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Updated: Feb 15, 2026

Novel 3D/VR Interactive Environment for MD Simulations, Visualization and Analysis
Published on: December 18, 2014
pyHVis3D: visualising molecular simulation deduced H-bond networks in 3D: application to T-cell receptor interactions
Bernhard Knapp1,2, Marta Alcala2, Hao Zhang3
1Department of Statistics, University of Oxford, 24-29 St Giles', Oxford OX1 3LB, UK.
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.
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