Useful links for protein identification

Summary of services that can be used for protein identification by database searching using mass and sequence data

This summary of useful services was compiled for use in the Advanced Lab Course in Protein Chemistry (Neurochemistry Group, Chris Weise) for rapid protein identification using peptide mass and protein sequence data obtained using mass spectrometric methods and/or N-terminal sequencing (Edman degradation).

Compiled by Chris Weise (last up-date March 06, 2003)

_{A First Choice of Tools}

Proteomic Tools at ExPASy
Searching, Browsing and Analysis Tools at EBI (EMBL European Bioinformatics Institute, Hinxton Hall, UK)
ConSurf (Server for the Identification of Functional Regions in Proteins by Surface-Mapping of Phylogenetic Information)
Brenda (Enzyme Information System)

Mass Searches (Input: MS data)

ProFound (Searches based on Mass Spectrometry Data)
Matrix Science Mascot (Searches based on Mass Spectrometry Data, generally very fast!)
ProteinProspector (Searches based on Mass Proteometry Data)
MOWSE at the HGMP-RC (Searches based on Peptide Masses)
Peptide Mass (Calculates mass from a sequence)

Sequence Similarity Searches (Input: Protein sequence data)

Blast: Running a Blast search at the NCBI
Prospector MS-Pattern: Search for a precise short sequence (option: mismatches allowed)
EBI: Database Searching, Browsing and Analysis Tools

EMBL: (link mentioned above)

Peptide Search: Protein identification by peptide mapping or peptide sequencing
PROPSEARCH: Compositional search using a sequence
BLAST2: Advanced BLAST2 Search Server

PatScan: Pattern scan of proteins or nucleotides

Major Public Institutions (Computational Services and Sequence Databases)

SWISS-PROT(Annotated Protein Sequences) + TREMBL
FlyBase (The Drosophila Genome)
EBI: European Bioinformatics Institute
EMBL: European Molecular Biology Laboratory
MIPS: Munich Information Center for Protein Sequences (Max-Planck-Institut für Biochemie in Martinsried)
NCBI: National Center for Biotechnology Information
Weizmann Institute of Science: Bioinformatics and Biological Computing

Databases of Structural Protein Properties

DOMO: Database of homologous protein domains.
PRODOM: The protein domain database
PROSITE: Database of protein families and domains
PDB: The Protein Data Bank (get a PDB structure)
PFAM: Protein families database of alignments and HMMs (Hidden Markov Models)
SCOP: Structural Classification of Proteins

Catalogues of Databases

INFOBIOGEN DBCAT: The Public Catalogue of Databases
SRS:Sequence Retrieval System Network Browser for Databanks in Molecular Biology

Further Information

Human Genome Project:

General Information

Proteome Research:

Proteomic databases: Human 2-D PAGE Databases for proteome analysis in health and disease
book contents: New Frontiers in Functional Genomics (Edited by M.R.Wilkins, K.L.Williams, R.D.Appel & D.F.Hochstrasser)

back to the main page