15916548

Source:http://linkedlifedata.com/resource/pubmed/id/15916548

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Predicate	Object
rdf:type	pubmed:Citation
lifeskim:mentions	umls-concept:C0035668, umls-concept:C0037949, umls-concept:C0205453, umls-concept:C0439534
pubmed:issue	Pt 3
pubmed:dateCreated	2005-5-26
pubmed:abstractText	Despite the importance of local structural detail for a mechanistic understanding of RNA catalysis and binding functions, RNA backbone conformation has been recalcitrant to analysis. There are too many variable dihedral angles per residue, and their raw empirical distributions are poorly clustered. This study applies quality-filtering techniques (using resolution, crystallographic B factor and all-atom-steric clashes) to the backbone dihedral angle distributions from a selected 8636 residue RNA database. With noise levels significantly decreased, clear signal appears for the underlying angle preferences. We analyse the multidimensional backbone dihedral distributions within sugar-to-sugar 'suites' rather than chemical residues due to the greater base interaction and steric interdependence within the suite. The final result is a small library of RNA backbone rotamers, each represented by a data cluster in seven-dimensional dihedral space, which should provide valid conformations for nearly all RNA backbones encountered in experimental structures. We are in the process of improving that library, and developing tools and applications for it in structure determination and analysis.
pubmed:language	eng
pubmed:journal	http://linkedlifedata.com/resource/pubmed/journal/7506897
pubmed:citationSubset	IM
pubmed:chemical	http://linkedlifedata.com/resource/pubmed/chemical/RNA
pubmed:status	MEDLINE
pubmed:month	Jun
pubmed:issn	0300-5127
pubmed:author	pubmed-author:ArendallW BWB, pubmed-author:MurrayL J WLJ, pubmed-author:RichardsonD CDC, pubmed-author:RichardsonJ SJS
pubmed:issnType	Print
pubmed:volume	33
pubmed:owner	NLM
pubmed:authorsComplete	Y
pubmed:pagination	485-7
pubmed:dateRevised	2006-11-15
pubmed:meshHeading	pubmed-meshheading:15916548-Crystallography, X-Ray, pubmed-meshheading:15916548-Models, Molecular, pubmed-meshheading:15916548-Nucleic Acid Conformation, pubmed-meshheading:15916548-RNA
pubmed:year	2005
pubmed:articleTitle	RNA backbone rotamers--finding your way in seven dimensions.
pubmed:affiliation	Department of Biochemistry, Duke University, Durham, NC 27710-3711, U.S.A.
pubmed:publicationType	Journal Article, Research Support, U.S. Gov't, P.H.S., Research Support, Non-U.S. Gov't, Research Support, N.I.H., Extramural