Related Databases & Prediction Websites
1. PubMed, Swiss-Prot and PDB
| URL |
Tool Description |
Country |
PubMed
|
National Library of Medicine Resource for publications in biological and biomedical sciences
|
USA
|
|
UniProt
|
UniPro Knowledgebase
|
Europe
|
|
Google Scholar
|
WWW-based Literature Search
|
USA
|
|
PDB
|
The RCSB Protein Data Bank
|
USA
|
|
|
|
2. Accessible Databases for antimicrobial peptides (AMPs)
Website
|
Database Description |
Country |
Year Published |
Peptaibols
|
A collection of peptaibols
|
England |
2003,2004 |
APD
|
The antimicrobial peptide database and analysis system for peptide discovery, timeline, nomenclature, classification, search, prediction and design
|
USA |
2004,2009,2016 |
| DAMPD (formerly ANTIMIC)
|
Dragon database for antimicrobial sequences |
South Africa/Saudi Arabia |
2004,2012 |
Cybase
|
The database of cyclic proteins
|
Australia |
2006,2008 |
| Defensins
|
Defensins knowledgebase |
Singapore |
2007 |
BACTIBASE
|
A data repository of bacteriocins
|
Canada/Tunisie |
2007,2010 |
PhytAMP
|
Plant AMPs
|
Canada/Tunisie |
2009 |
CAMP
|
A collection of AMPs including patented peptides and predicted peptides without activity data
|
India |
2010,2014,2016 |
YADAMP
|
Yet another database of AMPs
|
Italy |
2012 |
DADP
|
Database of amphibian defense peptides
|
Croatia |
2012 |
THIOBASE
|
Database of bacterial thiopeptides (containing macrocyclic core)
|
China |
2012 |
EnzyBase
|
Database of enzybiotics (lysins, autolysins, lysozymes, and large bacteriocins)
|
China |
2012 |
LAMP
|
A database linking other AMP databases
|
China |
2013,2020 |
MilkAMP
|
A database for milk AMPs
|
Canada |
2014 |
DBAASP
|
Database of AMPs with mainly synthetic peptides
|
Georgia |
2014,2016,2021 |
BaAMPs
|
Biofilm-active AMPs database
|
Italy |
2015 |
ANTISTAPHYBASE
|
A database for anti-Staphylococcal peptides and essential oils
|
France/Tunisia/Canada/USA |
2016 |
InverPep
|
Invertebrate AMPs
|
Colombia |
2017 |
AntiTbPdb
|
Anti-TB Peptides
|
India |
2018 |
DRAMP
|
Data Repository of Antimicrobial Peptides
|
China |
2019, 2022 |
|
|
|
|
3. Selected AMP prediction tools
Server
|
Description |
Country |
Year |
APD peptide predictor
|
Database-based classification and prediction of AMPs
|
USA
|
2004
|
|
BAGLE
|
A web-based bacteriocin genome mining tool
|
The Netherlands
|
2006
|
|
AntiBP
|
SVM, QM, or ANN prediction of AMPs
|
India
|
2007
|
|
AMPer
|
An automated discovery tool for gene-coded antimicrobial peptides
|
Canada
|
2007
|
|
CAMP Prediction
|
SVM, RF, ANN, or DA prediction of AMPs
| India
|
2010
|
|
antiSMASH
|
A web-based thiopeptide genome mining tool
|
The Netherlands
|
2011
|
|
AMPA
|
Antimicrobial sequence scanning system to predict potential AMP region from proteins
|
Spain
|
2012
|
|
AVPpred
|
SVM Prediction of antiviral peptides
|
India
|
2012
|
|
iAMP-2L
|
Two-layer Prediction of AMPs
|
China/USA
|
2013
|
|
CyPred
|
Prediction of circular proteins
|
Canada
|
2014
|
|
dPABBs
|
Prediction of anti-biofilm peptides
|
India
|
2016
|
|
AMP_Scanner
|
AMP scanner (>10 aa)
|
USA
|
2018
|
|
AMP parameter calculations and similarity using APD3
|
|
|
|
|
Main references for this webpage:
Wang, G., ed. (2017) Antimicrobial Peptides: Discovery, Design and Novel Therapeutic Strategies (2nd version), CABI, England.
Wang, G. (2015) Database resources dedicated to antimicrobial peptides. In "Antimicrobial Resistance and Food Safety: Methods and Techniques" (Chen, C.-Y., Yan, X., and Jackson, C.R., eds.), Academic Press, Boston, pp. 365-384.
Wang, G. (2007) Tool developments for structure-function studies of host defense peptides. Protein Pept. Lett. 14, 57-69 (containing a list of existing 8 AMP databases).
