ANTIMICROBIAL PEPTIDE REPOSITORY FOR BIOFILMS

B-AMP v2.0 is a structural and functional repository consisting of (i) 5766 AMPs from natural and synthetic sources, (ii) 2502 bacterial protein targets from a wide-range of bacterial species, and (iii) AMP-biofilm target models for well-known biofilm-forming pathogens. B-AMP provides search enabled information for AMPs and biofilm targets, that includes FASTA files, UniProt and PDB annotations, PDB and RoseTTAFold structural models, and PubMed references to scientific literature. For the 3D AMP-protein docking models, PDBQT IN/OUT files, 3D models and bond information is also provided. Taken together, B-AMP is a one-stop bioinformatics resource for AMP investigations related to biofilms, and can be leveraged for a range of studies across biofilm-forming pathogens and potential biofilm targets.

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

Dr. Ragothaman M Yennamalli

Assistant Professor
SASTRA Deemed to be University, India

Shashank Ravichandran

B.Tech. Bioinformatics
SASTRA Deemed to be University, India

Yatindrapravanan Narasimhan

B.Tech. Bioinformatics
SASTRA Deemed to be University, India

Sai Supriya Avatapalli

Remote Internship
Savitribai Phule Pune University, India

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

Ravichandran S, Avatapalli S, Narasimhan Y, Kaushik KS and Yennamalli RM (2022) 'Targeting' the search: An Upgraded Structural and Functional Repository of Antimicrobial Peptides for Biofilm Studies (B-AMP v2.0) with a Focus on Biofilm Protein Targets. Front. Cell. Infect. Microbiol. 12:1020391. doi: 10.3389/fcimb.2022.1020391

We will be updating this repository with additional AMP structures, Biofilm protein targets, and protein-peptide docking models. Last update was on Aug 10, 2022.

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.