ANTIMICROBIAL PEPTIDE REPOSITORY FOR BIOFILMS

B-AMP is an Antimicrobial Peptide (AMP) repository for biofilms, consisting of a vast library of 5552 structural AMP models, AMPs annotated to relevant biofilm literature, and protein-peptide interaction models with potential biofilm targets. B-AMP provides search enabled information of AMP structures, that includes easily accessible and downloadable FASTA files, PDB structures and their pictorial representation in 3D space. It also includes a filtered library of 2542 filtered peptides known to exhibit anti-Gram positive activity and 2397 peptides known to exhibit anti-Gram negative activity. Taken together, this user-friendly repository and structural and functional library can serve as a bioinformatics resource for AMP investigations across other biofilm targets and biofilm-forming pathogens.

MEET THE TEAM

Gandhar Tendulkar

M.Sc. Bioinformatics
University of Mumbai, India

Dr. Karishma S. Kaushik

Assistant Professor / Ramalingaswami Re-entry Fellow
Savitribai Phule Pune University, India

Rohit Awate

M.S. Computer Science
Northeastern University, USA

Shreeya Mhade

M.Sc. Bioinformatics
University of Mumbai, India

Stutee Panse

M.S. Biotechnology
The Pennsylvania State University, USA

HOW TO CITE US

Resources downloaded and/or used from B-AMP (as well as resources we have made available on GitHub), including FASTA files, PDB files, 3D models, AMP lists, code, should be cited with the link b-amp.karishmakaushiklab.com, and the following citation:

Mhade S, Panse S, Tendulkar G, Awate R, Narasimhan Y, Kadam S, Yennamalli RM and Kaushik KS (2021) AMPing Up the Search: A Structural and Functional Repository of Antimicrobial Peptides for Biofilm Studies, and a Case Study of Its Application to Corynebacterium striatum, an Emerging Pathogen. Front. Cell. Infect. Microbiol. 11:803774. doi: 10.3389/fcimb.2021.803774

We will be updating this repository with additional AMP structures, and protein-peptide docking models. Last update was on Jan 18, 2022. In this update, each AMP card was annotated and linked to its relevant biofilm literature.

While we have exercised multiple checks and continue to do so, B-AMP does not guarantee that the resources are free of errors. Please use resources at your own discretion and with verification.

This work is licensed under a Creative Commons Attribution 3.0 Unported License, with the exception of this website's code and additional utility code that aided this work, which is separately licensed under the GNU General Public License v3.0.