README.md

Overview

This repository contains data, code, and analysis for the simulations of molecular dynamics and affinity maturation presented in

Role of framework mutations and antibody flexibility in the evolution of broadly neutralizing antibodies

Victor Ovchinnikov^1,*, Joy E. Louveau^2,*, John P. Barton^3-6,*,†, Martin Karplus^1,7,#, and Arup K. Chakraborty^3-6,8,9,#

¹ Harvard University, Department of Chemistry and Chemical Biology (Cambridge, MA, United States)
² Massachusetts Institute of Technology, Harvard-MIT Division of Health Sciences and Technology (Cambridge, MA, United States)
³ Massachusetts Institute of Technology, Department of Chemical Engineering (Cambridge, MA, United States)
⁴ Massachusetts Institute of Technology, Department of Physics (Cambridge, MA, United States)
⁵ Massachusetts Institute of Technology, Institute for Medical Engineering and Science (Cambridge, MA, United States)
⁶ Ragon Institute of MGH, MIT and Harvard (Cambridge, MA, United States)
⁷ Université de Strasbourg, Laboratoire de Chimie Biophysique, ISIS (Strasbourg, France)
⁸ Massachusetts Institute of Technology, Department of Biological Engineering (Cambridge, MA, United States)
⁹ Massachusetts Institute of Technology, Department of Chemistry (Cambridge, MA, United States)
^* these authors contributed equally
^# correspondence to arupc@mit.edu or marci@tammy.harvard.edu
^† present address: University of California, Riverside, Department of Physics and Astronomy (Riverside, CA, United States)

See the iPython notebook analysis.ipynb for details on the affinity maturation simulations. Running this notebook requires the Python packages NumPy, pandas, and Matplotlib.

Matlab data and scripts for the molecular dynamics analysis are located in the molecular_dynamics/ folder. See the molecular_dynamics/README.md for details.