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Search tool help
PICI - Interaction tool help
BLAST search
Peptide Search
3D Similarity Search
PepBind Predict
Browsing help
Result help



SEARCH TOOL

 


Figure 1

A general search tool is present on all the pages of this web interface. This search tool is a simple, quick and convinient tool which can be used to search user defined queries in the database.

 

 


Figure 2

This database contains many search options which are broadly divided into three categories and is given as three search options (simple search, advanced search, and keyword search) under the search menu at the menu bar. These search options can be accessed at the search page shown in "Figure 2".

Keyword search- Keyword search tool searches the database by the keyword entered by the user (Figure 2a). User can perform search for all the words or the entered phrase.

Simple search- This option contains two search tools which can search the database for various protein database identification numbers (such as PDB and UniProt) or by entering protein name (Figure 2b). Users can search by different annotation accession numbers (such as for InterPro, Pfam, or Gene Ontology).

Advanced search- In advanced search category there are four search options which gives the user the option to search the database by their classification category, their functionality, their structure determination method, and search by the author name. (Figure 2c)

Search for database entries based on domain types can be done by the Domain search options with 40 different domain categories. This search generates a list of all the proteins falling in that category.

Search for database entries based on Peptide Length.

Search for database entries based on the Source Organism.

Proteins in the database can be searched by their cellular activity through the functionality search tool. PepBind dataset has been classified in nineteen categories given in the drop down menu (such as Cell cycle, Structural proteins, Cell adhesion, Transport, Calmodulin (CaM), Apoptosis, Signaling, Hormones, Transferases, Transcription, Gene regulation, Inhibitory complex, MHC, Immunoglobulin (Ig), Antibiotics, Other immune system proteins, Proteases, Other hydrolases, and Others.

Protein structures in the PepBind database can be searched by their structure determination method. (such as X-ray, NMR, Electron Microscope, etc)

Search by author name gives the user an option to search the database for the protein structures by the specific author.

All these search options with their parameters are joined by ‘AND’ operator for an intensive search.

All the proteins of specific classification, functionality and structure determination method can also be accessed by clicking the hyperlinks of the categories on the browse page.

 

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PICI - INTERACTION TOOL

 


Figure 3

PICI interaction tool calculates the hydrogen bonds and other interactions between the core protein and the peptide of the protein-peptide complexes from the PepBind databse. This tool computes the interaction details by entering the pdbid and the chain identifier of the protein sructure in the text box of the PICI Server interface. (Figure 3)

 


Figure 4

a - interaction file download
b - tabs for various interactions
c - residues participating in interaction are highlighted maroon
d - Jmol displaying interactions. Identified interacting residues colored maroon. Peptide chain is colored CPK
e - table displaying the interaction details

The interaction result page shows the peptide and the amino acid molecules from the other chains of the protein having various interactions in Jmol viewer applets and sequence display. (Figure 4)

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BLAST Search

 


Figure 5

The BLAST Search Tool (Figure 5) searches Similar amino acid sequences in the databases (PepBind, PDB, and SwissProt) as per the user given parameters. Users can choose from different matrices and and select penalties and threshold values.

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Peptide Search

 


Figure 6

The Peptide Search Tool (Figure 6) searches the PepBind database for the user given peptide sequence. Users can search peptides present in the database by exact sequence match or by BLAST search.

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3D Similarity Search

 


Figure 7

The 3D Similarity Search Tool (Figure 7) can search similar domains present in different structural databases. For this, we use web service of PDB, which uses the FATCAT algorithm to recognize homologous domains available at PepBind, SCOP, and PDP.

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PepBind Predict - Prediction tool for peptide binding

 


Figure 8

A binding prediction server which can predict the possible peptide binding domains in PepBind database for the user defined peptide sequence.

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BROWSE

 


Figure 9

Browse page (figure 9) can be accessed by clicking the browse menu on the menu bar. It shows the list of all the protein structures present in the database. This list also shows the classification, protein name, category, functionality, and author names for the relevant protein.

Dynamic links are given on the page to search the database or to go to the result page of a perticular protein.
1) By clicking on the PDBid button user can see the detailed result page for that protein.
2) By clicking on the classification user can search all the protein structures falling in that classification category.
3) By clicking on the functionality user can search all the proteins structures having that function.
4) By clicking on the author names user can search the list of proteins by that perticular author.

 


Figure 10

Protein structures can be browsed by different categories in the Category page, where all the peptide binding proteins are classified based on their functionality, peptide length, and their structure determination method. Category distribution has been shown as graphs on this page and links has been provided for each category to search the structures for specific category.

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RESULT

 

 


Figure 11

Result page for a perticular protein-peptide complex contains all the details for that protein structure divided in different categories which are added under relevant tabs of the result page. Top right corner of the result page contains linked images for downloading data files ( ) and printing ( ) the protein details in .pdf file format. (figure 11)

The Summary Tab contains data about protein's PDBid, name, classification, category, functionality, biological unit and keywords. Addition to this it also contains detailed data of the components of the proteins. It contains molecule name and source method for the polymers and if the polymer is an enzyme, then enzyme commission number of the enzyme.

This tab also contains data about the ligands present in the protein structure.

There are many internal and external links present in the content of the summary tab.
1) By clicking on the classification user can search all the protein structures falling in that classification category.
2) By clicking on the functionality user can search all the proteins structures having that function.
3) By clicking the EC number user can see the details of that enzyme from IUBMB (International Union of Biochemistry and Molecular Biology).
4) By clicking the UniProt id user can see the specific polypeptide reference in the UniProt database.
5) By clicking the Ligand Expo image ( ) for the ligands user can see the detailed information about that ligand.

 


Figure 12

The Sequence and Source Tab contains information about the type of chains, their sequence, the sequence length, and the UniProt reference for that chain (figure 12). The integrated sequence modification tool colors the single letter code amino acid sequence of the protein according to their biochemical properties (such as green for non-polar hydrophobic amino acids, yellow for uncharged polar amino acids, blue for positively charged amino acids, red for negatively charged amino acids, and black for non standard amino acids).

 

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