Molecular Modeling of Nucleic Acid Structure
dc.contributor.author | Cheatham, Thomas E. | |
dc.contributor.author | Brooks, Bernard R. | |
dc.contributor.author | Kollman, Peter A. | |
dc.date.accessioned | 2020-01-13T15:06:45Z | |
dc.date.available | 2020-01-13T15:06:45Z | |
dc.date.issued | 2001-09 | |
dc.identifier.citation | Cheatham, Thomas E.; Brooks, Bernard R.; Kollman, Peter A. (2001). "Molecular Modeling of Nucleic Acid Structure." Current Protocols in Nucleic Acid Chemistry 6(1): 7.5.1-7.5.12. | |
dc.identifier.issn | 1934-9270 | |
dc.identifier.issn | 1934-9289 | |
dc.identifier.uri | https://hdl.handle.net/2027.42/152650 | |
dc.description.abstract | This unit is the first in a series of four units covering the analysis of nucleic acid structure by molecular modeling. This unit provides an overview of computer simulation of nucleic acids. Topics include the static structure model, computational graphics and energy models, generation of an initial model, and characterization of the overall three‐dimensional structure. | |
dc.publisher | Wiley Periodicals, Inc. | |
dc.publisher | Data commission of the international union of crystallography | |
dc.title | Molecular Modeling of Nucleic Acid Structure | |
dc.type | Article | |
dc.rights.robots | IndexNoFollow | |
dc.subject.hlbsecondlevel | Biological Chemistry | |
dc.subject.hlbsecondlevel | Chemical Engineering | |
dc.subject.hlbsecondlevel | Chemistry | |
dc.subject.hlbsecondlevel | Public Health | |
dc.subject.hlbtoplevel | Engineering | |
dc.subject.hlbtoplevel | Health Sciences | |
dc.subject.hlbtoplevel | Science | |
dc.description.peerreviewed | Peer Reviewed | |
dc.description.bitstreamurl | https://deepblue.lib.umich.edu/bitstream/2027.42/152650/1/cpnc0705.pdf | |
dc.identifier.doi | 10.1002/0471142700.nc0705s06 | |
dc.identifier.source | Current Protocols in Nucleic Acid Chemistry | |
dc.identifier.citedreference | http://www.amber.ucsf.edu/amber | |
dc.identifier.citedreference | Schneider, B. and Kabelac, M. 1998. Stereochemistry of binding of metal cations and water to a phosphate group. J. Am. Chem. Soc. 120: 161 ‐ 165. | |
dc.identifier.citedreference | Schneider, B., Cohen, D.M., Schleifer, L., Srinivasan, A.R., Olson, W.K., and Berman, H.M. 1993. A systematic method for studying the spatial distribution of water molecules around nucleic acid bases. Biophys. J. 65: 2291 ‐ 2303. | |
dc.identifier.citedreference | Schneider, B., Neidle, S., and Berman, H.M. 1997. Conformations of the sugar‐phosphate backbone in helical DNA crystal structures. Biopolymers 42: 113 ‐ 124. | |
dc.identifier.citedreference | Stofer, E. and Lavery, R. 1994. Measuring the geometry of DNA grooves. Biopolymers 34: 337 ‐ 346. | |
dc.identifier.citedreference | Surles, M.C., Richardson, J.S., Richardson, D.C., and Brooks, F.P. 1994. Scuplting proteins interactively—Continual energy minimization embedded in a graphical modeling system. Protein Sci. 3: 198 ‐ 210. | |
dc.identifier.citedreference | Ulyanov, N.B. and James, T.L. 1995. Statistical analysis of DNA duplex structural features. Methods Enzymol. 261: 90 ‐ 120. | |
dc.identifier.citedreference | Vologodski, A.V. and Cozzarelli, N.R. 1994. Conformational and thermodynamic properties of supercoiled DNA. Annu. Rev. Biophys. Biomol. Struct. 23: 609 ‐ 643. | |
dc.identifier.citedreference | Wang, A.H., Quigley, G.J., Kolpak, F.J., Crawford, J.L., van Boom, J.H., van der Marel, G., and Rich, A. 1979. Molecular structure of a left‐handed double helical DNA fragment at atomic resolution. Nature 283: 743 ‐ 745. | |
dc.identifier.citedreference | http://igc.ethz.ch/gromos | |
dc.identifier.citedreference | http://honiglab.cpmc.columbia.edu/grasp | |
dc.identifier.citedreference | http://www.lobos.nih.gov/Charmm | |
