Basic Search

The user can input a search term in the search field and select the checkboxes to choose the specific fields they want to search.

Advance Search

Users can perform advance search by selecting multiple fields using logical operators like AND/OR. Users can build the query by using the "Add" button.

Peptide Search

Users can perform Peptide search to search for their query peptide sequence in the CancerPPD 2.0 Database. The module provides two search options:

• Identical Sequence Search: This option will search for identical peptide sequence in the database.
• Subsequence Search: This option will will search for peptides that contains a part of the query peptide.

SMILES Search

Users can perform SMILES search to search for the query SMILES sequence in the CancerPPD 2.0 Database. The module provides four search options:

• Substructure Search
• Exact Search
• Exact Fragment Search
• Superstructure Search

Browse by UniProt Proteins

Users can browse anticancer proteins mapped from UniProt.

Browse by Proteins

Users can browse anticancer proteins. The sequences with length greater than 40 were treated as proteins.

Browse by Peptide

Users can browse the unique anticancer peptides. It lists the number of entries for each peptide, the number of types of tissues effected, number of cell lines on which it has been tested and the number of different types of assays used to test each peptide.

Browse by Tissue

Users can browse the tissue types against which anticancer peptides have been tested. It lists the number of entries, number of unique peptides and the number of cell lines tested for a particular tissue type.

Browse by Cell Lines

Users can browse the the listed cell lines against which anticancer peptides have been tested. It also lists the total number of entries in CancerPPD 2.0 for each cell line.

Browse by Year of Publication

Users can browse the the listed cell lines against which anticancer peptides have been tested. It also lists the total number of entries in CancerPPD 2.0 for each cell line.

Browse by Assay

Users can browse the the listed assays using which anticancer peptides have been tested. It also lists the total number of entries, number of unique peptides and the total number of cell lines.

Browse by Length

Users can browse anticancer peptides in CancerPPD 2.0 based on their length. Sequences up to 40 amino acids are classified as peptides, while those exceeding 40 amino acids are classified as proteins.

Browse by Modifications

Users can browse various C-terminal modifications, N-terminal modifications as well as the chemical modifications that were incorporated in the anticancer peptides compiled in CancerPPD 2.0.

BLAST

Users can run a BLAST query against the CancerPPD 2.0 database. After submission of job it returns the list of peptides similar to the query peptide. The server also provides options to choose different parameters like weight matrix and expectation value.

Smith-Waterman Search

Users can run a Smith-Waterman search query against the CancerPPD 2.0 database. After submission of job it returns the list of peptides.

Mapping

User can select either SuperSearch to search for query PROTEIN sequence against peptides of CancerPPD or select SubSearch to search for query PEPTIDE sequence against the peptides of CancerPPD 2.0.

Structure Alignment

User can align their PDB structure with any of the CancerPPD 2.0 Structures

Alignment Result

HTTP Status Headers

Upon sending a request to the server the following HTTP response headers are returned by the CancerPPD 2.0 REST API:

Code	Description
200	The request was processed successfully.
400	Bad Request. Invalid data type.
404	Not Found. The requested data doesn't exist.
500	Internal server error. Most likely a temporary problem, but if the problem persists please contact us.

Query Fields

The CancerPPD 2.0 REST API offers access to the data through three distinct query fields: cancer type, cell line, and peptide sequence. Users can select from a diverse array of options within each field, enabling targeted retrieval of relevant data. Specifically, the cancer type query field encompasses 15 distinct cancer type parameters, while the cell line query field provides access to data from 45 different cell lines, contingent upon their significance within the database. Furthermore, the peptide sequence query field allows users to refine their search based on two parameters: Natural or Modified.

