The RiboWeb Project

1. Summary of Project Goals

One of the fundamental goals of modern molecular medicine is to understand how the structure of biological macromolecules produces their function. Our understanding of their structure comes from multiple experimental, theoretical and statistical data sources that appear in the literature and provide important fragments of information. RiboWeb is a prototype for new structural information resources that tightly link models and their coordinates with experimental (and other) data sources. The project initially focused on the structure of the prokaryotic 30S ribosomal subunit, which initiates the translation of mRNA into protein and is the site of action of numerous antibiotics; the project has since been expanded to include structural data pertaining to the entire ribosome of prokaryotes (but primarily E. coli). RiboWeb is composed of the following integrated information resources (which are available over the Internet):
 

• A knowledge base containing an ontology-based representation of the primary data relevant to the structure of the ribosome as well as supplementary functional data. In particular, we have encoded the main experimental results of approximately 200 articles that are key for ribosomal structure modeling in this knowledge base.
• Links within the knowledge base to the Medline references reporting these data and the special-purpose databases containing ribosomal sequences (e.g., the Ribosomal Database Project) as well as secondary and tertiary structures (e.g., the Protein Data Bank).
• Software components that test for compatibility and consistency between the primary data and structural models; that compute, display and evaluate new models based on user-specified interpretations of the primary data; and that use the knowledge base for other purposes such as supporting intelligent literature searching.
• An interface to the knowledge base to be used by the knowledge engineers. This includes facilities to create, edit, delete, and rename instances in the knowledge base as well as other entities of the underlying ontology.
• A structured query constructor, designed to be used by biologists, that guides the user in finding the information in the knowledge base for which s/he is searching.
• An XML-based syntax designed to exchange basic RNA molecular information.

2. Members of the RiboWeb Group

• Russ Altman
• Michael Bada
• Kevin Lauderdale
• Michelle Whirl-Carrillo

• Neil Abernethy
• Jenny Chai
• Cheng Che Chen
• Richard Chen
• Ramon Felciano
• John Gennari
• Steve Harvey
• Lawrence Hon
• Derrick Kondo
• Mark Musen
• Harry Noller
• Tom Rindfleisch
• Ya Li Wang
• Allison Waugh
• Bryn Weiser
• Julie Wu
• Michael Zuker

3. Shared Software and Data

1. RiboWeb.   This system contains most of the software components listed above, working in conjunction with the ribosomal knowledge base. The RiboWeb system is currently on an intranet. Please contact Dr. Altman if you are interested in collaborating in the use of the system.

 
2. The ribosomal knowledge base. We have created and are currently populating a knowledge base containing diverse scientific information and structural data related to the E. coli 30S ribosomal subunit. A demo version of the knowledge base is available for browsing.

 
3. Published 3-D models. This resource has been organized as part of the RiboWeb project to promote the sharing and distribution of available three-dimensional models of the E. coli 30S ribosomal subunit and 16S rRNA. It reports the currently available models, the coordinate systems used, the authors and referring publications, and contact information.

 
4. SStructView. SStructView is a Java applet which displays interactive secondary structures. The applet retrieves the secondary structure from a URL, displays it in a Web page, and responds to user interaction by identifying which objects the user clicked on and optionally calling a URL in response. The applet supports several levels of zooming and uses offscreen imaging for optimized performance. Java's virtual machine architecture allows the SStructView to be integrated into WWW pages and run on a number of different platforms.

 
5. The proteanD display program. We have published a paper in J. Mol. Graphics describing this program which is designed to display various representations of structural uncertainty for macromolecules, including overlapping stick drawings, ellipsoids of uncertainty, and secondary structure accessible volumes. These representations are closely related to our methodology for computing the structure of ribosomal RNA. The program runs on Silicon Graphics (SGI) machines and sample input files and binary executable code are available in ftp://ftp-smi.stanford.edu/pub/altman/tar.proteand.

 
6. RNAML. This is an XML-based syntax designed to exchange basic RNA molecular information. Using this syntax, one can represent and exchange data relating to sequence (including ambiguous positions, sequence numbering, and base modifications), secondary structure (including helices, base pairs, base triples, pseudoknots, and secondary structure layout), and tertiary structure (including intermolecular interactions).

 

4. Publications

Last update: 03/27/01
By: bada@smi.stanford.edu