rna backbone rotamers: introduction and updates laura weston murray july 27, 2008 roc meeting,...
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RNA Backbone Rotamers: Introduction and Updates
Laura Weston Murray
July 27, 2008
ROC Meeting, Berlin
Outline
• Background information on RNA backbone consensus conformers
• Applications and collaborations• Dataset update (in progress)
A Series of Tubes
1Q9A 1JJ2
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
Selection and Quality Filtering
• Dataset selection – resolution (3Å and better)
– variety
• B-factor– local reliability
• Sterics– Eliminate the impossible
1a
1a
#a
4s
5z
1a1a
1a
1a
1a
1e
1a
Applications
• Motif identification and description– But Gary will tell you more about that one.
• PHENIX• RNABC• Ribosome
Applications
• Motif identification and description– But Gary will tell you more about that one.
• PHENIX• RNABC• Ribosome
Applications
• Motif identification and description– But Gary will tell you more about that one.
• PHENIX• RNABC• Ribosome
RNABC: RNA Backbone Correction
Original
dihedral
RNABC conformation
RNABC correction
50S 1941-2
Applications
• Motif identification and description– But Gary will tell you more about that one.
• PHENIX• RNABC• Ribosome
RNA08
RNA03 RNA05 RNA08 est.
Files 132 171 200
Residues 86369486 15000
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