Proteomics is the prediction of protein structures by using computational technologies. Computation proteome annotation is the process of proteome database mining, which includes structure or fold prediction and functionality assignment. Here in this review methodologies of secondary structure prediction and problems of protein folding are discussed. Secondary structure predictions and pattern or fold recognition of proteins using the Internet resources are described. The enormous structural diversity of proteins begins with different amino acid sequences (primary structure) of polypeptide chains that fold into complex 3Dstructures. The final folded arrangement of the polypeptide chain is referred to as its conformation (secondary and tertiary structures). However, a special class of proteins known as chaperons is required to facilitate in vivo folding of a protein to form its native conformation. Although experimental determination of protein three-dimensional structure has become more efficient, the gap between the number of known sequences and the number of known structures is rapidly increasing. Protein structure prediction aims at reducing this sequence-structure gap Methods for abstracting protein structures from their sequences can be aimed at secondary structures or 3D structures (folding problems).There are four approaches to secondary structure prediction 1. Empirical statistical methods that use parameters derived from known 3D structures 2. Methods based on physicochemical properties of amino acid residues such as volume, exposure, hydrophobicity or hydrophilicity, charge, hydrogen bonding potential, and so on. 3. Methods based on prediction algorithms that use known structures of homologous proteins to assign secondary structures 4. Molecular mechanical methods that use force field parameters to model and assign secondary structures
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