What are Hemolytic Peptides?

Hemolytic peptides are short chains of amino acids that can disrupt red blood cell (RBC) membranes, leading to cell rupture — a process known as hemolysis. These peptides are often found in nature, such as in snake venoms, antimicrobial peptides, or human immune proteins.

How is This Useful in Therapeutics?

Predicting and controlling hemolytic activity supports multiple therapeutic advancements:

• Antimicrobial Peptides (AMPs): Non-hemolytic AMPs combat drug-resistant bacteria without harming human cells.
• Cancer Therapy: Some hemolytic peptides selectively target cancer cells — modifying them improves safety.
• Drug Delivery: Hemolytic peptides can enhance drug delivery across membranes when tuned to target diseased cells specifically.
• Antiviral and Anti-fungal Peptides: Safer, modified peptides can fight viruses or fungi without harming human cells.

Hemolytic Peptides: Action Mechanisms

Why This Matters for Therapeutics

Understanding these mechanisms helps design safer peptides:

• Pore-forming peptides: Can be modified to selectively target cancer or bacterial cells.
• Carpet-like peptides: Can be engineered to avoid damaging human cells.
• Toroidal model peptides: Provide insights into creating peptides that penetrate tough bacterial membranes while sparing human ones.

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 Hemolytik 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 Hemolytik 2.0 Database. The module provides four search options:

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

What is MAP Format?

MAP (Modified Amino acid Peptide) format is a structured representation specifically designed for modified peptides, particularly those containing non-natural residues or chemical modifications that aren't covered by standard one-letter amino acid codes. This format ensures consistency in representing peptide sequences across different computational tools and databases.

Why is MAP Format Important?

In peptide-based therapeutics and bioinformatics, especially when working with hemolytic peptides, accurate representation of both natural and non-natural residues is crucial. MAP format provides a reliable way to encode these sequences for computational analysis, predictive modeling, and database storage.

Need to Convert Your Sequences?

If you have raw peptide sequences and want to convert them into MAP format, you can easily do so using the tools and guidelines provided in the MAP repository developed by Raghava's group. This resource includes conversion utilities, examples, and detailed documentation to help you get started.

Explore the MAP Repository: https://webs.iiitd.edu.in/raghava/maprepo/

Dive deeper into MAP format structure, guidelines for representing modified residues, and how to use MAP files in peptide analysis workflows.

Browse by Source

Users can browse different sources of peptides or proteins.

Browse by Function

Users can browse the function of hemolytic peptides. It lists the number of entries of linear and cyclic peptides, the stereochemistry of peptides, and the number of non-hemolytic peptides.

Browse by Nature

Users can browse the unique hemolytic peptides by their nature. It lists the number of entries for different nature of peptides.

Browse by Length

Users can browse hemolytic peptides in Hemolytik 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.

BLAST

Users can run a BLAST query against the Hemolytik 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.

BLAST Result

Smith-Waterman Search

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

Smith-Waterman Result

Mapping

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

Mapping Result

Structure Alignment

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

Alignment Result

HTTP Status Headers

Upon sending a request to the server the following HTTP response headers are returned by the Hemolytik 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 Hemolytik 2.0 REST API offers access to the data through three distinct query fields: source, nature, and peptide sequence. Users can select from a diverse array of options within each field, enabling targeted retrieval of relevant data. Specifically, the nature query field encompasses 5 distinct nature parameters, while the source query field provides access to data from 12 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
Source	Human, Rat, Mouse, Fish, Sheep, Rabbit, Horse, Pig, Chicken, Porcine, Mus musculus, etc.	User can access data corresponding to particular source, this will return all the entries for the selected source.
Nature	Antimicrobial,Anticancer, Antifungal, Cytotoxic,CPP, etc.	User can access data corresponding to particular nature, this will return all the entries for the selected nature.
Peptide Sequence (seq)	Natural, Modified	Users can access data based on their selectedq 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 Hemolytik 2.0 REST API returns the data in JSON format. The response data consists of 16 fields:

Return Field	Description
ID	Unique identifier in the Hemolytik 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.
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.
Linear/Cyclic	Conformation of the peptide.
Stereo-chemistry	Stereo-chemistry of the peptide.
Chemical Modifications	Whether the peptide contains any non-natural residues or any other chemical modifications.
Length	Length of the peptide.
Nature	Nature of the peptide.
Source	The source of peptide used to measure the activity of peptide.
Origin	Origin of the peptide corresponding to that source.
Experimental Structure	The experimental structure of the peptide.
Non-Hemolytic	Whether the peptide is hemolytic or non-hemolytic.

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/hemolytik2/api/api.php?dataType=source&dataValue=Human"

-X flag is used to specify the HTTP request method. HTTP requests typically use methods such as GET, POST, PUT, DELETE, etc. Hemolytik 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/hemolytik2/api/api.php?dataType=source&dataValue=Human"

How to use ?

To access the data programmatically using Hemolytik 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 Hemolytik 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 Hemolytik 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/hemolytik2/api/api.php?dataType=source&dataValue=Human'

# 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)