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A method for computing the inter-residue interaction potentials for reduced amino acid alphabet

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.


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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
Publication: Journal of Biosciences
Publisher: Indian Academy of Science
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
URI: http://eprints.iisc.ac.in/id/eprint/15354

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