Molecular dynamics simulations of RNA: An in silico single molecule approach
dc.contributor.author | McDowell, S. Elizabeth | en_US |
dc.contributor.author | Špačková, Nad'A | en_US |
dc.contributor.author | Šponer, Ji[rcaron]í | en_US |
dc.contributor.author | Walter, Nils G. | en_US |
dc.date.accessioned | 2007-09-20T17:50:43Z | |
dc.date.available | 2008-04-03T18:43:52Z | en_US |
dc.date.issued | 2007-02-05 | en_US |
dc.identifier.citation | McDowell, S. Elizabeth; ŠpačkovÁ, Nad'a; Šponer, Ji[rcaron]Í; Walter, Nils G. (2007). "Molecular dynamics simulations of RNA: An in silico single molecule approach." Biopolymers 85(2): 169-184. <http://hdl.handle.net/2027.42/55864> | en_US |
dc.identifier.issn | 0006-3525 | en_US |
dc.identifier.issn | 1097-0282 | en_US |
dc.identifier.uri | https://hdl.handle.net/2027.42/55864 | |
dc.identifier.uri | http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=retrieve&db=pubmed&list_uids=17080418&dopt=citation | en_US |
dc.description.abstract | RNA molecules are now known to be involved in the processing of genetic information at all levels, taking on a wide variety of central roles in the cell. Understanding how RNA molecules carry out their biological functions will require an understanding of structure and dynamics at the atomistic level, which can be significantly improved by combining computational simulation with experiment. This review provides a critical survey of the state of molecular dynamics (MD) simulations of RNA, including a discussion of important current limitations of the technique and examples of its successful application. Several types of simulations are discussed in detail, including those of structured RNA molecules and their interactions with the surrounding solvent and ions, catalytic RNAs, and RNA–small molecule and RNA–protein complexes. Increased cooperation between theorists and experimentalists will allow expanded judicious use of MD simulations to complement conceptually related single molecule experiments. Such cooperation will open the door to a fundamental understanding of the structure–function relationships in diverse and complex RNA molecules. © 2006 Wiley Periodicals, Inc. Biopolymers 85:169–184, 2007. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com | en_US |
dc.format.extent | 926137 bytes | |
dc.format.extent | 3118 bytes | |
dc.format.mimetype | application/pdf | |
dc.format.mimetype | text/plain | |
dc.publisher | Wiley Subscription Services, Inc., A Wiley Company | en_US |
dc.subject.other | Chemistry | en_US |
dc.subject.other | Polymer and Materials Science | en_US |
dc.title | Molecular dynamics simulations of RNA: An in silico single molecule approach | en_US |
dc.type | Article | en_US |
dc.rights.robots | IndexNoFollow | en_US |
dc.subject.hlbsecondlevel | Chemical Engineering | en_US |
dc.subject.hlbsecondlevel | Chemistry | en_US |
dc.subject.hlbsecondlevel | Materials Science and Engineering | en_US |
dc.subject.hlbtoplevel | Engineering | en_US |
dc.subject.hlbtoplevel | Science | en_US |
dc.description.peerreviewed | Peer Reviewed | en_US |
dc.contributor.affiliationum | Biophysics Research Division, Single Molecule Analysis Group, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109-1055 | en_US |
dc.contributor.affiliationum | Department of Chemistry, Single Molecule Analysis Group, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109-1055 ; Department of Chemistry, Single Molecule Analysis Group, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109-1055 | en_US |
dc.contributor.affiliationother | Institute of Biophysics, Academy of Sciences of the Czech Republic, KrÁlovopolskÁ 135, 612 65 Brno, Czech Republic | en_US |
dc.contributor.affiliationother | Institute of Biophysics, Academy of Sciences of the Czech Republic, KrÁlovopolskÁ 135, 612 65 Brno, Czech Republic ; Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague ; Institute of Biophysics, Academy of Sciences of the Czech Republic, KrÁlovopolskÁ 135, 612 65 Brno, Czech Republic | en_US |
dc.identifier.pmid | 17080418 | en_US |
dc.description.bitstreamurl | http://deepblue.lib.umich.edu/bitstream/2027.42/55864/1/20620_ftp.pdf | en_US |
dc.identifier.doi | http://dx.doi.org/10.1002/bip.20620 | en_US |
dc.identifier.source | Biopolymers | en_US |
dc.owningcollname | Interdisciplinary and Peer-Reviewed |
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