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Issue 32, 2020
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KOBRA: a fluctuating elastic rod model for slender biological macromolecules

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Abstract

KOBRA (KirchOff Biological Rod Algorithm) is an algorithm and software package designed to perform dynamical simulations of elongated biomolecules such as those containing alpha-helices and coiled-coils. It represents these as coarsely-discretised Kirchoff rods, with linear elements that can stretch, bend and twist independently. These rods can have anisotropic and inhomogeneous parameters and bent or twisted equilibrium structures, allowing for a coarse-grained parameterisation of complex biological structures. Each element is non-inertial and subject to thermal fluctuations. The speed and simplicity of the algorithm allows KOBRA rods to easily access timescales from nanoseconds to seconds. To demonstrate this functionality, a KOBRA rod was parameterised using data from all-atom simulations of the Ndc80 protein complex, and compared against these simulations and negative-stain EM images. The distribution of bend angles and principal components were highly correlated between KOBRA, all-atom molecular dynamics, and experimental data. The properties of a hinge region, thought to be found at an unstructured loop, were studied. A C++ implementation of KOBRA is available under the GNU GPLv3 free software licence.

Graphical abstract: KOBRA: a fluctuating elastic rod model for slender biological macromolecules

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Supplementary files

Article information


Submitted
20 Mar 2020
Accepted
16 Jul 2020
First published
16 Jul 2020

This article is Open Access

Soft Matter, 2020,16, 7544-7555
Article type
Paper

KOBRA: a fluctuating elastic rod model for slender biological macromolecules

R. Welch, S. A. Harris, O. G. Harlen and D. J. Read, Soft Matter, 2020, 16, 7544
DOI: 10.1039/D0SM00491J

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