curp 3.0

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]. Also we applied it to a small protein to understand the features of local thermal transport of protein [3] [4] [5].

Offical website and tutorial can be found at https://curp.jp/.

(*) NOTE: CURP does not support atomic stress calculations on and after version 1.3.

pip install curp

git clone https://github.com/yamatolab/current-calculations-for-proteins.git
cd current-calculations-for-proteins
pip install .