A method for computing the inter-residue interaction potentials for reduced amino acid alphabet
| Autor: | Saraswathi Vishveswara, Abhinav Luthra, G. K. Ananthasuresh, Anupam Nath Jha |
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| Rok vydání: | 2007 |
| Předmět: |
chemistry.chemical_classification
Residue (complex analysis) Computer science Mechanical Engineering Computation Computational Biology Proteins General Medicine Interaction energy Molecular Biophysics Unit Peptide Mapping General Biochemistry Genetics and Molecular Biology Amino acid Crystallography Protein structure chemistry Predictive Value of Tests Sequence Analysis Protein Thermodynamics Critical assessment Multidimensional scaling Amino Acids Alphabet General Agricultural and Biological Sciences Algorithm |
| Zdroj: | Journal of Biosciences. 32:883-889 |
| ISSN: | 0973-7138 0250-5991 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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