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NORINE

http://bioinfo.lifl.fr/norine/

Description :
A database of nonribosomal peptides

GFS

http://gfs.unc.edu/cgi-bin/WebObjects/GFSWeb

Description :
Genome-based Fingerprint Scanning (GFS) takes as input an experimentally obtained peptide mass fingerprint, scans a genome sequence of interest, and outputs the most likely regions of the genome from which the mass fingerprint is derived.

PepConfDB

http://www.peptidome.org/products/list.htm A database of peptide conformations

ASC - Active Sequence Collection

http://bioinformatica.isa.cnr.it/ASC/

Description :
ASC (Active Sequences Collection) is a database of short amino acid sequences with known biological activity. The current version is substantially improved as compared to the previous release; it now includes more than 1300 different active short protein sequences, each sequence being linked to the corresponding PUBMED literature reference. The entries are organized in six sections (3 more than the previous release): AIRS (Autoimmunity Related Sequences), DVP (Delivery Vectors Peptides), SSP (Structure of Solved Peptides), BAC (BioACtive peptides), DORRS (Database Of RGD Related Sequences), and TRANSIT (TRANsglutamination SITes). This release is characterized by a relevant reorganization of the structural and functional information, and increase of literature references and links to other databases. Aim of ASC is to help elucidating the biological role of proteins and to help new-drugs discovery. The main feature of this collection is the focus on specific biological functions and the lack of "noisy" signal. The web address to access ASC database is: http://bioinformatica.isa.cnr.it/ASC/ which also offers a new query interface to compare protein sequences with the ASC collection, as well as an updating interface to allow contribution of new referenced active sequences from the users.

References :
Facchiano, A., Facchiano, A., and Facchiano, F. ASC (Active Sequences Collection) database: a new tool to assign functions to protein sequences. Nucleic Acids Research 2003 Database Issue, accepted.

CoPS

http://203.195.151.46/copsv2/index.html

Description :
Comprehensive peptide signature database

Defensins Knowledgebase

http://defensins.bii.a-star.edu.sg/

Description :
The defensins knowledgebase is a manually curated database and information source devoted to the defensin family of antimicrobial peptides. The current version of the database holds a comprehensive collection of over 350 defensin records each containing sequence, structure and activity information. A web-based interface provides access to the information and allows for text-based searching on various data fields. With the rapidly increasing interest in defensins, we hope that the knowledgebase will prove to be a valuable resource in the field of antimicrobial peptide research.

EROP-Moscow

http://erop.inbi.ras.ru/

Description :
Natural oligopeptides may regulate nearly all vital processes. To date, the chemical structures of nearly 6000 oligopeptides have been identified from more than 1000 organisms representing all the biological kingdoms. We have compiled the known physical, chemical, and biological properties of these oligopeptides - whether synthesized on ribosomes or by non-ribosomal enzymes - and have constructed an internet-accessible database, EROP-Moscow (Endogenous Regulatory OligoPeptides). This database enables users to perform rapid searches via many key features of the oligopeptides, and to carry out statistical analysis of all the available information. The database lists only those oligopeptides whose chemical structures have been completely determined (directly. or by translation from nucleotide sequences). It provides extensive links with the SwissProt-TrEMBL peptide-protein database, as well as with the PubMed biomedical bibliographic database. EROP-Moscow also contains data on many oligopeptides that are absent from other convenient databases, and is designed for extended use in classifying new natural oligopeptides and for production of novel peptide pharmaceuticals.

Aknowledgement :
This work has been supported by Grant 02-07-90175 from the Russian Foundation for Basic Research (RFBR) and by the Program "Molecular and Cellular Biology", RAS-10P (Russian Academy of Sciences).

FUNPEP

http://www.cmbi.kun.nl/swift/FUNPEP/gergo/

Description :
Low-complexity peptides capable of forming amyloid plaque

Peptaibol

http://www.cryst.bbk.ac.uk/peptaibol/

Description :
The Peptaibol Database is a sequence and structure resource for the unusual class of peptides known as peptaibols. The database includes sequence, biological source, and bibliographical data for the naturally-occurring peptaibols. Information is also collated for the growing number of peptaibol three-dimensional structures determined by either crystallography or NMR spectroscopy. The database can be obtained as a whole or can be queried by name, group, sequence motif, biological origin and/or literature reference.

Aknowledgement :
Major contributions to the collation of data were made by Drs. Chris Snook and Jasveen Chugh.

MHCPEP

http://wehih.wehi.edu.au/mhcpep/

Description :
MHC-binding peptides

PepSeeker

http://nwsr.bms.umist.ac.uk/cgi-bin/pepseeker/pepseek.pl

Description :
Peptide identification and ion information from proteome experiments

PeptideAtlas

http://www.peptideatlas.org/

Description :
The PeptideAtlas (1) is a multi-organism, publicly accessible compendium of peptides identified in a large set of LC-MS/MS proteomics experiments. Some of the experimental data have been already published; many are still unpublished. All results of sequence searching have subsequently been processed through PeptideProphet to derive a probability of correct identification for all results in a uniform manner to insure a high quality database. All peptides have been mapped to Ensembl and can be viewed as custom tracks on the Ensembl Genome Browser.

The PeptideAtlas will continue to grow as more datasets and organisms are added. We welcome data submissions, which we will incorporate into the atlas.

Recent develoments :
PeptideAtlas is a first step towards the goal of fully annotating and validating eukaryotic genomes by using experimentally observed protein-products. PeptideAtlas provides a process and a framework to accommodate proteome information generated by high-throughput proteomics technologies and is able to efficiently disseminate experimental data in the public domain. Its significance continues to grow as more data are submitted from diverse experiments, using different cellular compartments and enrichments methods. PeptideAtlas also provides a resource for the development of new avenues of research. The datasets will provide a rich source of data for computational scientists to develop and test new algorithms for proteomic analysis, gene-discovery and splice variant prediction. The need for public proteomics data repositories is recognized (3) and we intend PeptideAtlas to continue to grow as a public database and resource. We strongly encourage researchers to contribute their own MS/MS data to the PeptideAtlas project. In the near future, we will make builds for organisms such as mouse, Arabidopsis thaliana and Halobacterium sp. NRC-1, and continue to make subsets such as the Human Plasma PeptideAtlas (2). Also in the near future we hope to provide an interface to access representative spectra of peptides, and will provide a way to retrieve information on peptide modifications (such as phosphorylation, etc.).

References :
1. Desiere,F., Deutsch,E.W., Nesvizhskii,A.I., Mallick,P., King,N.L., Eng,J.K., Aderem,A., Boyle,R., Brunner,E., Donohoe,S. et al. (2005) Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. Genome Biol., 6, R9. http://genomebiology.com/2004/6/1/R9
2. Deutsch,E.W., Eng,J.K., Zhang,H., King,N.L., Nesvizhskii,A.I., Lin,B., Lee,H., Yi,E.C., Osssola,R. and Aebersold,R. (2005) Human Plasma PeptideAtlas. Proteomics., 5. http://www3.interscience.wiley.com/cgi-bin/abstract/110575153/ABSTRACT
3. Prince,J.T., Carlson,M.W., Wang,R., Lu,P. and Marcotte,E.M. (2004) The need for a public proteomics repository. Nat Biotechnol, 22, 471-472.

ANTIMIC

http://research.i2r.a-star.edu.sg/Templar/DB/ANTIMIC/ Database of natural antimicrobial peptides

APD - Antimicrobial Peptide Database

http://aps.unmc.edu/AP/main.php

Description :
Antimicrobial peptide database

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