AlphaFold of protein structures
ArchSchema for domain architecture display
BSBB program version screening Protein Data Bank and displaying structures of proteins similar to this submitted as a  query
ConSurf revealing conserved fragments in proteins
Database on Demand generating databases of peptides for application in proteomic studies
DeepGoWeb predicting protein function from sequence
FMODB annotating results of quantum mechanics calculations for proteins
Geomfinder comparing three-dimensional patterns in protein structures
HT-SAShttp://htsas.ibb.waw.plProgram displaying Medline keywords and abstracts attributed to query protein sequence and its homologs
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 protein resources
iLearnPlus predicting protein features on the basis of amino acid sequences
IMTECH Server providing access to bioinformatics tool designed in IMTECH, Chandigargh, India
InterPro of protein families
MarkUs designed  for finding of sequence-structure-function relationship
MisPred of mispredicted protein sequences together with search engine
Mol*Viewer for visualization of protein structures acquired from Protein Data Bank.
National Center for Biotechnology Information database of protein sequences, contains also tools for sequence alignments and homology searching
NCBI Peptidome of fragments used for protein indentification via mass spectrometry (proteotypic peptides)
PconsFamDatabase of structure predictions of protein families from Pfam database.
PDBPaint for visualization of protein structures from Protein Data Bank and annotated as pdb files
Pfam of protein families
PICR Identifier Cross-Referencing – program screening several protein sequence databases
Pôle Bioinformatique Lyonnais/NPS@ with the access to many programs able to process peptide sequences: e.g. constructing multiple alignments between sequences, secondary structure prediction calculating amino acids composition and profiles of physico-chemical features.
Protein Data Bank of protein structures
Protein Naming Utility database for protein nomenclature
Proteopedia containing structural information concerning proteins and other biomolecules
ProViz for visualization of protein structural and evolutionary features
SuperLooper2 designed for prediction loop structures in proteins
SpeeDB for Protein Data Bank screening using structural features as a query
UniProt (SwissProt/TrEMBL)
Major database of protein sequences. Some biologically active fragments of proteins are also annotated. Website contains tools for secondary structure prediction, binary and multiple alignments and calculation of physico-chemical features. Contains also computational tools enabling protein and peptide identification using mass spectrometry
University College of London for protein annotation and modeling
WABI server enabling searching in databases concerning information about proteins via keywords and amino acid sequences using programs finding sequence alignments (BLAST, MAFFT, FASTA)