Structure Mapping Working Group

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Structure Mapping Working Group
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RNA Secondary StructureExperimental Constraints

• Enzymatic Cleavage
• Paired nucleotides
• Unpaired nucleotides
• FMN Cleavage
• Us in GU pairs
• Chemical Modification (in vitro or in vivo)
• Nucleotides that are unpaired, at the ends of
  helices, or in or adjacent to GU pairs.
• SHAPE Data
• Probes backbone flexibility
• Microarray Data
• Explores accessibility

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Constrained Structure and PBP Prediction
E. coli 5S rRNA
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Color Annotation
E. coli 5S rRNA
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Immediate Goals

• Can we standardize methods to archive and
  transmit experimental constraints?
• Can we agree on best practices for implementing
  constraints for secondary structure prediction?
• Can we learn from each other to improve
  experimental and computational methods?

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Long-Term Goal

• Can we use low-resolution mapping and sequence
  data to identify motifs?
• Can this improve tertiary structure prediction?
• Can we write an NIH P01 to do a large scale
  mapping project to compare methods?

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Key Players

• Rob Knight
• Neocles Leontis
• Francois Major?
• Kevin Weeks
• Doug Turner
• Harry Noller or chemical modification mapper
• David Mathews

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