title: A method for computing the inter-residue interaction potentials for reduced amino acid alphabet.
abstract: Inter-residue potentials are extensively used in the design and evaluation of protein structures. However,dealing with all (20 x 20) interactions becomes computationally difficult 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 x 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.
authors.affiliation: Department of Biotechnology, Indian Institute of Technology-Guwahati, Guwahati 781 039, India.
authors.forename: Abhinav
authors.initials: A
authors.lastname: Luthra
authors.forename: Anupam Nath
authors.initials: AN
authors.lastname: Jha
authors.forename: G K
authors.initials: GK
authors.lastname: Ananthasuresh
authors.forename: Saraswathi
authors.initials: S
authors.lastname: Vishveswara
mesh_terms: D000596:Amino Acids / Q000737:chemistry / Q000378:metabolism*; D019295:Computational Biology / Q000379:methods*; D010449:Peptide Mapping; D011237:Predictive Value of Tests; D011506:Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D020539:Sequence Analysis, Protein; D013816:Thermodynamics
chemical_list: D000596:Amino Acids; D011506:Proteins