A set of python and R scripts for robust determination of protein allosteric signaling pathways are available to download @
https://github.com/LynaLuo-Lab/network_analysis_scripts
Botello-Smith, W., Luo, Y., Robust determination of protein allosteric signaling pathways, J. Chem. Theory Comput., 2019, 15, 2116-2126.
Botello-Smith, W., Luo, Y., Investigating protein-protein allosteric network using current-flow scheme, J. Comput. Chem, 2019
A set of python scripts for conducting uncertainty analysis are available to download @
https://github.com/LynaLuo-Lab/MD-data-uncertainty-analysis.git
A mouse Piezo1 all-atom model based on PBD ID 6B3R. Missing loops that are shorter than 20 amino aids are added using the loop remodeling approach.
https://github.com/LynaLuo-Lab/Piezo1-all-atomA mouse Piezo1 all atom model based on PBD ID 6B3R.
Botello-Smith W, Zhang H, Ozkan AD, Jiang W, Pham CN, Lacroix J and Luo Y, A molecular Mechanism for the Chemical Activation of the Mechanosensitive Piezo1 Channel, Nat. Commun., DOI: 10.1038/s41467-019-12501-1.
Generating 2D free energy landscape of resveratrol distirbution inside lipid bilayer using ggplot
https://github.com/LynaLuo-Lab/Membrane-Resveratrol.git
Q. Fei, D. Kent, W. Botello-Smith, F. Nur, S. Nur, A. Alsamarah, P. Chatterjee, M. Lambros, Y. Luo, Molecular mechanism of resveratrol’s lipid membrane protection, Sci. Rep., 2018, 8, 1587.