LAMP: A database linking antimicrobial peptide

User's Guide

Browse     Search     Tools      Statistical Info    Links    Disclaimer

The need to develop new classes of antibiotics with novel mechanisms of action against drug-resistant pathogens is becoming very urgent. Antimicrobial peptides (AMPs) have attracted much attention as potential substitutes for conventional antibiotics. Since the discovry of maganins, cecropins and defensins 30 years ago, antimicrobial peptides have been hailed as a potential solution to the dearth of novel antibiotic development. AMPs are genetically ancient members of innate defense systems. AMPs are attractive moleculars for clinical development: they can be sythesizes easily, kill drug-resistant bacteria and have a rapid antimicrobial mechanism.
AMPs in LAMP are short, of less than 100 amino acid residues and include natural and synthetic AMPs. AMPs in LAMP have been grouped into three catalogs by data source: experimental, predicted and patent and two catalogs by source: natural and synthetic..
LAMP has been created with an objective to provide a useful resource for AMP studies. This manually curated database currently holds 5547 AMP sequences including 3191 experimental AMPs from publicated articles or public databases,865 predicted AMPs from public databases, and 1491 patent AMPs from public patents. Information related to sequence, protein definition, accession numbers, activity, taxonomy of the source organism, target organisms with MIC values, and links to external databases like UniProt, PDB and InterPro. PubMed links are included here. The database will be updated monthly with additional sequences.

Browse

The database browse interface provides the users with a function of navigating the entire database and supply a download link for the download all AMPs stored in LAMP.

Search

We classified search into simple search and complex search in LAMP. Simple search allows users to search based on keywords like "defensins" or string searches like "lysozyme g" in full name or function field in main table.

Complex search allows users restrict the search to a particular field descriptor or a combination of varied field description.

All searches are case insensitive. A complete list of the field descriptors and their description is given below:

DESCRIPTORS
DESCRIPTION
LAMP Id
The unique identifier in LAMP. E.g. L01A003147
Protein name
The name of AMP, such as Defensin.
Uniprot Id
UniprotKB entry name, like P0C201.
Collection
The collection of AMPs, such as Experimental, Predicted, Patent.
Source
The source of the AMPs, such as Homo sapiens.
Domains
The name of domain, such as Alpha-defensin.
Activity
The activity of AMPs, such as Antibacterial,Antivirual.
Target Organism
The Target organism of AMPs against. E.g. E.coli
MIC
Minimum inhibitory concentration [MIC values] .

Tools

BLASTP
We only construct BLASTP AGAINST EnzyBase on Web Server. And we supply a link to NCBI BLASTP if you want to blast full datasets in NCBI.
BLASTP AGAINST EnzyBase: Users can search for similar sequences in EnzyBase.

Reference:
Altschul, S. F. et al. (1997), Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402.

FASTA format

FASTA format for sequences begins with a single-line description, followed by lines of sequence data. The description line is demarked from the sequence data by a greater-than ('>') symbol in the first column.

For example :
>L01AP01801|DEF1_HUMAN
ACYCRIPACIAGERRYGTCIYQGRLWAFCC

Statistical Info

The statical info interface provides data on distribution of sequence length, protein mass, isoelectric point and rank of domains and sources.

Links

The links interface provides the links to other antimicrobial peptide databases.It not only show the links but also give a brief introduction to other databases.

Disclaimer

The authors do not assume any responsibility for losses of any kind incurred by use of this database.
This work has been partly funded by the plan 2012 for Science and technology innovation action of Shanghai, China (grant 12DE1940500) and the ‘Yangtze river delta’ joint scientific and technological project of China (grant 10495810600).