dc.identifier.citedreference | http://www.msi.com | |
dc.identifier.citedreference | http://www.intsim.com | |
dc.identifier.citedreference | http://www.ks.uiuc.edu/Research/namd | |
dc.identifier.citedreference | http://dasher.wustl.edu/tinker | |
dc.identifier.citedreference | http://www.scripps.edu/case | |
dc.identifier.citedreference | http://www.eyesopen.com/babel.html | |
dc.identifier.citedreference | http://www.chem.qmw.ac.uk/iupac | |
dc.identifier.citedreference | http://www.sphere.ad.jp/hgs | |
dc.identifier.citedreference | http://www.rcsb.org/pdb | |
dc.identifier.citedreference | http://ndbserver.rutgers.edu | |
dc.identifier.citedreference | http://www.ccl.net/chemistry | |
dc.identifier.citedreference | http://cmm.info.nih.gov/intro_simulation/course_for_html.html | |
dc.identifier.citedreference | Abola, E.E., Bernstein, F.C., Bryant, S.H., Koetzle, T.F., and Weng, J. 1987. Protein Data Bank. In Crystallographic Databases—Information Content, Software Systems, Scientific Applications ( F.H. Allen, G. Bergerhoff, and R. Sievers, eds.)pp. 107 ‐ 132. Data commission of the international union of crystallography, Bonn/Cambridge/Chester. | |
dc.identifier.citedreference | Allen, F.H., Bellard, S., Brice, M.D., Cartright, B.A., Doubleday, A., Higgs, H., Hummelink, T., Hummelink‐Peters, B.G., Kennard, O., Motherwell, W.D.S., Rodgers, J.R., and Watson, D.G. 1979. The Cambridge Crystallographic Data Centre: Computer‐based search, retrieval, analysis and display of information. Acta Crystallogr. B35: 2331 ‐ 2339. | |
dc.identifier.citedreference | Altona, C. and Sundaralingam, M. 1972. Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of pseudorotation. J. Am. Chem. Soc. 94: 8205 ‐ 8212. | |
dc.identifier.citedreference | Arnott, S. and Hukins, D.W. 1972. Optimised parameters for A‐DNA and B‐DNA. Biochem. Biophys. Res. Commun. 47: 1504 ‐ 1509. | |
dc.identifier.citedreference | Babcock, M.S., Pednault, E.P., and Olson, W.K. 1994. Nucleic acid structure analysis. Mathematics for local Cartesian and helical structure parameters that are truly comparable between structures. J. Mol. Biol. 237: 125 ‐ 156. | |
dc.identifier.citedreference | Berman, H.M., Olson, W.K., Beveridge, D.L., Westbrook, J., Gelbin, A., Demeny, T., Hsieh, S.H., Srinivasan, A.R., and Schneider, B. 1992. The nucleic acid database—A comprehensive relational database of 3‐dimensional structures of nucleic acids. Biophys. J. 63: 751 ‐ 759. | |
dc.identifier.citedreference | Brion, P. and Westhof, E. 1997. Hierarchy and dynamics of RNA folding. Annu. Rev. Biophys. Biomol. Struct. 26: 113 ‐ 137. | |
dc.identifier.citedreference | Cheatham, T.E. III and Kollman, P.A. 1997. Molecular dynamics simulations highlight the structural differences in DNA:DNA, RNA:RNA and DNA:RNA hybrid duplexes. J. Amer. Chem. Soc. 119: 4805 ‐ 4825. | |
dc.identifier.citedreference | Clowney, L., Jain, S.C., Srinivasan, A.R., Westbrook, J., Olson, W.K., and Berman, H.M. 1996. Geometric parameters in nucleic acids: Nitrogenous bases. J. Amer. Chem. Soc. 118: 509 ‐ 518. | |
dc.identifier.citedreference | Cruz‐Neira, C., Sandin, D.J., DeFranti, T.A., Kenyon, R.V., and Hart, J.C. 1992. The CAVE: Audio visual experience automatic virtual environment. Commun. ACM 35: 65 ‐ 72. | |
dc.identifier.citedreference | Dickerson, R.E., Bansal, M., Calladine, C.R., Diekmann, S., Hunter, W., Kennard, O., von Kitzing, E., Lavery, R., Nelson, H.C.M., Olson, W.K., Saenger, W., Shakked, Z., Sklenar, H., Soumpasis, D.M., Tung, C.S., Wang, A.H., and Zhurkin, V.B. 1989. Definitions and nomenclature of nucleic acid structure components. Nuc. Acids Res. 17: 1797 ‐ 1803. | |
