Welch, RJ orcid.org/0000-0002-0135-0112, Harris, SA, Harlen, O orcid.org/0000-0002-4593-3547 et al. (1 more author) (2020) KOBRA: A Fluctuating Elastic Rod Model for Slender Biological Macromolecules. Soft Matter. ISSN 1744-683X
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. The rods can have anisotropic and inhomogeneous parameters and arbitrary 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 was compared against these simulations and negative-stain EM images. The distribution of bend angles 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 license.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Dates: |
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Institution: | The University of Leeds |
Academic Units: | The University of Leeds > Faculty of Engineering & Physical Sciences (Leeds) > School of Mathematics (Leeds) > Applied Mathematics (Leeds) The University of Leeds > Faculty of Engineering & Physical Sciences (Leeds) > School of Physics and Astronomy (Leeds) > Theoretical Physics (Leeds) |
Funding Information: | Funder Grant number EPSRC (Engineering and Physical Sciences Research Council) EP/S030697/1 |
Depositing User: | Symplectic Publications |
Date Deposited: | 23 Jul 2020 12:21 |
Last Modified: | 04 Aug 2020 10:42 |
Status: | Published online |
Publisher: | Royal Society of Chemistry |
Identification Number: | 10.1039/D0SM00491J |
Related URLs: | |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:163324 |