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a search for energy minimized sequences of proteins有哪些信誉好的足球投注网站能量最小化的蛋白质序列
A Search for Energy Minimized Sequences of Proteins 1 2 1 Anupam Nath Jha , G. K. Ananthasuresh *, Saraswathi Vishveshwara * 1 Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India, 2 Department of Mechanical Engineering, Indian Institute of Science, Bangalore, India Abstract In this paper, we present numerical evidence that supports the notion of minimization in the sequence space of proteins for a target conformation. We use the conformations of the real proteins in the Protein Data Bank (PDB) and present computationally efficient methods to identify the sequences with minimum energy. We use edge-weighted connectivity graph for ranking the residue sites with reduced amino acid alphabet and then use continuous optimization to obtain the energy-minimizing sequences. Our methods enable the computation of a lower bound as well as a tight upper bound for the energy of a given conformation. We validate our results by using three different inter-residue energy matrices for five proteins from protein data bank (PDB), and by comparing our energy-minimizing sequences with 80 million diverse sequences that are generated based on different considerations in each case. When we submitted some of our chosen energy-minimizing sequences to Basic Local Alignment Search Tool (BLAST), we obtained some sequences from non- redundant protein sequence database that are similar to ours with an E-value of the order of 10-7. In summary, we conclude that proteins show a trend towards minimizing energy in the sequence space but do not seem to adopt the global energy- minimizing sequence. The reason for this could be either that the existing energy matrices are not able to accurately
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