Metadata-Version: 2.1
Name: Curp
Version: 2.0
Summary: Inter-residue Current calculation in Proteins from MD             trajectory
Home-page: https://github.com/yamatolab/current-calculations-for-proteins
Author: Yamato's Lab
Author-email: yamato@nagoya-u.jp
License: UNKNOWN
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: MacOS
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Fortran
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Physics
Classifier: Topic :: Scientific/Engineering :: Chemistry
Requires-Python: >3.5,<3.7
Description-Content-Type: text/x-rst
License-File: LICENSE.txt
Requires-Dist: numpy (<1.17,>=1.11.2)
Requires-Dist: nose (==1.3.7)
Requires-Dist: mpi4py (>=1.2)
Requires-Dist: pygraphviz (<1.6,>1.2)
Requires-Dist: netcdf4 (<1.7,>=1.4.2)
Provides-Extra: dev
Requires-Dist: benchmarker (<5,>=4.0) ; extra == 'dev'

======================================
CURP: CURrent calculations in Proteins
======================================

.. image:: https://pepy.tech/badge/curp
    :target: https://pepy.tech/project/curp

**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.
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/>`_.

Installation
============
CURP requires Python3.6 with numpy to work.
You can install python here_, or anaconda there_.

.. _here: https://www.python.org/downloads/release/python-3613/
.. _there: https://www.anaconda.com/download

Install CURP via pip
--------------------

::

     pip install curp

Get CURP from source code 
-------------------------

You can get the source code from this repository and build by running following command.

::

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

Development
===========
Please read DEVELOP.rst before starting to develop CURP.

References
==========

.. [1] Ishikura, T.; Iwata, Y.; Hatano, T.; Yamato, T. Energy exchange network of inter-residue interactions within a thermally fluctuating protein molecule: A computational study. *J. Comput. Chem.* **2015**, 36:1709-1718

.. [2] Ota, T.; Yamato, T. Energy Exchange Network Model Demonstrates Protein Allosteric Transition: An Application to an Oxygen Sensor Protein. *J. Phys. Chem. B* **2019**, 123:768-775

.. [3] Yamato, T.; Wang, T.; Sugiura, W.; Laprévote, O.; Katagiri, T. Computational study on the thermal conductivity of a protein. *J. Phys. Chem. B* **2022**, 126:3029-3036

.. [4] Wang, T.; Yamato, T.; Sugiura, W; Site-selective heat current analysis of α-helical protein with linear-homopolymer-like model. *J. Phys. Chem. B* **2023**, 158

.. [5] Wang, T.; Yamato, T.; & Sugiura, W. Thermal Energy Transport through Nonbonded Native Contacts in Protein. *J. Phys. Chem. B* **2024**


