M. Scheurer, P. Rodenkirch, M. Siggel, R. C. Bernardi, K. Schulten,
E. Tajkhorshid, and T. Rudack.
PyContact: Rapid, customizable and visual analysis of non-covalent
interactions in MD simulations.
Biophysical Journal, 114:577-583, 2018.
(PMC: PMC5985026)
SCHE2018
Molecular dynamics (MD) simulations have become ubiquitous in all areas
of life sciences.
Size and model complexity of MD simulations are rapidly growing along
with increasing computing power and improved algorithms. This growth has
led to the production of a large
amount of simulation data that need to be filtered for relevant information
to address specific
biomedical and biochemical questions. One of the most relevant molecular
properties that can
be investigated by all-atom MD simulations is the time-dependent evolution
of the complex
non-covalent interaction networks governing such fundamental aspects as
molecular recognition,
binding strength, and mechanical and structural stability. Extracting,
evaluating and visualizing non-covalent interactions is a key task in the
daily work of structural biologists. We
have developed PyContact, an easy-to-use, highly flexible and intuitive
graphical user interface
(GUI)-based application, designed to provide a toolkit to investigate
biomolecular interactions
in MD trajectories. PyContact is designed to facilitate this task by enabling
identification of relevant non-covalent interactions in a comprehensible
manner. The
implementation of PyContact
as a stand-alone application enables rapid analysis and data visualization
without any additional programming requirement while preserving full in-
program
customization and extension
capabilities for advanced users. The statistical analysis representation is
interactively combined
with full mapping of the results on the molecular system through the
synergistic connection
between PyContact and VMD. We showcase the capabilities and scientific
significance of PyContact by analyzing and visualizing in great detail the
non-covalent interactions underlying the
ion permeation pathway of the human P2X3 receptor. As a
second application, we examine the
protein-protein interaction network of the mechanically ultrastable
cohesin-dockering complex.
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