Luthra, Abhinav and Jha, Anupam Nath and Ananthasuresh, GK and Vishveswara, Saraswathi (2007) A method for computing the inter-residue interaction potentials for reduced amino acid alphabet. In: Journal of Biosciences, 32 (5). pp. 883-889.
Inter-residue potentials are extensively used in the design and evaluation of protein structures. However, dealing with all (20×20) interactions becomes computationally diffi cult in extensive investigations. Hence, it is desirable to reduce the alphabet of 20 amino acids to a smaller number. Currently, several methods of reducing the residue types exist; however a critical assessment of these methods is not available. Towards this goal, here we review and evaluate different methods by comparing with the complete (20×20) matrix of Miyazawa-Jernigan potential, including a method of grouping adopted by us, based on multi dimensional scaling (MDS). The second goal of this paper is the computation of inter-residue interaction energies for the reduced amino acid alphabet, which has not been explicitly addressed in the literature until now. By using a least squares technique, we present a systematic method of obtaining the interaction energy values for any type of grouping scheme that reduces the amino acid alphabet. This can be valuable in designing the protein structures.
|Item Type:||Journal Article|
|Additional Information:||Copyright of this article belongs to Indian Academy of Science.|
|Department/Centre:||Division of Biological Sciences > Molecular Biophysics Unit
Division of Mechanical Sciences > Mechanical Engineering
|Date Deposited:||31 Jul 2008|
|Last Modified:||19 Sep 2010 04:48|
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