Method for Predicting Homology Modeling Accuracy from Amino Acid Sequence Alignment: the Power Function
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概要
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We have devised a power function (PF) that can predict the accuracy of a three-dimensional (3D) structure model of a protein using only amino acid sequence alignments. This Power Function (PF) consists of three parts; (1) the length of a model, (2) a homology identity percent value and (3) the agreement rate between PSI-PRED secondary structure prediction and the secondary structure judgment of a reference protein. The PF value is mathematically computed from the execution process of homology search tools, such as FASTA or various BLAST programs, to obtain the amino acid sequence alignments. There is a high correlation between the global distance test-total score (GDT_TS) value of the protein model based upon the PF score and the GDT_TSMAX value used as an index of protein modeling accuracy in the international contest Critical Assessment of Techniques for Protein Structure Prediction (CASP). Accordingly, the PF method is valuable for constructing a highly accurate model without wasteful calculations of homology modeling that is normally performed by an iterative method to move the main chain and side chains in the modeling process. Moreover, a model with higher accuracy can be obtained by combining the models ordered by the PF score with models sorted by the size of the CIRCLE score. The CIRCLE software is a 3D–1D program, in which energetic stabilization is estimated based upon the experimental environment of each amino acid residue in the protein solution or protein crystals.
著者
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Kamiya Kohei
Dep. Of Pharmacognosy And Natural Product Chemistry Fac. Of Pharmaceutical Sciences Kobe Gakuin Univ
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Iwadate Mitsuo
Department Of Biotechnology Tokyo University Of Agriculture And Technology
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Kanou Kazuhiko
Department of Biomolecular Design, School of Pharmaceutical Sciences, Kitasato University
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Terashi Genki
Department of Biomolecular Design, School of Pharmaceutical Sciences, Kitasato University
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Umeyama Hideaki
Department of Biomolecular Design, School of Pharmaceutical Sciences, Kitasato University
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Takeda-Shitaka Mayuko
Department of Biomolecular Design, School of Pharmaceutical Sciences, Kitasato University
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UMEYAMA HIDEAKI
Department of Biological Sciences, Chuo University
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IWADATE MITSUO
Department of Biological Sciences, Chuo University
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Iwadate Mitsuo
Department of Biological Sciences, Faculty of Science and Engineering, Chuo University
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IWADATE MITSUO
Department of Biological Science, Chuo University
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