CURP: CURrent calculations in Proteins

CURP permits to compute inter-residue flow of energy or heat and atomic stress tensors in a protein, given atomic coordinates and velocity trajectories obtained through molecular dynamics (MD). Energy flow data permit to picture an inter-residue Energy Exchange Network as a graph.

Within thermally fluctuating protein molecules under physiological conditions, tightly packed amino acid residues interact with each other through heat and energy exchanges. Non-uniform pattern of heat flow in proteins are illustrated and characterized with a theoretical model based on “local heat conductivity” between each residue pair. This model demonstrated characteristic features of “hidden dynamic allostery” in PDZ domain [1] and allosteric transition in the oxygen sensor domain of FixL [2].

Offical website and tutorial can be found at http://www.comp-biophys.com/yamato-lab/curp.html.

Installation

CURP requires Python2.7 with numpy to work. Python3 compatibility has yet to be realized. You can install python here, or anaconda there.

To install curp, run

pip install Curp

or your favorite python package manager, like conda or pipenv. You can get curp source code by running

git clone https://gitlab.com/yamato97/current-calculations-for-proteins.git

Then, go in the installed directory and use

pip install .

Development

Please read DEVELOP.rst before starting to develop CURP.

References