README.md

X-EISD: Extended Experimental Inferential Structure Determination

X-EISD is a Bayeian approach to perform Experimental Inferential Structure Determination of ensembles for intrinsically disordered proteins.

Program version: 0.2.0 - Latest update: April 03, 2020

Installation:

You can install eisd from the source:

git clone https://github.com/THGLab/X-EISD.git
cd X-EISD
pip install -e .

Git LFS data quota limit

If you are not able to download the data using git lfs, please try to download it directly from the following link: https://datadryad.org/stash/share/yrRQFe-bjpDqupDFtT_pxYJjrbT6cdhhUGNTVl-JLSA

Please unzip and copy the contents to the data directory in this repository. The size of the compressed data is 1.14 GB.

Dependencies:

The dependencies for X-EISD are only numpy and pandas libraries. A proper installation of the package will also install the requirements.

Citation:

Please cite the use of X-EISD as:

(1) James Lincoff, Mojtaba Haghighatlari, Mickael Krzeminski, Joao Teixeira, Gregory Neal-Gomes, Claudu Gardinaru, Julie Forman-Kay, Teresa Head-Gordon, https://www.nature.com/articles/s42004-020-0323-0
(2) David H. Brookes, and Teresa Head-Gordon, Experimental Inferential Structure Determination of Ensembles for Intrinsically Disordered Proteins, JACS 138, 2016, 4530-4538 DOI: 10.1021/jacs.6b00351

Getting Started

You can either follow along the sample_script.py in the repository or use the commnd line interface to run eisd:

python sample_script.py     # first modify sample_script based upon your request 

or

eisdshell -d/--datapath, -m/--mode, -s/--structure, -e/--epochs, -o/--output