LDLR-analysis

PCA of molecular dynamics simulations of the low-density lipoprotein receptor (LDLR) embedded in a membrane, used to assess how missense variants affect conformation and intramolecular interactions.

Contents

File	Description
PCA-LDLr-gmf.ipynb	PCA conformer plots (PC1 and PC2), clustered conformational states and trajectory motions

Method

Backbone atoms of each MD frame were extracted and aligned with trj_selection_dl.py and trj_align.py (Schrödinger Suite 2021v.2). Individual simulations were merged into a single trajectory and CMS file with trj_merge.py, and principal components were computed with trj_essential_dynamics.py. PCA conformer plots (PC1 × PC2, states and motions) are generated in the notebook with Matplotlib, Seaborn, NumPy and pandas.

Requirements

Python 3 with Jupyter and the libraries listed below. Trajectories and Schrödinger Suite outputs are not included in this repository.

pip install jupyter numpy pandas matplotlib seaborn

Author

Glaucio Monteiro Ferreira — Research Associate, Institute of Chemistry, University of São Paulo (IQ-USP) · LIBNM · Ferreira Lab · ORCID · FAPESP profile · gmf@usp.br