Proteins are polymers built from 20 different L-alpha-amino acids. Proteins are assembled from amino acids using information present in genes. Genes are transcribed into RNA, RNA is then subject to post-transcriptional modification and control, resulting in a mature mRNA that undergoes translation into a protein. mRNA is translated by ribosomes that match the three-base codons of the mRNA to the three-base anti-codons of the appropriate tRNA. The enzyme aminoacyl tRNA synthetase catalyzes the formation of covalent peptide bonds between amino acids forming the protein.
The two ends of the amino acid chain are referred to as the carboxy terminus (C-terminus) and the amino terminus (N-terminus) based on the nature of the free group on each extremity.
Comparative protein modeling – It uses previously solved structures as starting points, or templates. This is effective because it appears that although the number of actual proteins is vast, there is a limited set of tertiary structural motifs to which most proteins belong. Into 2 more types of modeling :
Identification of homologous interacting pairs – This method consists of searching whether the two sequences have homologues which form a complex in a database of known structures of complexes. Example :- InterPreTS (Interaction Prediction through Tertiary Structure)
Identification of structural patterns (target must be a structure) – The third method builds a library of known protein-protein interfaces from the Protein Data Bank. The sequences in the library are then clustered based on structural alignment and redundant sequences are eliminated. Example :- PRISM
Simons, K. T., Bonneau, R., Ruczinski, I., Baker, D.,(1999) Ab initio protein structure prediction of CASP III targets using ROSETTA, Proteins Suppl 3, 171-6.
Bates, P.A., Kelley, L.A., MacCallum, R.M. and Sternberg, M.J.E., (2001) Enhancement of Protein Modelling by Human Intervention in Applying the Automatic Programs 3D-JIGSAW and 3D-PSSM., Proteins: Structure, Function and Genetics, Suppl 5:39-46.
Tan S.H., Zhang Z., Ng S.K.,(2004) ADVICE: Automated Detection and Validation of Interaction by Co-Evolution.. Nucl. Ac. Res., 32 (Web Server issue):W69-72.
Aloy P.,Russell R.B, InterPreTS: Protein Interaction Prediction through Tertiary Structure., Bioinformatics, 19 (1), 161-162.
Ogmen U., Keskin O., Aytuna A.S., Nussinov R. and Gursoy A,(2005) PRISM: protein interactions by structural matching., Nucl. Ac. Res.,33 (Web Server issue):W331-336.