Resources

Vanderbilt:

https://medschool.vanderbilt.edu/biochemistry/

http://structbio.vanderbilt.edu/

 

Logistics:

BLAST: https://blast.ncbi.nlm.nih.gov/Blast.cgi

oligo calculator: http://biotools.nubic.northwestern.edu/OligoCalc.html

sequence editor: http://www.fr33.net/seqedit.php

UCSC genome browser: https://genome.ucsc.edu/

 

Structure INFO

RCSB protein data bank: http://www.rcsb.org

Q: Why is it still called the protein data bank? Check out the brown book on the principles of Nucleic acids   

NMR chemical shift database: http://www.bmrb.wisc.edu/

Electron Microscopy: http://www.emdatabank.org/

 

Explorations in RNA:

RNA 3D threading program: http://genesilico.pl/moderna/

RNA 3D motifs: http://iimcb.genesilico.pl/rnabricks

​RNA 3D motif atlas: http://rna.bgsu.edu/rna3dhub/pdb

RNA secondary structure: http://unafold.rna.albany.edu/

RNA secondary structure: http://rna.urmc.rochester.edu/

Non-canonical base pairs: http://prion.bchs.uh.edu/bp_type/bp_structure.html

Comparative RNA database: http://www.rna.icmb.utexas.edu/

Westhof Lab: http://www-ibmc.u-strasbg.fr/upr9002/westhof/index.html

 

Fun leisure reads:

Rediscovering RNA with Anna Pyle

Interactions that stabilize RNA tertiary structure (Pyle and Butcher)

RNA secondary structure adventure-land with Carl Woese and Harry Noller (RNA literature at its best!)