Proteomics prediction of protein structures

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. 

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A number of Web sites offer services in the secondary structure predictions of proteins using different approaches with varied accuracy. The Secondary structure prediction of ExPASy Proteomic tools (http //www.expasy.ch/tools/) provides pointers to different Web servers for predicting secondary structures of proteins. The ProtScale of ExPASy Proteomic tools produces conformational profiles by plotting statistical scales of various parameters (e.g., Chou and Fasman s conformational propensities, Levitt s conformational parameters) against residue positions. 

Structural genomics is the process of deter-miningthe three-dimensional structures of an organism s proteome (60). Predictions of protein function can be attempted from knowledge of the structure alone, or the additional information gained can be used to inform sequence-based methods of functional prediction (61). 

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. 

Z. Dosztanyi and P. Tompa, Prediction of Protein Disorder , in Methods in Molecular Biology (Totowa, NJ, United States), eds. B. Kobe, M. Guss and Th. Huber, Humana Press Inc, 2008, vol. 426, Structural Proteomics, p. 103. 

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