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

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)
  • IL MILIONE and SIR2008
  • Burla, M.C., Caliandro, R., Camalli, M., Carrozzini, B., Cascarano, G., De Caro L., Giacovazzo, C. Polidori, G., Siliqi, D., and Spagna, R.
  • IL MILIONE: a suite of computer programs for crystal structure solution of proteins.
  • J. Appl. Cryst. 40: 609-613. (2007)
  • Caliandro, R., Carrozzini, B., Cascarano, G., De Caro L., Giacovazzo, C. and Siliqi, D.
  • Advances in ab initio protein phasing by Patterson deconvolution techniques.
  • J. Appl. Cryst. 40: 883-890. (2007)
  • Caliandro, R., Carrozzini, B., Cascarano, G., De Caro L., Giacovazzo, C., Mazzone A. and Siliqi, D.
  • Ab initio phasing of proteins with heavy atoms at non-atomic resolution: pushing the size limit of solvable structures up to 7890 non-H atoms in the asymmetric unit.
  • J. Appl. Cryst. 41: 548-553. (2008)

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)
  • COMO ver. 1.2
  • Tong, L.
  • Combined molecular replacement
  • Acta Crystallogr. Sect. A Found. Crystallogr. 52: 782-784. (1996)
  • CNSsolve ver. 1.3
  • Brunger, A. T., Adams, P. D., Clore, G. M., Gros, P., Grosse-Kunstleve, R. W., Jiang, J.-S., Kuszewski, J., Nilges, N., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T., and Warren, G. L.
  • Crystallography & NMR System (CNS), A new software suite for macromolecular structure determination.
  • Acta Crystallogr. Sect. D Biol. Crystallogr. 54: 905-921. (1998)
  • Brunger, A. T.
  • Version 1.2 of the Crystallography and NMR System.
  • Nature Protocols 2: 2728-2733. 2007

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)

自動化

  • Lafire
  • Yao, M., Zhou, Y., and Tanaka, I.
  • LAFIRE: software for automating the refinement process of protein structure analysis.
  • Acta Crystallogr. Sect. D Biol. Crystallogr. 62: 189-196. (2006)
  • Zhou, Y., Yao, M., and Tanaka, I.
  • New algorithm for protein model building: extending partial model in map segment.
  • J. Appl. Cryst. 39: 57-63. (2006)
  • ARCIMBOLDO
  • Rodríguez, D.D., Grosse. C., Himmel, S., González, C., de Ilarduya I.M., Becker, S., Sheldrick and G.M., Usón, I.
  • Crystallographic ab initio protein structure solution below atomic resolution.
  • Nat. Methods 6: 651-653. (2009)

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/
  • eMovie
  • Hodis, E., Schreiber, G., Rother, K., and Sussman, J.L.
  • eMovie: a storyboard-based tool for making molecular movies.
  • Trends in Biochemical Sciences32: 199-204 (2007)
  • 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)
  • CCP4mg ver. 2.4.3
  • Potterton, L., McNicholas, S., Krissinel, E., Gruber, J., Cowtan, K., Emsley, P., Murshudov, G. N., Cohen, S., Perrakis, A., and Noble, M.
  • Developments in the CCP4 molecular-graphics project.
  • Acta Crystallogr. Sect. D Biol. Crystallogr. 60: 2288-2294 (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)
  • ClustalX
  • Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F., and Higgins, D. G.
  • The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.
  • Nucleic Acids Res. 24: 4876-4882 (1997)
  • CDPro
  • Sreerama, T.N. and Woody, R.W.
  • Computation and Analysis of Protein Circular Dichroism Spectra.
  • Methods Enzymol. 383: 318-351 (2004)
  • 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)

Biophysical Chemistry