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Veevers, Ruth and Hayward, Steven 
ORCID: https://orcid.org/0000-0001-6959-2604
(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 |
| UEA Research Groups: | Faculty of Science > Research Groups > Computational Biology |
| Depositing User: | Pure Connector |
| Date Deposited: | 27 Apr 2018 10:33 |
| Last Modified: | 20 Apr 2023 02:32 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/66845 |
| DOI: | 10.1016/j.jmgm.2018.04.013 |
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