Morphing and Docking Visualisation of Biomolecular Structures using Multi-Dimensional Scaling

Veevers, Ruth and Hayward, Steven (2018) Morphing and Docking Visualisation of Biomolecular Structures using Multi-Dimensional Scaling. Journal of Molecular Graphics and Modelling, 82. pp. 108-116. ISSN 1093-3263

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Abstract

Protein structures are often solved at atomic resolution in two states defining a functional movement but intervening conformations are usually unknown. Morphing methods generate intervening conformations between two known structures. When viewed as an animation using molecular graphics, a smooth, direct morph enables the eye to track changes in structure that might be otherwise missed. We present a morphing method that aims to linearly interpolate interatomic distances and which uses SMACOF (Scaling by MAjorisation of COmplicated Function) and multigrid techniques with a cut-off distance based weighting that optimizes the MolProbity score of intervening structures. The all-atom morphs are smooth, move directly between the two structures, and are shown, in general, to pass closer to a set of known intermediates than those generated using other methods. The techniques are also used for docking by putting the unbound structures in a “near-approach pose” and then morphing to the bound complex. The resulting GPU-accelerated tools are available on a webserver, Morphit_Pro, at http://morphit-pro.cmp.uea.ac.uk/ and more than 5000 domains movements available at the DynDom website can now be viewed as morphs http://morphit-pro.cmp.uea.ac.uk/dyndom/.

Item Type: Article
Faculty \ School: Faculty of Science > School of Computing Sciences
Depositing User: Pure Connector
Date Deposited: 27 Apr 2018 10:33
Last Modified: 26 May 2020 00:02
URI: https://ueaeprints.uea.ac.uk/id/eprint/66845
DOI: 10.1016/j.jmgm.2018.04.013

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