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RNA links and information
RNA links and information
[Home] [Search Engines] [Protein information] [Wayne's RNA world]
101229:
This has not been edited for a long time and some of links are quite
probably dead. It is still at the vintage 2002 + my references.
There are the usual excuses I can offer. Mostly, I have been busy,
I only used this occasionally, and AOL stopped hosting web pages.
In short, I had no incentive to fix or maintain it.
051007: some improvements.
The page was constructed mainly to suit my own interests at
some particular time in vintage 2002. It was not updated for
some time, but recently, I at least went through to verify the
links. I added one important link (my own of course), and tracked
down a few links that were nearly lost, but otherwise, it is still
about 2002 vintage. I didn't write it as a general resource since
other web sites that are properly maintained can provide that.
RNA secondary structure prediction servers [top]
RNA secondary structure prediction servers [top]
Michael Zuker's flagship MFOLD server. Other applications are also available at this new web site.
Ivo Hofacker's flagship Vienna package server.
Product of the Belozersky Institute (Moscow State University). The difference between this approach and the traditional RNA secondary structure prediction stratagies is that this method examines sequence alignments. The thermodynamics is the same as the above two programs. Therefore, if all you have is one sequence, this server cannot improve the thermodynamic predictions, but if you have several homologous sequences and a good alignment, it should improve your predictions.
vsfold5: RNA pseudoknot prediction server
Vsfold is my own secondary structure prediction program based upon thermodynamics and using a physical model I discovered during my research. The concepts of this work were originally published as part of a filtering program of the suboptimal structures predicted using mfold in the GCG package (see PubMed 11735286, PubMed 11735287, Plos One and JCSB). All such programs have their limitations and your mileage (kilometers) may vary. All the same, I care about the physics and vsfold4/5 often does better at the standard benchmark RNA structures.
RNA structure software information [top]
RNA structure software information [top]
RNA secondary structure calculations:
RNA symbols
standard abbreviations for various types of bases used in RNA sequences.
Vienna Package: Ivo Hofacker's web page.
The Vienna Package Reference manual (v 1.4)
Michael Zuker's web page contains a host of information and links.
The rules for RNA secondary structure calculations.
Other RNA information resources [top]
Other RNA information resources [top]
useful databases for RNA [top]
The "PDB" equivalent for RNA. The NDB (Nucleic acid DataBase project) was originally located only at Rutgers University, but now has mirror sites in Japan and San Diego.
Something that needs a lot more study (IMHO). Glad to see they managed to get it up and running finally. (University of Queensland).
Information resource for genetics at Cold Springs Harbor Laboratory.
The university of Tokyo Human Genome Center web server Offers a way to search for a variety of gene related issues from a single website.
Useful links to RNA world [top]
This web resource lists Internet links on RNA related topics: Databases, Web Tools, Sequences, RNA secondary structure data, RNA structure software, Books, Tutorials, and lots more.
Rather similar to RNA World at IMB Jena. (link appears to be dead anyway)
The RNA society in the US.
Harvard Dept of MCB - Biology Links: Not specifically devoted to RNA, but provides many useful Links to biology related databases throughout the world.
general info [top]
Standard nucleotide sequence abbreviations
A way to register for online documentation of the Wisconsin.
A Structure for DNA (Nature April 2, 1953)(link probably dead)
Nucleic Acid Resources (link probably dead)
Experiment I-DNA structure (link probably dead)
RNA structure definitions [top]
Madison format: (Leontis and Westhof)
The models presented by Leontis and Westhof is a good place to begin visualizing 3D structures for RNA. I'm not 100% certain that the nomenclature is in full in agreement with the Madison project, but it is the best description so far available (AFAIK). Note, there used to be some 3D figures and examples, but seem to have disappeared.
The Madison format (with Mc-Sym):
Geometric Classification of Non-Canonical Basepairing (taken from the Mc-Sym website because the original site at Stanford seems to be a broken link)
The initial definitions (developed by Tinoco and printed in RNA world first edition) contains Tinoco's list of non-Watson Crick pairings for RNA. Originally cited in The RNA World (1993) and currently posted at JENA.
Standard nucleotide sequence abbreviations
RNA Research Groups [top]
RNA Research Groups [top]
This is hardly complete. It is basically stuff that I happened to save somewhere during some of my searches and managed to remember to write it down here. The presence or absence of anyone is of no personal intension on my part (as far as I know). Anyone who feels I have intensionally missed them can holler at me here. At any rate these are some RNA research groups, and I'll try to add others as I get around to it.
A loose association of research groups at the University of Bern whose research deals with the structure and function of RNA and related nucleic acid molecules.
David Case' group at the Scripts Institute. Part of the Amber forcefield for Molecular dynamics simulations afficionados.
The one who found the first self-splicing intron. NMR structure.
(Department of Chemistry, Yale University) Crothers was one of the early pioneers of RNA thermodynamic studies. Several of the parameters in mfold and the Vienna package originate form his work (and remain essentially unchanged).
(University of Texas at Austin) Basically protein/RNA interactions: currently studying (actually searching for) aptomers to be used binding to such vermin as the AIDS virus. (Link appears to be dead)
The Comparative RNA Web Site: Phylogeny and comparative sequence analysis.
Kawai Laboratory for Structural Biology
Among the early pioneers on ribosomal RNA structure and function research and essentially a household name in RNA/protein research circles. Most notable for proposing that the RNA of the ribosome was the function, and the proteins were the scaffold -- a result that has been largely confirmed in recent years through tRNA footprinting and metal ion cleavage. Other information on Noller's lab can be found here.
Host for the Madison format RNA structure definitions, amoung other things.
A great place to learn about introns. Features a recently opened database for studying introns.
Molecular Information Theory Group: theory of molecular machines.
TBI Theoretical Biochemistry Group
Home of the famous Vienna Package.
(University of Strassburg) One of the early folk in 3D RNA structure. He determined the structure of tRNA(Ala) back in the when some computers still had front panels, took up large rooms and took 10 hours to calculate things we take for granted they can do (now) at the push of the [return] button.
The Zuker lab: home of the famous MFOLD.
last update: 05.10.07
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