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

Databases of protein domains and families

UniProt - the universal protein resource (including UniProtKB -Swiss-Prot and TrEMBL-, UniRef, UniParc) Around UniProtKB - links to related databases and portals HAMAP - Portal to microbial UniProtKB/Swiss-Prot entries SwissVar - Portal to human diseases and variant information in UniProtKB/Swiss-Prot UniPathway - Metabolic pathways database ViralZone - Portal to viral UniProtKB/Swiss-Prot entries HPI - Human Proteomics Initiative PPAP - Plant Proteome Annotation Project Tox-Prot - Toxin Annotation Project 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 Resources of Proteins Domains and Functional Sites PROSITE - Database of protein families and domains BLOCKS - BLOCKS db Gene3D - Structural and Functional Annotation of Protein Families Panther - Functional classification system Pfam - Protein families db (HMM derived) [Mirrors at JFRC (USA), CCBB (South Korea) Institute, UK, Karolinska Institutet (Sweden)] PIRSF - Protein classification system PRINTS - Protein Motif fingerprint db ProDom - Protein domain db (Automatically generated) SBASE - SBASE domain db SMART - Simple Modular Architecture Research Tool SUPERFAMILY - Library of profile HMMs representing all proteins of known structure STRING - Search Tool for the Retrieval of Interacting Genes/Proteins TIGRFAMs - TIGR protein families db BIND - Biomolecular Interaction Network Database DIP - Database of Interacting Proteins MINT - Molecular INTeraction database HPRD - Human Protein Reference Database IntAct BioGRID - General Repository for Interaction Dataset PPI - JCB Protein-Protein Interaction Website PMD - Protein Mutant db

Pattern and profile searches

InterPro Scan - Integrated search in PROSITE, Pfam, PRINTS and other family and domain databases Hits - Relationships between protein sequences and motifs ScanProsite - Scans a sequence against PROSITE or a pattern against the UniProt Knowledgebase (Swiss-Prot and TrEMBL) HamapScan - Scans a sequence against the HAMAP families MotifScan - Scans a sequence against protein profile databases (including PROSITE) Pfam HMM search - Scans a sequence against the Pfam protein families db [At Washington University or at Sanger Centre] ProDom - Compares sequences 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 3of5 - Complex Pattern Search - e.g. to search for a motif with 3 basic AA in 5 positions ELM - Eukaryotic Linear Motif resource for functional sites in proteins PRATT - Interactively generates conserved patterns from a series of unaligned proteins; [at EBI / ExPASy ] PPSEARCH - Scans a sequence against PROSITE (allows a graphical output); at EBI PROSITE scan - Scans a sequence against PROSITE (allows mismatches); at PBIL PATTINPROT - Scans a protein sequence or a protein database for one or several pattern(s); at PBIL SMART - Simple Modular Architecture Research Tool; at EMBL TEIRESIAS - Generate patterns from a collection of unaligned protein or DNA sequences; at IBM 9aaTAD - Prediction of Nine Amino Acid Transactivation Domain