Input
The accepted files extentions are: .fasta, .pdb, .gz, .zip, .tgz and .tar.gz
Compressed files should include either .pdb or .fasta files (not both). Including other types of files/directoies/mixed file types within a compressed input file will prevent the analysis of all input data.
The input sequence is in fasta format, has a .fasta file extention and includes at least 40 amino acids
The input structure is in PDB format, has a .pdb file extention and includes at least 40 amino acids
The coordinates of at least the backbone atoms must be included within the input structure file (i.e.; Ca=C-alpha carbon, C=carbon, N=nitrogen, O=oxygen)
A valid PDB id from the Protein Data Bank

NOTE: whether using a sequence or a structureas an input, the approximate location of an ABRs should have 10 to 15 flanking amino acids on each side, otherwise the prediction may be inaccurate.

An example of a fasta input Paratome

Output
A HTML file with the sequences/chains on which ABRs were found with the ABRs highlighted, the ABRs and their location within the input sequence or structure. For sequences, the location of the ABRs is according to their sequential numbering along the sequence. For structures, the location of the ABRs is accoridng to their ATOM field numbering within the PDB file. ABRs residues that appear in the SEQRES field but not in the ATOM filed are marked with *

An example of a HTML output file Paratome

A text file that includes all sequences/structure chains that were analyzed. For sequences/structure chains for which ABRs were found, their location is indicated according to their sequential numbering along the sequence. For structures, the location of the ABRs is accoridng to their ATOM field numbering within the PDB file. Sequences/structure chains for which no ABRs were found, an explanation is included within the text file

An example of a text output file Paratome

Visualization
The HTML output file contains a link for each analyzed strucure which enables to visualize the input structure with the ABRs highlighted.

A JMOL vizualization of Anti-IL-15 antibody ABRs (PDB id 2XQB) Paratome