Supply Code for MDPI Molecules 2020 Draft

FlowChart

HBOS

• detection.py, calcualte the HBOS score for each residue of proteins in a folder

  Used to identify the potential anomalous residue in proteins

  Each row in the output csv file contains: protein id, chain id, residue index, residue name, d-sidechain, d-block, phi, psi, chi-1, HBOS of d-sidechain, HBOS of d-block, HBOS of phi, HBOS of psi, HBOS of chi-1

  python -W ignore HBOS/detection.py datasetFolder Analysis

• NCSAnomaly.py, calcualte the HBOS score for each residue of proteins in a folder

  Used to generate the reference

  Considering NCS byremoving the chains having 95% similarity or above with any other chains in the same protein

  Each row in the output csv file contains: protein id, chain id, residue index, residue name, d-sidechain, d-block, phi, psi, chi-1, HBOS of d-sidechain, HBOS of d-block, HBOS of phi, HBOS of psi, HBOS of chi-1

  python -W ignore HBOS/NCSAnomaly.py datasetFolder Analysis

• resolution.py, download cif files by resolution

  Download cif files by release time with RCSB search engine, save them into a download folder

  Use resolution.py to select the cif files downloaded within the specified resolution range by meta data in the corresponding xml files, default range is 0 to 4 angstrom

  python HBOS/resolution.py cifFolder targetFolder

• labelling.py, check the label in validation reports for each residue labelled by HBOS score with meta data in the corresponding xml files

  python HBOS/labelling.py detection.cvs, "detection.cvs" is the output of "detection.py"

• count.py and countResidue.py, count residue numbers in a dataset for different types of residues

  python -W ignore count.py cifFolder

  python countResidue.py count.csv, "count.csv" is the output of "count.py"

• DSSP.py and DSSPResidue.py, check the identify of secondary structure (Helix, Sheet, et. al.) for each residue labelled by HBOS score

  python DSSP.py detection.py, "detection.py" is the output of "detection.py"

  python DSSPResidue.py dssp.csv, "dssp.csv" is the output of "DSSP.py"

Analysis

• Contains the HBOS database

Plots

• Some MATLAB functions used for plotting the figures in the draft

Datasets

• protein list for each dataset

Setup

• The code was written in Python 2.7
• Need BioPython 1.69 or above installed
• Need DSSP module installed

  conda install -c salilab dssp

• Support cif files only