Computation proteome annotation

Computation proteome annotation is the process of proteome database mining, which includes structure/fold prediction and functionality assignment. Methodologies of secondary structure prediction and problems of protein folding are discussed. Approaches to identify functional sites are presented. Protein structure databases are surveyed. Secondary structure predictions and pattern/fold recognition of proteins using the Internet resources are described. 

A. Ceroni, K. Maass, H. Geyer, R. Geyer, A. Dell, and S. M. Haslam, GlycoWorkbench A tool for the computer-assisted annotation of mass spectra of glycans, J. Proteome Res., 7 (2008) 1650-1659. 

Computational proteomics refers to the large-scale generation and analysis of 3D protein structural information. Accurate prediction of protein contact maps is the beginning and essential step for computational proteomics. The major resource for computational proteomics is the currently available information on protein and nucleic acid structures. The 3D-GENOM1CS (www.sbg.bio.ic.au.uk/3dgenomics/) and PDB (http // www.rcsb.org/pdb/), and other databases provide a broad range of structural and functional annotations for proteins from sequenced genomes and protein 3D structures, which make a solid foundation for computational proteomics. 

EMBL Nucleotide Sequence Database. SWISS-PROT consists of core sequence data with minimal redundancy, citation and extensive annotations including protein function, post-translational modifications, domain sites, protein structural information, diseases associated with protein deficiencies and variants. SWISS-PROT and TrEMBL are available at EBI site, http //www.ebi.ac.uk/swissprot/, and ExPASy site, http //www.expasy.ch/sprot/. From the SWISS-PROT and TrEMBL page of ExPASy site, click Full text search (under Access to SWISS-PROT and TrEMBL) to open the search page (Figure 11.3). Enter the keyword string (use Boolean expression if required), check SWISS-PROT box, and click the Submit button. Select the desired entry from the returned list to view the annotated sequence data in Swiss-Prot format. An output in the fasta format can be requested. Links to BLAST, feature table, some ExPASy proteomic tools (e.g., Compute pI/Mw, ProtParam, ProfileScan, ProtScale, PeptideMass, ScanProsite), and structure (SWISS-MODEL) are provided on the page. 

Increasing reproducibility of available separation techniques and sensitivity and affordability of mass spectrometers, as well as the desire and need to automate the identification process, have caused peptide mass fingerprinting and MS/MS sequencing to gain importance and to become the method of choice for many proteomics laboratories. Several tools are available to assist users in the interpretation of mass spectrometry data. Peptldent (http //www.expasy.org/tools/peptident.html) on the ExPASy server follows the concept of the other tools from the ExPASy proteomics suite, in that it takes into account annotation available in the SWISS-PROT/TrEMBL database, in particular as post-translational modifications and processing are concerned. The user can paste peptide masses (monoisotopic or average) into the Peptldent form, but peptide mass data can also be uploaded from a file on the user s local computer. Supported file formats are .pkm ... 

Gattiker, A., Michoud, K., Rivoire, C., et al. (2003) Automated annotation of microbial proteomes in SWISS-PROT. Comput. Biol. Chem. 27, 49-58. 

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