Query Field (..dataType)	Parameter (..dataValue)	Description
Cancer Type (cancer_type)	Breast Cancer, Lung Cancer, Ovarian Cancer, Cervical Cancer, Colon Cancer, Skin Cancer, Blood Cancer, Prostate Cancer, Liver Cancer, etc.	User can access data corresponding to particular cancer type, this will return all the entries for the selected cancer type.
Cell Line (cell_line)	MCF-7, A-549, HeLa, PC-3, HepG-2, MDA-MB-231, HCT-116, Jurkat, K-562, MDA-MB-435S, HT-1080, DU-145, HL-60, Caco-2, HMLER, etc.	User can access data corresponding to particular cell line, this will return all the entries for the selected cell line.
Peptide Sequence (seq)	Natural, Modified	Users can access data based on their selected parameter. Selecting "Natural" will retrieve entries featuring sequences composed solely of natural amino acid residues, and devoid of any chemical modifications. Conversely, selecting "Modified" will retrieve entries characterized by sequences containing non-natural residues or having any chemical modifications.

Return Fields

Once the request has been processed successfully, the CancerPPD 2.0 REST API returns the data in JSON format. The response data consists of 16 fields:

Return Field	Description
CancerPPD 2.0 ID	Unique identifier in the CancerPPD 2.0 database for that entry.
PMID	Article PMID corresponding to that entry.
Year	Year of publication of that entry.
Sequence	Sequence of the peptide.
Name	Name of the peptide.
Length	Length of the peptide.
Linear/Cyclic	Conformation of the peptide.
Chirality	Sterechemistry of the peptide.
Chemical Modifications	Whether the peptide contains any non-natural residues or any other chemical modifications.
C-Ter Modifications	Whether the C-terminal end of the peptide contains an entity or it is free.
N-Ter Modifications	Whether the N-terminal end of the peptide contains an entity or it is free.
Cell Line	Anticancer property of the peptide tested against which cell line.
Cancer Type	The cancer type corresponding to that cell line.
Assay	Type of assay used to measure the anticancer activity of the peptide.
Test Time	Time after which the anticancer activity was measured or found to be significant.
Tissue Effected	The tissue effected corresponding to that cancer type.

CURL

cURL, short for "Client URL," is a command-line tool and library for transferring data with URLs. It supports a wide range of protocols, including HTTP, HTTPS, FTP, FTPS, SCP, SFTP, LDAP, TFTP, and many others. Example Command:

curl -X GET "https://webs.iiitd.edu.in/cancerppd2/api/api.php?dataType=cell_line&dataValue=A-549"

-X flag is used to specify the HTTP request method. HTTP requests typically use methods such as GET, POST, PUT, DELETE, etc. CancerPPD 2.0 REST API allows only GET request method.

wget

wget is a command-line utility for downloading files from the web. It supports downloading files via HTTP, HTTPS, and FTP protocols in Linux environments. Example Command:

wget "https://webs.iiitd.edu.in/raghava/cancerppd2/api/api.php?dataType=cell_line&dataValue=A-549"

How to use ?

To access the data programmatically using CancerPPD 2.0 REST API, user simply needs to select the query field and its corresponding query term and hit "Execute".

After clicking "Execute" the output will contain the cURL command, wget command, request URL and the server response.

Python Example

Below is a very simple example of how to use the CancerPPD 2.0 REST API using Python. It sends a GET request to the API endpoint, retrieves the JSON response containing data, and parses it into a pandas DataFrame for further analysis. This example demonstrates the basic process of accessing data from the CancerPPD 2.0 REST API and manipulating it within a Python environment.

import requests
import pandas as pd

# Define the URL for the API request
url = 'https://webs.iiitd.edu.in/raghava/cancerppd2/api/api.php?dataType=cancer_type&dataValue=Fibrosarcoma'

# Send a GET request to the API
response = requests.get(url)

# Check if the request was successful (status code 200)
if response.status_code == 200:
    # Print the JSON response from the API
    print(response.json())

    # Parse the JSON data and store it in a pandas DataFrame
    json_data = response.json()
    df = pd.DataFrame(json_data['data'])

    # Visualize the DataFrame
    print(df.head())  # Display the first few rows of the DataFrame

else:
    # Print an error message if the request was not successful
    print('Error:', response.status_code)