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    • Keywords


      Inter-residue potential; multidimensional scaling; protein folding and design; reduced MJ matrix

    • Abstract


      Inter-residue potentials are extensively used in the design and evaluation of protein structures. However, dealing with all (20×20) 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 (20×20) 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.

    • Author Affiliations


      Abhinav Luthra1 Anupam Nath Jha2 G K Ananthasuresh3 Saraswathi Vishveswara2

      1. Department of Biotechnology, Indian Institute of Technology-Guwahati, Guwahati 781 039, India
      2. Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
      3. Department of Mechanical Engineering, Indian Institute of Science, Bangalore 560 012, India
    • Dates

  • Journal of Biosciences | News

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      Posted on July 25, 2019

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