NameLinkDescription
AlphaFoldhttps://alphafold.ebi.ac.uk/Database of protein structures
ArchSchemahttp://www.ebi.ac.uk/Tools/archschema/Program for domain architecture display
BSBBhttp://bioserver1.physics.iisc.ernet.in/bssb/BLAST program version screening Protein Data Bank and displaying structures of proteins similar to this submitted as a  query
ConSurfhttp://consurf.tau.ac.il/2016/Program revealing conserved fragments in proteins
Database on Demandhttp://www.ebi.ac.uk/pride/dodProgram generating databases of peptides for application in proteomic studies
DeepGoWebhttps://deepgo.cbrc.kaust.edu.sa/deepgo/Program predicting protein function from sequence
FMODBhttps://drugdesign.riken.jp/FMODB/Database annotating results of quantum mechanics calculations for proteins
Geomfinderhttp://appsbio.utalca.cl/geomfinder/Program 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 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 protein resources
iLearnPlushttps://ilearnplus.erc.monash.edu/Program predicting protein features on the basis of amino acid sequences
IMTECH Serverhttp://www.imtech.res.in/raghava/Server providing access to bioinformatics tool designed in IMTECH, Chandigargh, India
InterProhttp://www.ebi.ac.uk/interpro/Database of protein families
MarkUshttp://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:Mark-UsServer designed  for finding of sequence-structure-function relationship
MisPredhttp://mispred.enzim.hu/Database of mispredicted protein sequences together with search engine
Mol*Viewerhttps://molstar.org/Progrm for visualization of protein structures acquired from Protein Data Bank.
National Center for Biotechnology Informationhttp://www.ncbi.nlm.nih.gov/guide/proteins/Major database of protein sequences, contains also tools for sequence alignments and homology searching
NCBI Peptidomehttp://www.ncbi.nlm.nih.gov/peptidomeDatabase of fragments used for protein indentification via mass spectrometry (proteotypic peptides)
PconsFamDatabase of structure predictions of protein families from Pfam database.
PDBPainthttp://cbdm.mdc-berlin.de/~pdbpaint/Program for visualization of protein structures from Protein Data Bank and annotated as pdb files
Pfamhttp://pfam.xfam.org/Database of protein families
PICRhttp://www.ebi.ac.uk/Tools/picrProtein Identifier Cross-Referencing – program screening several protein sequence databases
Pôle Bioinformatique Lyonnais/NPS@http://pbil.univ-lyon1.fr/Server 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 Bankhttp://www.wwpdb.org/Database of protein structures
Protein Naming Utilityhttp://www.jcvi.org/pn-utility/web/smarty_wrapper/about.phpRules database for protein nomenclature
Proteopediahttp://www.proteopedia.org/wiki/index.php/Main_PageWebsite containing structural information concerning proteins and other biomolecules
ProVizhttp://proviz.ucd.ie/Program for visualization of protein structural and evolutionary features
SuperLooper2http://proteinformatics.charite.de/ngl-tools/sl2/start.phpProgram designed for prediction loop structures in proteins
SpeeDBhttp://www.parallelcomputing.ca/Program for Protein Data Bank screening using structural features as a query
UniProt (SwissProt/TrEMBL)http://www.expasy.org
http://beta.uniprot.org/		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 Londonhttp://bioinf.cs.ucl.ac.uk/Server for protein annotation and modeling
WABIhttp://cyclamen.ddbj.nig.ac.jp/newsoap9/ http://www.xml.nig.ac.jp/index.htmlWeb server enabling searching in databases concerning information about proteins via keywords and amino acid sequences using programs finding sequence alignments (BLAST, MAFFT, FASTA)