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Home » 2011 » August » 11 » Tools For Protein Function Assignment
8:54 PM
Tools For Protein Function Assignment

Tools for protein function assignment
  1. Scan or search for patterns, motifs, profiles, domains, families
    • ScanProsite (Scan a protein sequence against PROSITE pattern database at ExPASy, CH)
    • PROSCAN (Scan a protein sequence against PROSITE pattern database allowing mismatches at PBIL, Lyon, Fr)
    • PPSearch (Scan a protein sequence against PROSITE pattern database with graphical output at EBI, UK)
    • PFSCAN (Scan protein against different profile databases at ISREC; also searches PROSITE and Pfam patterns)
    • FingerPRINTScan (Scan a protein sequence against protein motif fingerprints database PRINTS)
    • BLOCKS Search (Scan a protein against BLOCKS database; also searches PRINTS)
    • eMOTIF-Scan (Scan for motifs that describe protein families or superfamilies at Stanford University, USA)
    • Scansite (Prediction of protein signaling sequence motifs at MIT, Cambridge, USA)
    • MEME (Multiple EM for Motive Elicitation: Motive discovery at San Diego Supercomputer Centre, SDSC, Ca, USA)
    • eMotif-maker (Build motifs that describe protein families or superfamilies at Stanford University, USA)
    • Meta-MEME (Buid motif at San Diego Supercomputer Centre, SDSC, Ca, USA)
    • CDART (Conserved Domain Architecture Retrieval Tool at NCBI, USA)
    • SearchPfam at Wustl or EBI (Search a protein against Pfam domain/family database)
    • InterProScan (Search a protein against the integrated protein domains and functional sites database InterPro at EBI, UK)
    • CD-Search (Search a protein against conserved domain database CDD with RPS-BLAST at NCBI, USA)
    • COGnitor (Search a protein agains the COG database at NCBI)
    • iProClass Search (Search a protein against PIR's integrated protein class database at Georgetown University, USA)
    • SMART (Simple Modular Architecture Research Tool at EMBL; also searches Pfam)
    • PROCAT (Search a protein structure agains the PROCAT database of 3D enzyme active site templates)
    • ConSurf (Identification of functional regions in proteins by surface-mapping of phylogenetic information at Tel Aviv University, Israel)
    • ProDom (Automatically generated protein domain database at Toulouse, Fr)
    • Modules (Mobile protein domains database at EMBL)
    • SBASE (Protein domain library at ICGEB, Trieste, It)
    • HSSP (Database of homology-derived structures and sequences of proteins at EBI)
    • 3Motif (Find protein (domain)s with defined 3D motifs at Stanford University, USA (runs only with Chime plugin))
    • eMATRIX Search (Function prediction by sequence analysis using minimal-risk scoring matrices at Stanford University, USA)
    • GeneQuiz (Automated analysis of protein sequences at EMBL)
  2. Search, computation and analysis of pathways
    • KEGG (Search and computation tools at KEGG pathway database, Kyoto, Jp)
    • aMAZE (Query tools for metabolic and signal transduction pathway analysis at ULB, Belgium)
  3. Protein-protein interactions
    • DIP (Search Database of Interacting Proteins at UCLA, USA)
    • PreBIND (Locate biomolecular interaction information in the scientific literature at the Samuel Lunenfeld Research Institute, Canada)
    • BIND (Biomolecular Interaction Network Database at the Samuel Lunenfeld Research Institute, Canada )
    • BINDBLAST (Search BIND database with BLAST)
    • MINT (Molecular INTeraction database at Rome University, It)
    • GRID (General Repository of Interaction Datasets at the Samuel Lunenfeld Research Institute, Canada)
    • PPI viewer (Mammalian protein-protein interaction database and viewer at RIKEN, Japan)
    • STRING (database of predicted functional associations among genes/proteins at the EMBL)
    • InterPrets (Interaction prediction through structure at the EMBL)
  4. Protein Annotation
    • PAA (Protein Annotator's Assistant at EBI, UK)
    • AAT (Analysis and Annotation Tool for finding genes in genomic sequences at Michigan Tech, USA)
    • Artemis (Free (large-) DNA sequence viewer and annotation tool at the Sanger Institute, UK)
    • Gene Ontology tools (Universal function annotation vocabulary by the Gene Ontology Consortium)
  5. Automatic alert for related new sequence
    • PubCrawler (Automated alerting service that scans daily updates to PubMed and GenBank databases at Trinity College Dublin, Ireland)
    • Swiss-Shop (Automatically receive alerts upon new submissions of related protein sequences)
    • New microbial Genomes Notification (Receive notifications by e-mail about new complete genomes in GenBank)

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