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Common Peptide Databases


Peptides are important molecules with diverse biological functions and biomedical uses such as hormones, transmitters, and modulators of numerous biological processes.Both naturally occurring and synthetic peptides are used in therapeutic applications. Scientist have constructed many peptides database, which at the time of writing contains thousands of individual peptide entries.

These databases have a web-based user interface with a simple search function, advanced text search, and BLAST search capabilities. Database has biological and medical applications, for example, to predict the binding partners of biologically interesting peptides, to develop peptide based therapeutic or diagnostic agents, or to predict molecular targets or binding specificities of peptides resulting from phage display selection.Here we provide links to all the web servers/tools which are developed for peptides with special emphasis on therapeutic peptides.
Abbreviation Name Description Organization
AHTPDB Database of antihypertensive peptides It contains around 6000 entries of about 1700 unique peptides. Each entry provides comprehensive information about a peptide that includes its sequence, inhibitory concentration (IC50), log value of inhibitory concentration (pIC50) and toxicity. These peptides have been collected & complied from published literature and existing databases like ACEpepDB, BIOPEP and EROP-Moscow database. Institute of Microbial Technology, India.
LAMP Database of antimicrobial peptides AMPs in LAMP are short, of less than 100 amino acid residues and include natural, synthetic and predicted AMPs. AMPs in LAMP had been grouped into three catalogs by data source: experimental, predicted, and patent. This manually curated database currently holds 5547 AMP sequences, including 3904 natural and 1643 synthetic AMPs. Fudan University, China
Antimicrobial Combination Networks Database annotating information about combinations of antimicrobial drugs and peptides The initial release of the database focused on antimicrobial combinations that have been experimentally tested against Pseudomonas aeruginosa, Staphylococcus aureus, Escherichia coli, Listeria monocytogenes and Candida albicans, which are prominent pathogenic organisms and are well-known for their wide and growing resistance to conventional antimicrobials. Besides maintaining these data collections, we are extending literature screening to a wider collection of organisms. University of Minho, Portugal
APD Database of antimicrobial and anticancer peptides The Antimicrobial Peptide Database (APD) contains 2890 antimicrobial peptides from six kingdoms with the following activity . University of Nebraska Medical Center, USA
AVPdb Database of antiviral peptides AVPdb is the first comprehensive database of Antiviral Peptides (AVPs) targeting about 60 medically important viruses. It is a manually curated, open source archive having experimentally verified 2683 AVPs including 624 modified AVPs. Institute of Microbial Technology, India
CancerPPD Database of anticancer peptides Data was curated manually from both published articles, patents as well as from other repositories. The important feature of cancerPPD is that it also provides information related to various chemical modifications like non-natural, D-amino acids, modified-amino acid like ornithine. The database is cross-linked with various other related resources in order to provide comprehensive information related to ACPs. Institute of Microbial Technology, India
TumorHoPe Database of tumor-recognizing peptides TumorHoPe is a manually curated comprehensive database containing 744 entries of experimentally characterized tumor homing peptides. These peptides recognize tumor tissues and tumor associated micro environment, including tumor metastasis. Thus, they can be used to deliver drugs selectively in tumors. Institute of Microbial Technology, India
CPPsite Database of cell-penetrating peptides CPPsite 2.0 is an updated version of database CPPsite, it contains around 1700 unique cell penetrating peptides (CPPs) alongwith their secondary & tertiary structure. This database maintains experimentally validated CPPs (linear & cyclic; modified & non-natural residues) and wide range of cargos (nucleic acids, proteins, nanoparticles, PNA) delivered in cells using these peptides. Institute of Microbial Technology, India
BioTherapi Metabase of peptides revealing bioactivity and useful as drugs This include all the relevant information about the use of Peptides/Proteins in drug and synthesis of new peptides. It also cover problems, in their formulation, synthesis and delivery process. Institute of Microbial Technology,India
EROP-Moscow Database of biologically active peptides EROP-Moscow is a curated oligopeptide (2-50 amino acid residues) sequence database which strives to provide a high level of annotations (such as descriptions of the structure of an oligopeptide, its source and function, post-translational modifications, etc.). A. N. Bach Institute of Biochemistry, Russian Academy of Sciences
