[Databases of protein domains and families]   [Pattern and profile searches]

Databases of protein domains and families
  • PROSITE - Database of protein families and domains
  • UniProt - the universal protein resource (includes UniProtKB, UniRef, UniParc)
  • Around UniProtKB - links to related databases and portals
    • HAMAP - UniProtKB family classification and annotation
    • SwissVar - Portal to human UniProtKB/Swiss-Prot variants implied in diseases
    • ViralZone - Portal to viral UniProtKB/Swiss-Prot entries
    • CPAP - Chordata (includes human) Protein Annotation Program
    • PPAP - Plant Protein Annotation Program
    • Tox-Prot - Animal toxin annotation program
  • neXtProt - A knowledge platform dedicated to human proteins
  • Swiss Human Plasma protein dataset - Novartis/Geneprot MicroProt2 dataset from Human Plasma samples
  • NCBI protein resources

  • InterPro - Integrated database of protein domains and functional sites
  • CDD - The Conserved Domain Database: A resource for the annotation of functional units in proteins
  • CATH / Gene3D - A resource that provides information on the evolutionary relationships of protein domains
  • Panther - Functional classification system of genes
  • Pfam - Database of protein families (HMM derived)
  • PIRSF - Protein classification system based on whole proteins
  • SMART - Simple Modular (protein) Architecture Research Tool
  • SUPERFAMILY - Database of profile HMMs representing all proteins of known structure
  • STRING - Search Tool for the Retrieval of Interacting Genes/Proteins
  • TIGRFAMs - Database of protein families, featuring curated multiple sequence alignments, hidden Markov models (HMMs) and annotation

  • DIP - Database of Interacting Proteins
  • MINT - Molecular INTeraction database
  • HPRD - Human Protein Reference Database
  • IntAct - Database system and analysis tools for protein interaction data
  • BioGRID - Biological General Repository for Interaction Dataset
  • PPI - The Jena Protein-Protein Interaction Website

Pattern and profile searches
  • ScanProsite - Scan proteins for matches against the PROSITE collection of motifs as well as against your own patterns
  • InterPro Scan - Integrated search in PROSITE, Pfam, HAMAP, PRINTS and the other InterPro databases
  • Hits - Relationships between protein sequences and motifs
  • HAMAP-Scan - Scans several protein sequences or a whole genome against HAMAP profiles
  • MotifScan - Scans a sequence against several protein profile databases (including PROSITE)
  • HMMER - Biosequence analysis using profile hidden Markov Models
  • SUPERFAMILY Sequence Search - Assign SCOP domains to your sequences using the SUPERFAMILY hidden Markov models
  • 3of5ComplexPatternSearch - e.g. to search a sequence with a motif with 3 basic AA in 5 positions
  • ELM - Eukaryotic Linear Motif resource for scanning a sequence against functional site motifs
  • PRATT - Interactively generates conserved patterns from a series of unaligned proteins
  • PPSEARCH - Scans a sequence against all PROSITE patterns (allows a graphical output) (at EBI)
  • PATTINPROT - Scans a protein sequence or a protein database against one or several pattern(s) (at PBIL)
  • SMART - Simple Modular Architecture Research Tool (at EMBL)