Understanding Tools and Techniques in Protein Structure Prediction

Abstract

Protein structure prediction is an important area of protein science. Every protein has a primary structure, its sequence; a secondary structure, the helices and sheets; tertiary structure, the fold of the protein; and for some, the quaternary structure, multimeric formation of its polypeptide subunits. Protein structure has been experimented for the past several decades by physical and chemical methods. The dawn of protein sequencing began early in 1950s upon complete sequencing of insulin and then, ribonuclease. A key step towards the rapid increase in the number of sequenced proteins by 1980s was the development of automated sequencers followed by advances in mass spectrometry for structure identities. Structural knowledge is vital for complete understanding of life at the molecular level. An understanding of protein structure can lead to derivation of functions and mechanisms of their action. Bioinformatics is a novel approach in recent investigations on sequence analysis and structure prediction of proteins. With the advent of bioinformatics, it has been made possible to understand the relationship between amino acid sequence and three-dimensional structure in proteins. The central challenge of bioinformatics is the rationalization of the mass of sequence information not only to derive efficient means of storage and retrieval of sequence data, but also to design more analysis tools. Thus, there is a continual need to convert sequence information into biochemical and biophysical knowledge; to decipher the structural, functional and evolutionary clues encoded in the language of biological sequences (Attwood & Parry-Smith, 2003). Protein sequence information is stored in databases made available in the public domain to access, analyse and retrieve sequence and structural data. In general, protein databases may be classified as Primary and Secondary databases, composite protein pattern databases and structure classification databases. Primary and secondary databases address different aspects of protein analysis, because they store different levels of protein information. Primary databases are the central repositories of protein sequences, while secondary databases are based on the analysis of sequences of the primary ones. Composite protein pattern databases have emerged with a view to create a unified database of protein families. Protein structure classification databases have been established based on the structural similarities and common evolutionary origins of proteins. A number of tools are also