AAindex of indices describing physicochemical properties, sufficient for prediction of peptide properties, e.g. QSAR approach
ANNIE creating protein sequence annotations. Accepts peptide sequences as a queries.
BETASCAN for amyloid propensity prediction
BioCatalogue for registering, browsing and annotating web services in the area of life sciences
BioDBcore providing access to few catalogues of biological databases and to information about current and proposed standards of database description
bioDBnet of biological databases
Bioinformatics Links Directory 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
BioMart providing access to biological databases
Bio-PEPA providing framework for the modelling and analysis of biological systems
BioSharing providing access to databases from the area of life sciences
BioStar concerning bioinformatics
Bio-TDS providing access to many programs form the area of chemistry, biochemistry and molecular biology
Bioware  Website providing access to several programs utilizing protein and peptide sequences
ChEMBL of low molecular compounds including peptides
ChemSpider of low molecular compounds including peptides
CheShift-2 predicting chemical shifts from protein or peptide structures and validating predicted structures using NMR data
CPipe for prediction of cytesine reactivity and possible functional role.
Dichrocalc for prediction of circular dichroism spectra
EBI Search Engine for screening databases provided by European Bioinformatics Institute. Proteins and peptides are among of compounds annotated in database.
FoldAmyloid for amyloid propensity prediction
GOBLET for bioinformatics education
Heatmapper for display data and results as heat maps
Hyperlink Management System providing access to biological databases e.g. protein resources
IBIVU providing access to programs aligning amino acid sequences, predicting secondary structures as well as other bioinformatics tools
IMTECH Server giving Access to bioinformatics tool designed in IMTECH, Chandigargh, India
iScienceSearch finding information about chemical compounds (including peptides)in chemical databases. Enables text search, input of peptide sequences or structures drawn using molecule editor.
KEGG of genes, proteins, enzymes, metabolic pathways and compounds, including peptides
LabWorm providing access to databases and other bioinformatics tools, e.g. concerning proteins and peptides
MetaBase wiki-metaserver providing access to biological databases
MetaComBio 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.
myExperiment supporting social sharing of bioinformatics workflows
NAR Collection providing access to biological databases described in the Nucleic Acids Research
National Genomics Data center metabase
NCBI Taxonomy database metabase
NRPSsp predicting presence of nonribosomal peptides synthase adenylation domains in protein sequences
OLS lookup service
OMICtools providing access to biological and chemical databases and programs, e.g. concerning peptides
Ontobee of biological, chemical and other ontology
PepSMI converting peptide sequences into SMILES representations
PlifePred,in/raghava/plifepred/file_mod.phpProgram predicting peptide half-life in blood
PLIP for screening Protein Data Bank for information about protein-ligand interactions. Peptides are included among ligands
POSSUM for generation PSSM sequence features
PubChemhttp://pubchem.ncbi.nlm.nih.govDatabase of low molecular compounds including peptides
PVS designed to measure site variability in groups of protein sequences. Accepts also peptide sequences as a queries.
SCOWLP of protein domains interacting with ligands, e.g. with peptides
The Peptide Resource Page providing information about peptides as well as access to some bioinformatics tools
Tools and Data Services Registry enabling access to databases and other bioinformatics tools, e.g. concerning peptides
Venny for construction of Venn diagrams
WABI server enabling searching in biological databases