学会関係
タンパク質立体構造関連
放射光施設
共同研究先など
- 高エネルギー加速器研究機構 構造生物学研究センター（千田俊哉先生）
- 横浜市立大学生命ナノシステム科学研究科構造科学研究室（佐藤衛先生）
- 静岡県立大学薬学部生命物理化学研究室（橋本博先生）
- 大阪大学蛋白質研究所超分子構造解析学研究系（中川敦史先生）
- 熊本大学大学院薬学教育部機能分子構造解析学分野（山縣ゆり子先生）
- 熊本大学環境安全センター（山口佳宏先生）
構造解析プログラム関係
総合
- CCP4 ver. 6.5
- Winn, M. D., Ballard, C. C., Cowtan, K. D., Dodson, E. J., Emsley, P., Evans, P..R., Keegan, R. M., Krissinel, E. B., Leslie, A. G., McCoy, A., McNicholas, S. J., Murshudov, G. N., Pannu, N. S., Potterton, E. A., Powell, H. R., Read, R. J., Vagin, A., Wilson, K. S.
Overview of the CCP4 suite and current developments.
Acta Crystallogr. Sect. D Biol. Crystallogr. 67: 235-242. (2011)
- PHENIX ver. 1.10
- Adams, P. D., Afonine, P. V., Bunkoczi, G., Chen, V. B., Davis, I. W., Echols, N., Headd, J. J., Hung, L. W., Kapral, G. J., Grosse-Kunstleve, R. W., McCoy, A. J., Moriarty, N. W., Oeffner, R., Read, R. J., Richardson, D. C., Richardson, J. S., Terwilliger, T. C. and Zwart, P. H.,
PHENIX: a comprehensive Python-based system for macromolecular structure solution.
Acta Crystallogr. Sect. D Biol. Crystallogr. 66: 213-221. (2010)
回折データ処理
- MOSFLM ver. 7.0.9
- Leslie, A. G. W., Powell, H. R.
Processing Diffraction Data with Mosflm
Evolving Methods for Macromolecular Crystallography245: 41-51. (2007)
- XDS Program Package
- Kabsch, W.
XDS
Acta Crystallogr. Sect. D Biol. Crystallogr. 66: 125-132. (2010)
- DIALS framework
- Waterman, D.G., Winter, G., Parkhurst, J.M., Fuentes-Montero, L., Hattne, J., Brewster, A., Sauter, N.K., Evans, G.
The DIALS framework for integration software
CCP4 Newsl. Protein Crystallogr.49: 16-19. (2013)
位相決定・精密化
- SHELX
- Sheldrick, G. M.
A short history of SHELX.
Acta Crystallogr. Sect. A Found. Crystallogr. 64: 112-122. (2008)
化合物cifデータなど
- HIC-Up
- Kleywegt, G. J.
Crystallographic refinement of ligand complexes.
Acta Crystallogr. Sect. D Biol. Crystallogr. 63: 94-100 (2007)
- PRODRG2 Server
- A. W. Schuettelkopf and D. M. F. van Aalten
PRODRG - a tool for high-throughput crystallography of protein-ligand complexes.
Acta Crystallogr. Sect. D Biol. Crystallogr. 60: 1355-1363 (2004)
モデル構築
- Coot ver. 0.8
- Emsley, P., Lohkamp, B., Scott, W. G., and Cowton, K.
Features and Development of Coot.
Acta Crystallogr. Sect. D Biol. Crystallogr. 66: 486-501. (2010)
- PyMOL ver. 1.7
- The PyMOL Molecular Graphics System, Version 1.4.1, Schrödinger, LLC.
- CueMol
- http://www.cuemol.org/
- Chimera
- Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., and Ferrin, T. E.
UCSF Chimera--a visualization system for exploratory research and analysis.
J. Comput. Chem. 25: 1605-1612 (2004)
その他
- PISA
- Krissinel, E., and Henrick, K.
Inference of macromolecular assemblies from crystalline state.
J. Mol. Biol. 372: 774-797 (2007)
- TLSMD
- TLSMD
Painter, J., and Merritt, E. A.
Optimal description of a protein structure in terms of multiple groups undergoing TLS motion.
Acta Crystallogr. Sect. D Biol. Crystallogr. 62: 439-450 (2006)
- server
Painter, J., and Merritt, E. A.
TLSMD web server for the generation of multi-group TLS models.
J. Appl. Cryst. 39: 109-111. (2006)
- MEGA 5
- Rost, B., Yachdav, G., and Liu, J.
MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods.
Mol. Biol. Evol.28: 2731-2739 (2011)
- PredictProtein
- Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., and Kumar, S.
The PredictProtein server
Nucleic Acids Res.32: W321-W326 (2003)
- ExPASy ProtParam tool
- Gasteiger E., Hoogland C., Gattiker A., Duvaud S., Wilkins M.R., Appel R.D., and Bairoch A.
Protein Identification and Analysis Tools on the ExPASy Server
The Proteomics Protocols Handbook, (ed) John M. Walker, 571-607 (2005)
- Anomalous Scattering Coefficients
- Ethan A Merritt
