NameLinkDescription
AAindexhttp://www.genome.ad.jp/aaindexDatabase of indices describing physicochemical properties, sufficient for prediction of peptide properties, e.g. QSAR approach
ANNIEhttp://annie.bii.a-star.edu.sgProgram creating protein sequence annotations. Accepts peptide sequences as a queries.
BETASCANhttp://groups.csail.mit.edu/cb/betascan/Program for amyloid propensity prediction
BioCataloguehttp://www.biocatalogue.org/Interface for registering, browsing and annotating web services in the area of life sciences
BioDBcorehttp://biocurator.org/biodbcore.shtmlWebsite providing access to few catalogues of biological databases and to information about current and proposed standards of database description
bioDBnethttp://biodbnet.abcc.ncifcrf.gov/Network of biological databases
Bioinformatics Links Directoryhttp://bioinformatics.ca/links_directory/Website providing access to programs described in the Web Server Issues of the journal: “Nucleic Acids Research” and to some other programs processing protein and peptide sequences
BioMarthttp://www.biomart.org/index.htmlServer providing access to biological databases
Bio-PEPAhttp://homepages.inf.ed.ac.uk/jeh/Bio-PEPA/biopepa.htmlWebsite providing framework for the modelling and analysis of biological systems
BioSharinghttps://biosharing.org/Metabase providing access to databases from the area of life sciences
BioStarhttp://www.biostars.org/Forum concerning bioinformatics
Bio-TDShttp://biotds.org/Metaserver providing access to many programs form the area of chemistry, biochemistry and molecular biology
Biowarehttp://bioware.ucd.ie/~compass/biowareweb/  Website providing access to several programs utilizing protein and peptide sequences
ChEMBLhttps://www.ebi.ac.uk/chembldb/Database of low molecular compounds including peptides
ChemSpiderhttp://www.chemspider.com/Default.aspxDatabase of low molecular compounds including peptides
CheShift-2http://www.cheshift.com/Program predicting chemical shifts from protein or peptide structures and validating predicted structures using NMR data
CPipehttp://cpipe.explora-biotech.com/cpipe/start.pyProgram for prediction of cytesine reactivity and possible functional role.
Dichrocalchttp://comp.chem.nottingham.ac.uk/dichrocalc/Program for prediction of circular dichroism spectra
EBI Search Enginehttps://www.ebi.ac.uk/Program for screening databases provided by European Bioinformatics Institute. Proteins and peptides are among of compounds annotated in database.
FoldAmyloidhttp://antares.protres.ru/fold-amyloid/oga.cgiProgram for amyloid propensity prediction
GOBLEThttp://www.mygoblet.org/Website for bioinformatics education
Heatmapperhttp://www.heatmapper.ca/Program for display data and results as heat maps
Hyperlink Management Systemhttp://biodb.jp/Server providing access to biological databases e.g. protein resources
IBIVUhttp://www.ibi.vu.nl/Server providing access to programs aligning amino acid sequences, predicting secondary structures as well as other bioinformatics tools
IMTECH Serverhttp://www.imtech.res.in/raghava/Server giving Access to bioinformatics tool designed in IMTECH, Chandigargh, India
iScienceSearch  http://www.isciencesearch.com/index.htmlProgram finding information about chemical compounds (including peptides)in chemical databases. Enables text search, input of peptide sequences or structures drawn using molecule editor.
KEGGhttp://www.genome.jp/kegg/Database of genes, proteins, enzymes, metabolic pathways and compounds, including peptides
LabWormhttps://labworm.com/Website providing access to databases and other bioinformatics tools, e.g. concerning proteins and peptides
MetaBasehttp://metadatabase.org/wiki/Main_PageThe wiki-metaserver providing access to biological databases
MetaComBiohttp://www.uwm.edu.pl/metachemibio/index.php/about-metacombioMetabase of low-molecular weight chemical compounds, including peptidees. Peptides are annotated using chemical codes.
Metal Detectorhttp://metaldetector.dsi.unifi.itProgram predicting potential sites of metal binding.
myExperimenthttp://wiki.myexperiment.org/index.php/Main_PageWebsite supporting social sharing of bioinformatics workflows
NAR Collectionhttp://www.oxfordjournals.org/our_journals/nar/database/c/Website providing access to biological databases described in the Nucleic Acids Research
NCBI Taxonomy databasehttp://www.ncbi.nlm.nih.gov/taxonomyDatabase of species of living organisms
NRPSsphttp://www.nrpssp.com/execute.phpProgram predicting presence of nonribosomal peptides synthase adenylation domains in protein sequences
OLShttps://ebi.ac.uk/ols/ontologies/Ontology lookup service
OMICtoolshttp://omictools.com/sp.com/execute.phpMetaserver providing access to biological and chemical databases and programs, e.g. concerning peptides
Ontobeehttp://www.ontobee.org/Database of biological, chemical and other ontology
PepSMIhttps://www.novoprolabs.com/tools/convert-peptides-to-smile-stringProgram converting peptide sequences into SMILES representations
PlifePredhttps://webs.iiitd.edu,in/raghava/plifepred/file_mod.phpProgram predicting peptide half-life in blood
PLIPhttps://projects.biotec.tu-dresden.de/plip-web/plip/indexProgram for screening Protein Data Bank for information about protein-ligand interactions. Peptides are included among ligands
POSSUMhttp://possum.erc.monash.edu/Program for generation PSSM sequence features
PubChemhttp://pubchem.ncbi.nlm.nih.govDatabase of low molecular compounds including peptides
PVShttp://imed.med.ucm.es/PVS/Program designed to measure site variability in groups of protein sequences. Accepts also peptide sequences as a queries.
SCOWLPhttp://www.scowlp.org/scowlp/Database of protein domains interacting with ligands, e.g. with peptides
The Peptide Resource Pagehttp://www.peptideresource.com/Website providing information about peptides as well as access to some bioinformatics tools
Tools and Data Services Registryhttps://bio.tools/Metaserver enabling access to databases and other bioinformatics tools, e.g. concerning peptides
WABIhttp://www.xml.nig.ac.jp/index.htmlWeb server enabling searching in biological databases