PDB-Scrapper

Web Crawler to Extract data from PDB(Protein Data Bank) Files.

Software Requirements(in Fedora(i.e Linux) OS):

• Perl

• Modules Required(Can be installed using CPAN:
  1. DBI (for Connecting to Database)]
  2. LWP::Simple (for Web Crawling)
  3. IO::String (for Web Crawling)

• MySQL Server

Features of the crawler

• This script is capable of extracting the following information:

1. Experiment Type(Eg.X-Ray Diffraction,NMR)
2. Protein Type(Eg.Lectin)
3. Resolution of the structure
4. R-factor

• For each Individual Chain in a structure,the code:

1. Determines the type of the chain(Protein/DNA/RNA)
2. Extracts the Primary Sequence(from the FASTA file)

• The code discards the extract data on the following conditions:

1. The Chain contains any unknown residue
2. There is no protein chains in the structure(only DNA or/and RNA)