SwePep Database of biologically active peptides including sophisticated computing tools for peptide mass spectra interpretation SwePep is an endogenous peptide database developed by the Laboratory for Biological and Medical Mass Spectrometry at Uppsala University to aid mass spectrometric identifications. At this stage the information in SwePep is biased to the species handled by the developers, ie. rat, and mouse. Uppsala University, Swedens
Brainpeps Database of peptides passing through the blood-brain barrier Brainpeps® is a resource of blood-brain barrier properties of peptides. This database is managed by Ghent University. The database is linked to a manuscript entitled "Brainpeps: the blood-brain barrier peptide database", in which the BBB methods and responses are clarified and correlated to each other. Ghent University,Belgium
Cybase Database of cyclic proteins and peptides with various bioactivities These proteins are found in the plants of the Rubiaceae and Violaceae and our specific goals include: determining the role that cyclotides play in plants, discovering the mechanism of action of the wide range of biological activities displayed by the cyclotides (including anti-HIV, anti-bacterial and insecticidal activity), characterising the genetics of the cyclotides and further discovery of novel cyclotides. University of Queensland , Australia
Hmrbase Database of hormones Hormones are the chemical messengers of the body which convey the message from one part to another. On the basis of chemical composition, there are two types of hormones: (a) Peptides (b) Non-peptides. The action of both types of hormone is mediated through Receptors which receive the signal and relay it to the destination. Receptors of polypeptide/protein hormones are located in the plasma membrane and regulate various intracellular functions by changing the activity of a particular enzyme. Institute of Microbial Technology, India
NeuroPedia Database of neuropeptides including library of mass spectra NeuroPedia is a neuropeptide encyclopedia of peptide sequences (including genomic and taxonomic information) and spectral libraries of identified MS/MS spectra of homolog neuropeptides from multiple species. Searching neuropeptide MS/MS data against known NeuroPedia sequences will improve the sensitivity of database search tools. Moreover, the availability of neuropeptide spectral libraries will also enable the utilization of spectral library search tools, which are known to further improve the sensitivity of peptide identification. University of California San Diego ,USA
NeuroPep Database of neuropeptides The current release of the database (version 1.0, 2014-11-26) holds 5949 non-redundant neuropeptide entries originating from 493 organisms belonging to 65 neuropeptide families. The data were collected from various resources including MEDLINE abstracts, full papers, UniProt,database at www.neuropeptides.nl and Neuropedia. All the entries in NeuroPep have been manually checked. Huazhong University of Science and Technology, China
ParaPep Database of antiparasitic peptides It is a manually curated repository of experimentally validated anti-parasitic peptides and their structures. Data have been collected from research papers, published patents and other databases. The current release of ParaPep contains 863 anti-parasite peptide entries, which have been tested against 12 different types of parasites. Institute of Microbial Technology, India
THPdb Database of therapeutic peptides Therapeutic peptides are modified in different ways so as to alter their properties and then sold under different brand names by various companies. THPdb provides detailed description of such brands in a user-friendly way to enable quick access of relevant information on the peptides. All information compiled in this database has been extracted from research papers, patents, pharmaceutical company websites catering to product details, drugbank, US-FDA and others. Institute of Microbial Technology, India
WALTZ-DB Database of amyloid hexapeptides The majority of the data comes from electron microscopy and FTIR experiments done by the Switch lab. Apart from that class of data we also provide the amyloid annotation for several other short peptides found in current scientific research papers. Switch Laboratory, Belgium

Reference:


Mandava S, Makowski L, Devarapalli S, Uzubell J, Rodi DJ: RELIC--a bioinformatics server for combinatorial peptide analysis and identification of protein-ligand interaction sites. Proteomics. 2004, 4 (5): 1439-1460. 10.1002/pmic.200300680.

Valuev VP, Afonnikov DA, Ponomarenko MP, Milanesi L, Kolchanov NA: ASPD (Artificially Selected Proteins/Peptides Database): a database of proteins and peptides evolved in vitro. Nucleic Acids Res. 2002, 30 (1): 200-202. 10.1093/nar/30.1.200.

Wade D, Englund J: Synthetic antibiotic peptides database. Protein Pept Lett. 2002, 9 (1): 53-57. 10.2174/0929866023408986.

Wang Z, Wang G: APD: the Antimicrobial Peptide Database. Nucleic Acids Res. 2004, 32 (Database issue): D590-2. 10.1093/nar/gkh025.
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