| Databases of protein domains and families |
- PROSITE - Database of protein families and domains
- UniProt - the universal protein resource (includes UniProtKB, UniRef, UniParc)
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Around UniProtKB - links to related databases and portals
- HAMAP - Portal to UniProtKB microbial families
- SwissVar - Portal to human UniProtKB/Swiss-Prot variants implied in diseases
- UniPathway - Resource for the exploration and annotation of metabolic pathways
- 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
- PROSITE - Database of protein families and domains
- InterPro - Integrated database of protein domains and functional sites
- BLOCKS - BLOCKS database (N.B. not updated since 2008)
- Gene3D - Structural and functional annotation of protein families
- Panther - Functional classification system of genes
- Pfam - Database of protein families (HMM derived)
- PIRSF - Protein classification system based on whole proteins
- PRINTS - Database of protein fingerprints (goups of conserved motifs)
- ProDom - Database of protein domains automatically generated from UniProtKB
- SBASE - Database of protein domain sequences and related computational tools
- 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
- PROSITE - Database of protein families and domains
- 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
- PMD - Protein Mutant Database (last modified March 2007)
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| 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)
- Pfam HMM search - Scans a sequence against the Pfam protein family HMMs
- ProDom - Compares a sequence with ProDom search utility
- SUPERFAMILY Sequence Search - Assign SCOP domains to your sequences using the SUPERFAMILY hidden Markov models
- FingerPRINTScan - Scans a protein sequence against the PRINTS Protein Fingerprint Database
- 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)
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