|
International
Tables for Crystallography Volume F Crystallography of biological macromolecules Edited by M. G. Rossmann and E. Arnold © International Union of Crystallography 2006 |
International Tables for Crystallography (2006). Vol. F. ch. 24.2, pp. 657-662
https://doi.org/10.1107/97809553602060000719 Chapter 24.2. The Nucleic Acid Database (NDB)
aThe Nucleic Acid Database Project, Department of Chemistry, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854-8077, USA |
References
Allen, F. H., Bellard, S., Brice, M. D., Cartwright, B. A., Doubleday, A., Higgs, H., Hummelink, T., Hummelink-Peters, B. G., Kennard, O., Motherwell, W. D. S., Rodgers, J. R. & Watson, D. G. (1979). The Cambridge Crystallographic Data Centre: computer-based search, retrieval, analysis and display of information. Acta Cryst. B35, 2331–2339.Google Scholar
Berman, H. M., Olson, W. K., Beveridge, D. L., Westbrook, J., Gelbin, A., Demeny, T., Hsieh, S. H., Srinivasan, A. R. & Schneider, B. (1992). The Nucleic Acid Database – a comprehensive relational database of three-dimensional structures of nucleic acids. Biophys. J. 63, 751–759.Google Scholar
Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N. & Bourne, P. E. (2000). The Protein Data Bank. Nucleic Acids Res. 28, 235–242.Google Scholar
Bernstein, F. C., Koetzle, T. F., Williams, G. J., Meyer, E. E., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T. & Tasumi, M. (1977). Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535–542.Google Scholar
Bourne, P., Berman, H. M., Watenpaugh, K., Westbrook, J. D. & Fitzgerald, P. M. D. (1997). The macromolecular Crystallographic Information File (mmCIF). Methods Enzymol. 277, 571–590.Google Scholar
Brünger, A. T. (1992). X-PLOR. Version 3.1. A system for X-ray crystallography and NMR. Yale University Press, New Haven, CT, USA.Google Scholar
Clowney, L., Jain, S. C., Srinivasan, A. R., Westbrook, J., Olson, W. K. & Berman, H. M. (1996). Geometric parameters in nucleic acids: nitrogenous bases. J. Am. Chem. Soc. 118, 509–518.Google Scholar
Feng, Z., Hsieh, S.-H., Gelbin, A. & Westbrook, J. (1998). MAXIT: macromolecular exchange and input tool. NDB-120. Rutgers University, New Brunswick, NJ, USA.Google Scholar
Feng, Z., Westbrook, J. & Berman, H. M. (1998). NUCheck. NDB-407. Rutgers University, New Brunswick, NJ, USA.Google Scholar
Gelbin, A., Schneider, B., Clowney, L., Hsieh, S.-H., Olson, W. K. & Berman, H. M. (1996). Geometric parameters in nucleic acids: sugar and phosphate constituents. J. Am. Chem. Soc. 118, 519–528.Google Scholar
Grzeskowiak, K., Yanagi, K., Privé, G. G. & Dickerson, R. E. (1991). The structure of B-helical C-G-A-T-C-G-A-T-C-G and comparison with C-C-A-A-C-G-T-T-G-G: the effect of base pair reversal. J. Biol. Chem. 266, 8861–8883.Google Scholar
Lavery, R. & Sklenar, H. (1989). Defining the structure of irregular nucleic acids: conventions and principles. J. Biomol. Struct. Dyn. 6, 655–667.Google Scholar
Parkinson, G., Vojtechovsky, J., Clowney, L., Brünger, A. T. & Berman, H. M. (1996). New parameters for the refinement of nucleic acid-containing structures. Acta Cryst. D52, 57–64.Google Scholar
Sayle, R. & Milner-White, E. J. (1995). RasMol: biomolecular graphics for all. Trends Biochem. Sci. 20, 374.Google Scholar
Schneider, B., Neidle, S. & Berman, H. M. (1997). Conformations of the sugar–phosphate backbone in helical DNA crystal structures. Biopolymers, 42, 113–124.Google Scholar
Scott, W. G., Finch, J. T. & Klug, A. (1995). The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage. Cell, 81, 991–1002.Google Scholar
Vaguine, A. A., Richelle, J. & Wodak, S. J. (1999). SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model. Acta Cryst. D55, 191–205.Google Scholar
Westbrook, J. (1998). AutoDep input tool. NDB-406. Rutgers University, New Brunswick, NJ, USA.Google Scholar