Morphing and docking visualisation of biomolecular structures using multi-dimensional scaling

Ruth Veevers, Steven Hayward

Research output: Contribution to journalArticlepeer-review

5 Citations (Scopus)
22 Downloads (Pure)


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 and more than 5000 domains movements available at the DynDom website can now be viewed as morphs
Original languageEnglish
Pages (from-to)108-116
Number of pages9
JournalJournal of Molecular Graphics and Modelling
Early online date25 Apr 2018
Publication statusPublished - Jun 2018

Cite this