pyHVis3D: visualising molecular simulation deduced H-bond networks in 3D: application to T-cell receptor interactions

Bioinformatics. 2018 Jun 1;34(11):1941-1943. doi: 10.1093/bioinformatics/btx842.

Abstract

Motivation: Hydrogen bonds (H-bonds) play an essential role for many molecular interactions but are also often transient, making visualising them in a flexible system challenging.

Results: We provide pyHVis3D which allows for an easy to interpret 3D visualisation of H-bonds resulting from molecular simulations. We demonstrate the power of pyHVis3D by using it to explain the changes in experimentally measured binding affinities for three T-cell receptor/peptide/MHC complexes and mutants of each of these complexes.

Availability and implementation: pyHVis3D can be downloaded for free from http://opig.stats.ox.ac.uk/resources.

Contact: science.bernhard.knapp@gmail.com.

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Computational Biology / methods*
  • Humans
  • Hydrogen Bonding
  • Molecular Dynamics Simulation*
  • Mutation
  • Protein Conformation
  • Receptors, Antigen, T-Cell / chemistry
  • Receptors, Antigen, T-Cell / genetics
  • Receptors, Antigen, T-Cell / metabolism*
  • Software*

Substances

  • Receptors, Antigen, T-Cell