Nucleic acid visualization with UCSF Chimera

Nucleic Acids Research

Volumn 34, Issue 4, 2006, Pages

  Couch, Gregory S ^b   Hendrix, Donna K ^a   Ferrin, Thomas E ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEIC ACID; NUCLEIC ACID BASE; SUGAR; CARBOHYDRATE; DNA; RNA;

ANALYTICAL EQUIPMENT; ARTICLE; BASE PAIRING; CHIMERA; COMPUTER GRAPHICS; COMPUTER PROGRAM; COMPUTER SYSTEM; CONTROLLED STUDY; GEOMETRY; NUCLEIC ACID STRUCTURE; PRIORITY JOURNAL; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; INTERNET;

BACTERIA (MICROORGANISMS);

BASE PAIRING; CARBOHYDRATES; COMPUTER GRAPHICS; DNA; INTERNET; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; RNA; SOFTWARE;

EID: 33644860901     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gnj031     Document Type: Article

References (29)

1. Batey,R.T., Gilbert,S.D. and Montange,R.K. (2004) Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine. Nature, 432, 411-415.
2. Serganov,A., Yuan,Y.R., Pikovskaya,O., Polonskaia,A., Malinina,L., Phan,A.T., Hobartner,C., Micura,R., Breaker,R.R. and Patel,D.J. (2004) Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs. Chem. Biol., 11, 1729-1741.
3. Krasilnikov,A.S., Yang,X., Pan,T. and Mondragon,A. (2003) Crystal structure of the specificity domain of ribonuclease P. Nature, 421, 760-764.
4. Krasilnikov,A.S., Xiao,Y., Pan,T. and Mondragon,A. (2004) Basis for structural diversity in homologous RNAs. Science, 306, 104-107.
5. Adams,P.L., Stahley,M.R., Kosek,A.B., Wang,J. and Strobel,S.A. (2004) Crystal structure of a self-splicing group I intron with both exons. Nature, 430, 45-50.
6. Golden,B.L., Kim,H. and Chase,E. (2005) Crystal structure of a phage Twort group I ribozyme-product complex. Nature Struct. Mol. Biol., 12, 82-89.
7. Wimberly,B.T., Brodersen,D.E., Clemons,W.M. Jr, Morgan-Warren,R.J., Carter,A.P., Vonrhein,C., Hartsch,T. and Ramakrishnan,V. (2000) Structure of the 30S ribosomal subunit. Nature, 407, 327-339.
8. Ban,N., Nissen,P., Hansen,J., Moore,P.B. and Steitz,T.A. (2000) The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science, 289, 905-920.
9. Harms,J., Schluenzen,F., Zarivach,R., Bashan,A., Gat,S., Agmon,I., Bartels,H., Franceschi,F. and Yonath,A. (2001) High resolution structure of the large ribosomal subunit from a mesophilic eubacterium. Cell, 107, 679-688.
10. Schuwirth,B.S., Borovinskaya,M.A., Hau,C.W., Zhang,W., Vila-Sanjurjo,A., Holton,J.M. and Cate,J.H. (2005) Structures of the bacterial ribosome at 3.5 A resolution. Science, 310, 827-834.
11. Luger,K., Mader,A.W., Richmond,R.K., Sargent,D.F. and Richmond,T.J. (1997) Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature, 389, 251-260.
12. Edayathumangalam,R.S., Weyermann,P., Gottesfeld,J.M., Dervan,P.B. and Luger,K. (2004) Molecular recognition of the nucleosomal 'supergroove'. Proc. Natl Acad. Sci. USA, 101, 6864-6869.
13. Holbrook,S.R. (2005) RNA structure: The long and the short of it. Curr. Opin. Struct. Biol., 15, 302-308.
14. Klosterman,P.S., Tamura,M., Holbrook,S.R. and Brenner,S.E. (2002) SCOR: a Structural Classification of RNA database. Nucleic Acids Res., 30, 392-394.
15. Tamura,M., Hendrix,D.K., Klosterman,P.S., Schimmelman,N.R., Brenner,S.E. and Holbrook,S.R. (2004) SCOR: Structural Classification of RNA, version 2.0. Nucleic Acids Res., 32, D182-D184.
16. Richardson,J.S. (1981) The anatomy and taxonomy of protein structure. Adv. Protein Chem., 34, 167-339.
17. Pettersen,E.F., Goddard,T.D., Huang,C.C., Couch,G.S., Greenblatt,D.M., Meng,E.C. and Ferrin,T.E. (2004) UCSF Chimera - a visualization system for exploratory research and analysis. J. Comput. Chem., 25, 1605-1612.
18. Saenger,W. (1983) Principles of Nucleic Acid Structure. Springer-Verlag, New York, NY.
19. Carson,M. and Bugg,C.E. (1986) Algorithm for ribbon models of proteins. J. Mol. Graph., 4, 121-122.
20. Foley,J.D., van Dam,A., Feiner,S.K. and Hughes,J.F. (1990) Computer Graphics: Principles and Practice, 2nd edn. Addison-Wesley, Reading, MA.
21. Olson,W.K., Bansal,M., Burley,S.K., Dickerson,R.E., Gerstein,M., Harvey,S.C., Heinemann,U., Lu,X.J., Neidle,S., Shakked,Z. et al. (2001) A standard reference frame for the description of nucleic acid base-pair geometry. J. Mol. Biol., 313, 229-237.
22. Lu,X.J. and Olson,W.K. (2003) 3DNA: A software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res., 31, 5108-5121.
23. Branden,C.-I. and Tooze,J. (1991) Introduction to Protein Structure, 1st edn. Garland Publishing, Inc,
24. Carson,M. (1997) Ribbons. In Carter,C.W.Jr and Sweet,R.M. (eds), Methods in Enzymology, Macromolecular Crystallography Part B. Academic Press, 277, pp. 493-502.
25. Massire,C., Gaspin,C. and Westhof,E. (1994) DRAWNA: A program for drawing schematic views of nucleic acids. J. Mol. Graph., 12, 201-206196.
26. Goddard,T.D., Huang,C.C. and Ferrin,T.E. (2005) Software extensions to UCSF Chimera for interactive visualization of large molecular assemblies. Structure, 13, 473-482.
27. Drew,H.R., Wing,R.M., Takano,T., Broka,C., Tanaka,S., Itakura,K. and Dickerson,R.E. (1981) Structure of a B-DNA dodecamer: Conformation and dynamics. Proc. Natl Acad. Sci. USA, 78, 2179-2183.
28. Kopka,M.L., Yoon,C., Goodsell,D., Pjura,P. and Dickerson,R.E. (1985) Binding of an antitumor drug to DNA, Netropsin and C-G-C-G-A-A-T-T-BrC-G-C-G. J. Mol. Biol., 183, 553-563.
29. Lu,M. and Steitz,T.A. (2000) Structure of Escherichia coli ribosomal protein L25 complexed with a 5S rRNA fragment at 1.8-A resolution. Proc. Natl Acad. Sci. USA, 97, 2023-2028.