Protein Function Assignment

Protein Function Assignment

Search Pattern, motif, Profiles domains, families

ScanProsite (Search a protein sequence against PROSITE pattern database at ExPASy, CH)

PPSearch (Search a protein sequence against PROSITE pattern database with graphical output at EBI, UK)

FingerPRINTScan (Search a protein sequence against protein motif fingerprints database PRINTS )

Scansite (Prediction of protein signaling sequence motifs at HIM, Boston, USA)

SearchPfam at Wustl or EBI (Search a protein against Pfam domain/family database)

CD-Search (Search a protein against CDD domain database, including Pfam and SMART, with RPS-BLAST at NCBI, USA)

eMOTIF Search (Assign putative function to new proteins by sequence comparison with IDENTIFY motif database at Stanford University, USA)

PROCAT (Search a protein structure agains the PROCAT database of 3D enzyme active site templates)

Meta-MEME (motive buiding at San Diego Supercomputer Centre, SDSC, Ca, USA)

eMOTIF Maker (Generate motifs that describe protein families or superfamilies ats Stanford University, USA)

Modules (mobile protein domains database)

HSSP (Database of homology-derived structures and sequences of proteins at EBI)

eMATRIX Search (Function prediction by sequence analysis using minimal-risk scoring matrices at Stanford University, USA)

PROSCAN (Search a protein sequence against PROSITE pattern database allowing mismatches at PBIL, Lyon, Fr)

PFSCAN (Search protein against different profile databases at ISREC; also searches PROSITE and Pfam patterns)

BLOCKS Search (Search a protein against BLOCKS database; also searches PRINTS)

DART (Domain Architecture Retrieval Tool at NCBI, USA)

InterProScan or InterPro Search (Search a protein against the integrated protein domains and functional sites database InterPro at EBI, UK)

COGnitor (Search a protein agains the COG database at NCBI)

iProCass 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)

MEME (Multiple EM for Motive Elicitation: Motive discovery at San Diego Supercomputer Centre, SDSC, Ca, USA)

ProDom (Protein domain database at Toulouse, Fr)

DOMO (homologous protein domain families database)

SBASE (Protein domain library at ICGEB, It)

3Motif (Find protein (domain)s with defined 3D motifs at Stanford University, USA (runs only with Netscape and Chime plugin)

GeneQuiz (Automated analysis of protein sequences at EMBL)

Search, computation & analysis of pathways

KEGG (Search and computation tools at KEGG pathway database, Kyoto, Jp)

aMAZE (Query tools for pathway analysis at EBI, UK)

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, Toronto, Canada )

BINDBLAST (Search BIND database with BLAST)

ProNet Online (Database of interacting proteins from Myriad Genetics, US)

BIND (Biomolecular Interaction Network Database at the Samuel Lunenfeld Research Institute Toronto, Canada )

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)

Protein Annotation

PAA (Protein Annotator's Assistant at EBI, UK)

Artemis (Free (large-) DNA sequence viewer and annotation tool at the Sanger Center, UK)

AAT (Analysis and Annotation Tool for finding genes in genomic sequences at Michigan Tech, USA)

AmiGO and other tools (Universal function annotation vocabulary by the Gene Ontology Consortium )