FAMSD: A Powerful Protein Modeling Platform that Combines Alignment Methods, Homology Modeling, 3D Structure Quality Estimation and Molecular Dynamics

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概要

• 論文の詳細を見る

• The prediction of a protein three-dimensional (3D) structure is one of the most important challenges in computational structural biology. We have developed an automatic protein 3D structure prediction method called FAMSD. FAMSD is based on a comparative modeling method which consists of the following four steps: (1) generating and selecting sequence alignments between target and template proteins; (2) constructing 3D structure models based on each selected alignment; (3) selecting the best 3D structure model and (4) refining the selected model. In the FAMSD method, sequence alignment programs such as a series of BLAST programs, SP3 and SPARKS2 programs, the homology modeling program FAMS (Full Automatic Modeling System), the model quality estimation program CIRCLE and the molecular dynamics program APRICOT were used in combination to construct high quality protein models. To assess the FAMSD method we have participated in the 8th Critical Assessment of Techniques for Protein Structure Prediction (CASP8) experiment. The results of our original assessment indicate that the FAMSD method offers excellent capability in packing side-chains with the correct torsion angles while avoiding the formation of atom–atom collisions. Since side-chain packing plays a significant role in defining the biological function of proteins, this method is a valuable resource in biological, pharmaceutical and medicinal research efforts.

• 公益社団法人　日本薬学会の論文

著者

• Kanou Kazuhiko

  School of Pharmacy, Kitasato University

• Hirata Tomoko

  School of Pharmacy, Kitasato University

• Terashi Genki

  School of Pharmacy, Kitasato University

• Takeda-shitaka Mayuko

  School Of Pharmaceutical Sciences Kitasato University

• Kamiya Kohei

  Dep. Of Pharmacognosy And Natural Product Chemistry Fac. Of Pharmaceutical Sciences Kobe Gakuin Univ

• Iwadate Mitsuo

  Department Of Biotechnology Tokyo University Of Agriculture And Technology

• Umeyama Hideaki

  School Of Pharmaceutical Sciences Kitasato University

• IWADATE MITSUO

  Department of Biological Sciences, Chuo University

関連論文

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• Structural Studies of the Interactions of Normal and Abnormal Human Plasmins with Bovine Basic Pancreatic Trypsin Inhibitor
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