Conformational Entropy as a Potential Liability of Computationally Designed Antibodies

This repository contains the full analysis code to reproduce our results on the conformational landscape of designed single-domain antibodies, published in Biomolecules.

Reproducibility information

Simulations were run using GROMACS 2019.3 and PLUMED 2.6 (git commit 8859093) with 32 replicas. Analysis was performed in a Jupyter notebook using python 3.7.6, numpy 1.18.1 and mdtraj 1.9.3.

Dataset

The full dataset including trajectories can be found on Zenodo. It includes the following data:

• simulations/: Gromacs tpr runtime files and PLUMED input
• trajectories/: xtc trajectories, deposited Gaussian hills, PLUMED post-processing script and computed total bias (to calculate the per-frame weight)
• analysis/: The analysis notebook ana.ipynb, template folder structures for the clustering procedure, and structures sampled from the trajectories and clusters