research