Table 1 Brief descriptions of databases and tools integrated in the PeptideMine server

1.

STRING (version 7) [4]

Database of known and predicted protein-protein interaction.

Protein-Protein Interaction data and sequence of interacting partners are sourced from STRING database

2.

Gene Ontology Annotation (for 6 genomes) and Ontology file (.obo) for Biological Process, Molecular Function and Cellular Compartment [33, 38]

GOA project provides high-quality GO annotations to proteins reported in Uniprot

GOA files are used to obtain the individual GO annotations of gene products. .obo files are used to obtain description of GO terms based on GO Ids obtained from GOA files.

3.

Pfam (version 22) [39]

Pfam is a database of protein families, represented as multiple sequence alignments and HMM models

Pfam is used as the target database to obtain the domain architecture of query sequence and its interacting partners using hmmpfam.

4.

AAindex (version 7.0) [29]

AAindex is a database of amino acid physicochemical properties, substitution matrices and statistical protein contact potentials.

Data from AAindex is used to generate plots using 516 Amino Acid Indices. An amino acid index is a set of 20 numerical values representing various physico-chemical and biochemical properties of amino acids.

5.

DOMINE (version 1.1) [36]

DOMINE is a database of known and predicted protein domain (domain-domain) interactions. It contains domain-domain interactions reported in PDB along with interactions predicted using various computational approaches using Pfam domain definitions.

Pre-computed domain-domain interaction from DOMINE is used to provide additional support for a protein-peptide interaction. Domine is used in PeptideMine as it reports domain-domain based on the Pfam definitions.

6.

BLASTP (version 2.2.17) [23]

BLASTP or Protein BLAST is a tool for searching protein sequence databases using a protein sequence as query.

BLASTP is used as one of the search programs in PeptideMine server. BLASTP is used to search the database of interacting partners' sequence to obtain homologues sequence in the interacting sequence space

7.

hmmpfam (HMMER suite version 2.2) [37]

hmmpfam is part of the HMMER suite. hmmpfam use a sequence file as it input and search against a database of hmmfiles to identify significantly similar sequence matches.

hmmpfam is used to obtain the domain architecture of a query protein sequence and its interacting partner.

8.

ScanProsite (version 1.17) [26]

ScanProsite tool allows to scan protein sequence against the PROSITE database.

Used to identify the functional sites in individual peptides. Used as a search option to identify functional patterns from the

9.

PSIPRED (version 2.5) [34]

PSIPRED is a tool for protein secondary structure from amino acid sequence based on position-specific scoring matrices

PSIPRED is used to predict the secondary structure from the sequence of interacting partner.

10

DISOPRED (version 2.1) [35]

DISOPRED is a tool for the prediction of disorder from the amino acid sequence.

DISOPRED is used to predict the disorder region from the sequence of interacting partner

11.

SEQPLOT (version 1.1) [30]

SEQPLOT is a web-utility developed to generate AAindex based plots for a protein sequence

SEQPLOT is used to generate plots using three different amino acid indices from AAINDEX database.

12.

MView (version 1.49) [43]

MView is a visualization tool for converting the results of a sequence database search into the form of a coloured multiple alignment of hits stacked against the query.

Visualization of BLASTP search results in multiple sequence alignment format is provided using MView.