Method for Predicting Homology Modeling Accuracy from Amino Acid Sequence Alignment: the Power Function

• Iwadate Mitsuo

  Department of Biological Sciences, Faculty of Science and Engineering, Chuo University

• Kanou Kazuhiko

  Department of Biomolecular Design, School of Pharmaceutical Sciences, Kitasato University

• Terashi Genki

  Department of Biomolecular Design, School of Pharmaceutical Sciences, Kitasato University

• Umeyama Hideaki

  Department of Biomolecular Design, School of Pharmaceutical Sciences, Kitasato University

• Takeda-Shitaka Mayuko

  Department of Biomolecular Design, School of Pharmaceutical Sciences, Kitasato University

抄録

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_TS_MAX 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.

収録刊行物

• ＣＨＥＭＩＣＡＬ　＆　ＰＨＡＲＭＡＣＥＵＴＩＣＡＬ　ＢＵＬＬＥＴＩＮ

  ＣＨＥＭＩＣＡＬ　＆　ＰＨＡＲＭＡＣＥＵＴＩＣＡＬ　ＢＵＬＬＥＴＩＮ 58 (1), 1-10, 2010

  公益社団法人 日本薬学会

キーワード

• power function
• comparative modeling
• homology modeling
• protein modeling accuracy

詳細情報

• CRID: 1390282679146507264
• NII論文ID: 130000140755
• NII書誌ID: AA00602100
• DOI: 10.1248/cpb.58.1
• ISSN: 13475223
• ISSN: 00092363
• NDL書誌ID: 10497744
• Web Site: https://ndlsearch.ndl.go.jp/books/R000000004-I10497744
• Web Site: http://www.jstage.jst.go.jp/article/cpb/58/1/58_1_1/_pdf
• 本文言語コード: en
• データソース種別:
  • JaLC
  • NDL
  • Crossref
  • CiNii Articles
• 抄録ライセンスフラグ: 使用不可