3DIANA: 3D Domain Interaction Analysis: A Toolbox for Quaternary Structure Modeling

Biophysical Journal
Joan SeguraJosé María Carazo

Abstract

Electron microscopy (EM) is experiencing a revolution with the advent of a new generation of Direct Electron Detectors, enabling a broad range of large and flexible structures to be resolved well below 1 nm resolution. Although EM techniques are evolving to the point of directly obtaining structural data at near-atomic resolution, for many molecules the attainable resolution might not be enough to propose high-resolution structural models. However, accessing information on atomic coordinates is a necessary step toward a deeper understanding of the molecular mechanisms that allow proteins to perform specific tasks. For that reason, methods for the integration of EM three-dimensional maps with x-ray and NMR structural data are being developed, a modeling task that is normally referred to as fitting, resulting in the so called hybrid models. In this work, we present a novel application-3DIANA-specially targeted to those cases in which the EM map resolution is medium or low and additional experimental structural information is scarce or even lacking. In this way, 3DIANA statistically evaluates proposed/potential contacts between protein domains, presents a complete catalog of both structurally resolved and predicted interacting reg...Continue Reading

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Citations

May 18, 2017·IUCrJ·Felix SimkovicDaniel J Rigden
Jul 19, 2018·Bioinformatics·Ruben Sanchez-GarciaJoan Segura
Oct 4, 2017·Protein Science : a Publication of the Protein Society·Pablo Conesa MingoJose María Carazo
Jul 3, 2021·International Journal of Molecular Sciences·Kuan-Hsi Chen, Yuh-Jyh Hu

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Methods Mentioned

BETA
NMR

Software Mentioned

DIMERO
Rosetta
Chimera viewer
HADDOCK
3DIANA
Chimera 3D viewer
PatchDock
DIANA
Jsmol
HMMER

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