The Coordinator:

• Neocles Leontis, the Principal Investigator on this grant will serve as the Coordinator of the ROC. He is Professor of Chemistry at Bowling Green State University. His research focuses on the analysis, description, and annotation of RNA structural motifs and the integration of sequence and 3D data to construct accurate RNA alignments for 3D modeling and phylogenetic analysis. In collaboration with Eric Westhof, he formulated an unambiguous and descriptive nomenclature of RNA basepairing types that has been adopted by RNAML and the Nucleic Acid Database and has defined isostericity matrices for basepair families for analyzing sequence alignments (Leontis & Westhof 2001; Leontis et al. 2002)

Initial Steering Committee:

• Russ Altman (Stanford University) has expertise in ontology design for RNA and structured representations of experimental and structural information. He initiated the effort for developing RNAML and has developed RiboWeb, a database of structural experimental information on the ribosome. He has extensive experience with biological ontologies (e.g. GO).
  

• Helen Berman (Rutgers University) is the Director of the Research Collaboratory for Structural Bioinformatics, which runs the Protein Data Bank and the Nucleic Acids Databank. She has 15 years of experience in building a community based ontology and in creating one data resource -- the NDB and directing and reengineering another -- the PDB.
  

• Steve Brenner (University of California at Berkeley) is a computational biologist studying the structural and evolutionary relationships of biological macromolecules. He is a cofounder of the SCOR: Structural Classification of RNA database. He discovered the prevalence of alternative splicing functionally coupled to nonsense-mediated mRNA decay and an apparent regulatory mechanism. He pioneered target selection for structural genomics, and he is one of the cofounders of the SCOP: Structural Classification of Proteins database.
  

• James Brown (North Carolina State University) is the curator of the RNase P Database. The Brown lab has developed a rigorous comparative approach for the study of RNA structure; comparative inferences form the basis for biochemical analysis of RNAs in order to determine the roles of the structural elements of which these are comprised. The RNase P Database is a community service based on these comparative studies.
  

• Steve Holbrook (Lawrence Berkeley National Laboratory) has solved crystal structures of RNA oligonucleotides, transfer RNA, and RNA binding proteins; he co-founded the SCOR database for Structural Classification of RNA and is developing methods for identification and annotation of functional RNAs in genomic sequences.
  

• François Major (Université de Montréal, Canada) is a computer scientist specializing in structural bioinformatics and 3D modeling. He has developed the RNA modeling program MC-Sym and, more recently, the MC-Annotate program to identify base pairing patterns and base stacking in RNA 3D structures. He coordinated the definition of RNAML and developed a series of tools to parse and generate RNAML objects.
  

• Jane Richardson (Duke University) has been recognized internationally with a MacArthur Fellowship for her contributions to determination, analysis visualization and validation of protein 3D structure. In recent work, she is developing tools to validate backbone conformations in RNA structures.
  

• Eric Westhof (IBMC, Strasbourg, France) is the leading authority worldwide on the 3D modeling of complex, biologically active RNA molecules. He is also a crystallographer. He collaborates widely to model biologically important RNA molecules incorporating diverse experimental data and sequence information.
  

• Jamie Williamson (Scripps Institute) is a biophysical chemist who has employed NMR spectroscopy, thermodynamic methods, and crystallography to characterize RNA-protein interactions. Jamie Williamson will link to the NMR structure determination community.

Initial Advisory Board:

• Jennifer Doudna (University of California, Berkeley) has solved the crystal structures of many important catalytic RNAs, greatly expanding our knowledge of RNA 3D structure and ribozyme function.
  

• Stephen C. Harvey (Georgia Institute of Technology) uses modeling, bioinformatic and simulation methods to investigate structure/function relationships in the ribosome, tRNAs, tmRNA. The YAMMP molecular modeling package from his laboratory allows multiscale representation of RNA structures during refinement and simulations.
  

• David Mathews (University of Rochester) is a young investigator working in RNA thermodynamics secondary structure prediction. He is a collaborator of Douglas Turner and Michael Zuker. His primary research interest is predicting RNA secondary structure from sequence. He has expertise in both parameterizing the widely used thermodynamic nearest neighbor parameters in collaboration with Douglas Turner and in designing novel algorithms for improved structure prediction.
  

• Anna Marie Pyle (Yale University) Dr. Pyle uses the group II intron as a model system for studying ribozyme catalysis, RNA folding, and RNA-protein interactions. She also studies the mechanisms of RNA helicase enzymes, which are molecular motors that unwind RNA and displace proteins from RNA binding sites. This work is complemented by the development of new computational approaches for analyzing RNA conformation.

Network Participants:

• Michael Ashburner (Cambridge University, UK) and Suzanna Lewis (University of California, Berkeley Drosophila Genome Project) have in the last two years been developing, together with colleagues Lincoln Stein of the Cold Spring Harbor Laboratory and Richard Durbin of the Wellcome Trust's Sanger Institute in Hinxton, a Sequence Ontology (song.sf.net) to be used for the annotation of sequence data. The content is centrally managed and edited by Karen Eilbeck in Berkeley, who is funded by the Gene Ontology grant from NIH-NHGRI. Using the SO to describe sequence data allows this information to be more easily exchanged (in, for example GFF3 syntax), compared, and queried in and across databases. They will work closely with the ROC to integrate the RO with the SO in order that the community sees one comprehensive ontology (see attached letter).
  

• Alex Bateman (Sanger Institute, UK) is founding member of Pfam and Rfam. Rfam is a curated collection of RNA families and domains that is used internationally for genomic analysis and for training RNA analysis tools. The Rfam database currently uses a small ontology to classify its data. Dr. Bateman is committed to contribute to an international effort to develop a unified ontology (see attached letter).
  

• David Case (The Scripps Research Institute) is leader of the AMBER development team and a leading innovator in molecular simulation. He represents the molecular dynamics simulation community and will participate in discussions related to description and characterization of motif dynamics (see attached letter).
  

• Sean Eddy (Washington University) has pioneered the use of stochastic context-free grammars for creating probabilistic models of RNA sequences for database searching and sequence comparison and alignment. He has extensive experience with RNA analysis software development and with the development of the Distributed Annotation System for community-driven genome annotation, and the Pfam and Rfam databases (see attached letter).
  

• David Engelke, (University of Michigan), is a leading molecular biologist studying the biosynthesis of small, functional RNAs in nuclei. He makes use of biochemistry, genetics, and cytological methods to study the behavior of RNAs and ribonucleoproteins in yeast and mammals. Additional projects have involved nucleic acid technology, including RNA-based therapies and diagnostics. He will provide input from the point of view of end-users working at the bench (see attached letter).
  

• Christine Gaspin is a Permanent Researcher in bioinformatics at the National Institute of Agronomical Research (Toulouse, France) where she promotes the use of the CSP formalism (Constraint Satisfaction Problem) for representing RNA secondary structures and searching for RNA Motifs. She is also involved in RNA searching by developing new algorithms models with the aim to integrate available data and knowledge (see letter attached).
  

• Peter Moore (Yale University) has determined the low-resolution structure of the 30S ribosome with neutron scattering and recently collaborated with Tom Steitz to determine the high-resolution structure of the 50S ribosome by x-ray crystallography. He has also determined numerous RNA structures by NMR spectroscopy. His work has identified numerous RNA motifs, such as the sarcin loop, 5S loop E, and the kink-turns.