Requirements
============
 * Linux (CentOS 7.3 or similar)
 * gcc (>=4.8.5)
 * AmberTools (2014 or above; http://ambermd.org/)
 * R (>=3.0; https://www.r-project.org/)
 * The Bio3D R packages
    * Install the bio3d R package from CRAN (>=2.3-4) (http://thegrantlab.org/bio3d/): Within R, type `install.packages("bio3d")`
    * For path analysis, you may also need to install the latest bio3d.core and bio3d.cna packages. Check https://bitbucket.org/Grantlab/bio3d/ for instructions.
 * The igraph R package (>=1.1.1; http://igraph.org/r/): `install.packages("igraph")`
 * VMD [Optional] (>=1.9.3; http://www.ks.uiuc.edu/Research/vmd/)


Quick Start
===========
## Calculate contact statistics from MD simulations
 * cd contact
 * make 
 * (Edit "mdlist" file to match your case; See contact/readme for details)
 * ./creat_mean_contact.sh mdlist 4   
 * (NOTE: "4" indicates the number of cores to use and can be adjusted)
 * cd ..

## Residue wise difference contact network
 * cd bar
 * (Edit "run_bar.r" file to match your case)
 * Rscript run_bar.r
 * (To visualize results, open files with VMD: vmd -e bar.vmd)
 * cd ..

## Community analysis
 * cd community
 * (Edit "run_community_analysis.r" to match your case)
 * R 
 * (In the R session, type "source('run_community_analysis.r')"
 * (Adjust the plot in the poped-up window and save it as a pdf/eps file; Optionally, try commented out lines in the bottom of "run_community_analysis.r" for alternative ways to plot and for modularity evaluations)
 * (To visualize results, open files with VMD in a linux shell (color the protein by chain IDs): vmd network.pdb. NOTE: you may need to append the content in the community/append.vmdrc file to ~/.vmdrc; otherwise, colors in the VMD graphic may not match those in the R plot window)
 * cd ..

## Suboptimal path analysis
 * cd path
 * check out the "readme" file for instructions

## Citation
Yao XQ and Hamelberg D. Residue-residue contact changes during functional processes define allosteric communication pathways. J Chem Theory Comput (2022), 18:1173–1187. https://doi.org/10.1021/acs.jctc.1c00669
Yao XQ, Momin M, and Hamelberg D. Elucidating allosteric communications in proteins with difference contact network analysis. J Chem Inf Model (2018) 58:1325-1330. https://doi.org/10.1021/acs.jcim.8b00250