Validation and quality assessment of macromolecular structures using complex network analysis
Jure Pražnikar · Zenodo (CERN European Organization for Nuclear Research) · 2019
Protein model analysis For details see the paper: https://www.nature.com/articles/s41598-019-38658-9 The R script (Filename: ProtModAna.r) was used to analyze protein models. The script reads the PDB file, converts the 3D protein model into a graph and calculates mean node degree, Zscore, poor and long subgraphs. Smooth mean and standard deviation was calculated using data source (raw_data.csv), with a window length [0.8N, 1.2N], where N is the length of protein (Filename: SmoothData.csv). USAGE Test run Save "ProtModAna.r" and "SmoothData.csv" in to the same directory and run R script "ProtModAna.r". Custom analyze The user can change the path to the data file "SmoothData.csv". Note that this file is required to calculate the Zscore. To validate the protein model, change the line where the R script reads the PDB file (see lines 19 and 20 in "ProtModAna.r")