A method for computing the inter-residue interaction potentials for reduced amino acid alphabet.
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.
Luthra
Abhinav
A
Department of Biotechnology, Indian Institute of Technology-Guwahati, Guwahati 781 039, India.
Jha
Anupam Nath
AN
Ananthasuresh
G K
GK
Vishveswara
Saraswathi
S
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
D000596:Amino Acids; D011506:Proteins