Applications of contact predictions to structural biology

IUCrJ
Felix SimkovicDaniel J Rigden

Abstract

Evolutionary pressure on residue interactions, intramolecular or intermolecular, that are important for protein structure or function can lead to covariance between the two positions. Recent methodological advances allow much more accurate contact predictions to be derived from this evolutionary covariance signal. The practical application of contact predictions has largely been confined to structural bioinformatics, yet, as this work seeks to demonstrate, the data can be of enormous value to the structural biologist working in X-ray crystallo-graphy, cryo-EM or NMR. Integrative structural bioinformatics packages such as Rosetta can already exploit contact predictions in a variety of ways. The contribution of contact predictions begins at construct design, where structural domains may need to be expressed separately and contact predictions can help to predict domain limits. Structure solution by molecular replacement (MR) benefits from contact predictions in diverse ways: in difficult cases, more accurate search models can be constructed using ab initio modelling when predictions are available, while intermolecular contact predictions can allow the construction of larger, oligomeric search models. Furthermore, MR using supersec...Continue Reading

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Citations

Dec 5, 2017·Acta Crystallographica. Section D, Structural Biology·Jens M H ThomasDaniel J Rigden
Aug 7, 2017·F1000Research·Saulo de Oliveira, Charlotte Deane
Oct 17, 2018·Nature Microbiology·Yassine CherrakEric Durand
Dec 4, 2019·Acta Crystallographica. Section D, Structural Biology·Adam J SimpkinDaniel J Rigden
Mar 16, 2019·BMC Bioinformatics·Joseph LuttrellZheng Wang
Dec 1, 2018·Bioinformatics·Seung Hwan HongJooyoung Lee
Mar 30, 2018·Frontiers in Cellular and Infection Microbiology·Christian StutzerChristine Maritz-Olivier
Jan 29, 2021·Bioinformatics·Filomeno Sánchez RodríguezDaniel J Rigden
Apr 15, 2020·The Journal of Physical Chemistry. B·Jiangyan Feng, Diwakar Shukla
Apr 27, 2021·Bioinformatics·Chloé QuignotJessica Andreani
May 23, 2021·Briefings in Bioinformatics·Luciano A Abriata, Matteo Dal Peraro
Aug 31, 2017·Journal of Chemical Information and Modeling·Pernille SønderbyGünther H J Peters
May 19, 2020·Journal of Chemical Information and Modeling·Doo Nam KimKarissa Y Sanbonmatsu

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Methods Mentioned

BETA
NMR
X-ray
SANS
electron paramagnetic resonance

Software Mentioned

MetaPSICOV
gamma
PatchDock
CS
– BORGES
Buccaneer
PconsC
ConKit
ARP
SwarmDock

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