dc.identifier.citedreference | Elhassan, M.A. and Calladine, C.R. 1995. The assessment of the geometry of dinucleotide steps in double helical DNA; a new local calculation scheme. J. Mol. Biol. 251: 648 ‐ 664. | |
dc.identifier.citedreference | Erie, D.A., Breslauer, K.J., and Olson, W.K. 1993. A Monte Carlo method for generating structures of short single‐stranded DNA sequences. Biopolymers 33: 75 ‐ 105. | |
dc.identifier.citedreference | Gelbin, A., Schneider, B., Clowney, L., Hsieh, S.‐H., Olson, W.K., and Berman, H.M. 1996. Geometric parameters in nucleic acids: Sugar and phosphate constituents. J. Amer. Chem. Soc. 118: 519 ‐ 529. | |
dc.identifier.citedreference | Hecht, S. 1996. Bioorganic Chemistry: Nucleic Acids ( S. Hecht, ed.) pp. 512. Oxford University Press, New York. | |
dc.identifier.citedreference | JCBN. 1983. IUPAC‐IUB Joint Commission on Biochemical Nomenclature (JCBN). Abbreviations and symbols for the description of conformations of polynucleotide chains. Recommendations 1982. Eur. J. Biochem. 131: 9 ‐ 15. | |
dc.identifier.citedreference | Lavery, R. and Sklenar, H. 1988. The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. J. Biomol. Struct. Dyn. 6: 63 ‐ 91. | |
dc.identifier.citedreference | Leclerc, F., Srinivasan, J., and Cedergren, R. 1997. Predicting RNA structures: The model of the RNA element binding Rev meets the NMR structure. Folding Des. 2: 141 ‐ 147. | |
dc.identifier.citedreference | Lu, X.‐J. and Olson, W.K. 1999. Resolving the discrepancies among nucleic acid conformational analyses. J. Mol. Biol. 285: 1563 ‐ 1575. | |
dc.identifier.citedreference | Lu, X.‐J., Babcock, M.S., and Olson, W. K. 1999. Overview of nucleic acid analysis programs. J. Biomol. Struct. Dyn. 16: 833 ‐ 843. | |
dc.identifier.citedreference | Macke, T. and Case, D.A. 1998. Modeling unusual nucleic acid structures. In Molecular Modeling of Nucleic Acids ( N.B. Leontis and J. Santa Lucia, eds.)pp. 379 ‐ 393. ACS, Washington, D.C. | |
dc.identifier.citedreference | Major, F., Turcotte, M., Gautheret, D., LaPalme, G., Fillion, E., and Cedergren, R. 1991. The combination of symbolic and numerical computation for three‐dimensional modeling of RNA. Science 253: 1255 ‐ 1260. | |
dc.identifier.citedreference | Nielsen, P.E., Egholm, M., Berg, R.H., and Buchardt, O. 1991. Sequence‐selective recognition of DNA by strand displacement with a thymine‐substituted polyamide. Science 254: 1497 ‐ 1500. | |
dc.identifier.citedreference | Olson, W.K. 1996. Simulating DNA at low resolution. Curr. Opin. Struct. Biol. 6: 242 ‐ 256. | |
dc.identifier.citedreference | Pearlman, D.A., Case, D.A., Caldwell, J.W., Ross, W.S., Cheatham, T.E., Debolt, S., Ferguson, D., Seibel, G., and Kollman, P. 1995. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structure and energetic properties of molecules. Comp. Phys. Comm. 91: 1 ‐ 41. | |
dc.identifier.citedreference | Saenger, W. 1984. Principles of Nucleic Acid Structure. Springer Advanced Texts in Chemistry ( C.E. Cantor, ed.). Springer‐Verlag, New York. | |
dc.identifier.citedreference | Schlick, T. 1995. Modeling superhelical DNA: Recent analytical and dynamical approaches. Curr. Opin. Struct. Biol. 5: 245 ‐ 252. | |
dc.owningcollname | Interdisciplinary and Peer-Reviewed |
Files in this item
Remediation of Harmful Language
The University of Michigan Library aims to describe library materials in a way that respects the people and communities who create, use, and are represented in our collections. Report harmful or offensive language in catalog records, finding aids, or elsewhere in our collections anonymously through our metadata feedback form. More information at Remediation of Harmful Language.
Accessibility
If you are unable to use this file in its current format, please select the Contact Us link and we can modify it to make it more accessible to you.