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 searches across any or all fields of the PEPlife2 database using logical operators like AND/OR. Users can build the query by using the "Add" button.

Peptide Search

User can search the query sequence against whole PEPlife2 database. Search result will provide user either with exactly identical peptide or matching peptides with the given query sequence. 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 search peptides using SMILES notation in the PEPlife 2.0 Database. The module provides four search options:

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

Browse by Half-life (converted into seconds)

Users can browse peptide entries from PEPlife2 database using Half-life in seconds.

Browse by Organism / Media

This module allows user to perform search on the basis of organism type. Enter the search term, and choose the field(s) in which you want to search. Each field is provided with an example button.

Browse by Year

Users can browse peptides by the year of publication present in PEPlife 2.O database

Browse by Assay

Users can browse the assays used to evaluate peptide half-life present in PEPlife 2.O database.

Browse by Length

Users can browse peptides 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 Chemical Modifications

Users can browse various C-terminal modifications, N-terminal modifications as well as the chemical modifications present in PEPlife 2.0.

BLAST

Users can run a BLAST query against the PEPlife 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 PEPlife 2.0 database. After submission of job it returns the list of peptides.

Mapping

User can select either SuperSearch to search for query peptide sequence against peptides of PEPlife2 or select SubSearch to search for query peptide sequence against the peptides of PEPlife 2.0.

Structure Alignment

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

Alignment Result

HTTP Status Headers

Upon sending a request to the server the following HTTP response headers are returned by the PEPlife 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 PEPlife 2.0 REST API offers access to the data through three distinct query fields: organism / media, linear / cyclic, and peptide sequence. The PEPlife2 REST API provides users programmatic access to peptide and protein half-life data without requiring manual downloads. It allows users to filter data based on three main query fields: Organism/media, Protease present, Linear/Cyclic, Peptide/Protein Sequence with various option. After selecting any query field, the API generates a wget, CURL and Request URL command for direct data accession. Then result are returned by the server in JSON format which can be downloaded from the Server Response box.

Query Field (..dataType)	Parameter (..dataValue)	Description
Organism / Media (org)	Mouse, dogs, rats, Pigs, Cell line/tissue, DPP-IV, RhNEP, Monkeys, mice, Cats, Buffer, MBP, PBS etc.	User can access data corresponding to particular organism / media, this will return all the entries for the selected organism / media.
Linear or Cyclic (lin_cyc)	Linear or Cyclic	User can access data corresponding to its structure linear or cyclic.
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 PEPlife 2.0 REST API returns the data in JSON format. The response data consists of 16 fields:

Return Field	Description
PEPlife 2.0 ID	Unique identifier in the PEPlife 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.
Origin	Origin of Corresponding peptide
Nature	Nature of the Peptide
Incubation Time	Incubation time of Peptide
Concentration	Concentration of peptide used in the study
Half-life	Half life of corresponding peptide
Half life Unit	Unit in which half life was given
Protease present	Protease present in that particular organism.
Assay	Type of assay used to measure half life of the peptide.
Test sample	Organism which was used to measure half life.
In-Vivo or In-vitro	Half life measured in-vivo or in-vitro
Reference	Refernce of the paper
Patent Number	It give Patent Number if any
Dose Route	It gives the Route of administration of peptide

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 "curl -X GET "https://webs.iiitd.edu.in/raghava/peplife2/api/api.php?dataType=lin_cyc&dataValue=Linear"
                            "

-X flag is used to specify the HTTP request method. HTTP requests typically use methods such as GET, POST, PUT, DELETE, etc. PEPlife 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/peplife2/api/api.php?dataType=lin_cyc&dataValue=Linear"

How to use ?

To access the data programmatically using PEPlife 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 PEPlife 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 PEPlife 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/peplife2/api/api.php?dataType=organism&dataValue=Mouse'

# 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)