rna backbone rotamers: introduction and updates laura weston murray july 27, 2008 roc meeting,...
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![Page 1: RNA Backbone Rotamers: Introduction and Updates Laura Weston Murray July 27, 2008 ROC Meeting, Berlin](https://reader035.vdocuments.site/reader035/viewer/2022070412/56649d555503460f94a32703/html5/thumbnails/1.jpg)
RNA Backbone Rotamers: Introduction and Updates
Laura Weston Murray
July 27, 2008
ROC Meeting, Berlin
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Outline
• Background information on RNA backbone consensus conformers
• Applications and collaborations• Dataset update (in progress)
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A Series of Tubes
1Q9A 1JJ2
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Classification Consensus
• Selected and quality-filtered dataset• Nomenclature to translate among
residue, dinucleotide, suite descriptions• Applied and cross-referenced methods
– 7D visualization– Pseudo-electron density contours– Multi-dimensional binning– Pseudotorsion analysis
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Selection and Quality Filtering
• Dataset selection – resolution (3Å and better)
– variety
• B-factor– local reliability
• Sterics– Eliminate the impossible
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1a
1a
#a
4s
5z
1a1a
1a
1a
1a
1e
1a
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Applications
• Motif identification and description– But Gary will tell you more about that one.
• PHENIX• RNABC• Ribosome
![Page 12: RNA Backbone Rotamers: Introduction and Updates Laura Weston Murray July 27, 2008 ROC Meeting, Berlin](https://reader035.vdocuments.site/reader035/viewer/2022070412/56649d555503460f94a32703/html5/thumbnails/12.jpg)
Applications
• Motif identification and description– But Gary will tell you more about that one.
• PHENIX• RNABC• Ribosome
![Page 13: RNA Backbone Rotamers: Introduction and Updates Laura Weston Murray July 27, 2008 ROC Meeting, Berlin](https://reader035.vdocuments.site/reader035/viewer/2022070412/56649d555503460f94a32703/html5/thumbnails/13.jpg)
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Applications
• Motif identification and description– But Gary will tell you more about that one.
• PHENIX• RNABC• Ribosome
![Page 15: RNA Backbone Rotamers: Introduction and Updates Laura Weston Murray July 27, 2008 ROC Meeting, Berlin](https://reader035.vdocuments.site/reader035/viewer/2022070412/56649d555503460f94a32703/html5/thumbnails/15.jpg)
RNABC: RNA Backbone Correction
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Original
dihedral
RNABC conformation
RNABC correction
50S 1941-2
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Applications
• Motif identification and description– But Gary will tell you more about that one.
• PHENIX• RNABC• Ribosome
![Page 18: RNA Backbone Rotamers: Introduction and Updates Laura Weston Murray July 27, 2008 ROC Meeting, Berlin](https://reader035.vdocuments.site/reader035/viewer/2022070412/56649d555503460f94a32703/html5/thumbnails/18.jpg)
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RNA08
RNA03 RNA05 RNA08 est.
Files 132 171 200
Residues 86369486 15000
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Acknowledgements
Richardson Lab Rutgers-Prague Georgia Tech Yale
Jane Richardson Helen Berman Loren Williams Anna-Marie Pyle
David Richardson Bohdan Schneider Eli Hershkovitz John Westbrook
Gary Kapral Zdenek Moravek Kevin Keating
Bryan Arendall David Micallef
Lizbeth Videau Daniela Hamova
Ian Davis
Funding
NIH HHMI NSF ROC
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