FAMSD: A Powerful Protein Modeling Platform that Combines Alignment Methods, Homology Modeling, 3D Structure Quality Estimation and Molecular Dynamics
-
- Kanou Kazuhiko
- School of Pharmacy, Kitasato University
-
- Iwadate Mitsuo
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University
-
- Hirata Tomoko
- School of Pharmacy, Kitasato University
-
- Terashi Genki
- School of Pharmacy, Kitasato University
-
- Umeyama Hideaki
- School of Pharmacy, Kitasato University
-
- Takeda-Shitaka Mayuko
- School of Pharmacy, Kitasato University
この論文をさがす
抄録
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.
収録刊行物
-
- CHEMICAL & PHARMACEUTICAL BULLETIN
-
CHEMICAL & PHARMACEUTICAL BULLETIN 57 (12), 1335-1342, 2009
公益社団法人 日本薬学会
- Tweet
キーワード
詳細情報 詳細情報について
-
- CRID
- 1390001204170887936
-
- NII論文ID
- 130000124531
-
- NII書誌ID
- AA00602100
-
- ISSN
- 13475223
- 00092363
-
- NDL書誌ID
- 10455062
-
- 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