In today’s tip I am going to feature a resource that I found recently. I’ve been updating our dbSNP tutorial, which Mary & Trey will be presenting at workshops in Morocco, and also our free PDB tutorial, which is sponsored by the RCSB PDB team. I have therefore been thinking about protein structures and small sequence variations a lot lately. As I explored the latest Database issue of NAR looking for resources to do a tip on, I found an article describing the VnD (genetic Variation and Drug) resource, which can also be accessed at the URL www.vandd.org, according to the NAR article. The article is “VnD: a structure-centric database of disease-related SNPs and drugs“, and figure one shows a veritable Who’s Who of protein, variation and disease resources, so I had to investigate.
What I found at VnD made me sure that this was a resource that I wanted to feature in a tip. VnD is from the Korean Bioinformation Center, or KOBIC, who has a list of databases and tools that they provide. I’ll save the rest of the KOBIC resources for another post & concentrate on VnD here. Compiling data from resources such as RefSeq, OMIM, UniProt, PDB, DrugBank, dbSNP, GAD and more might have been cool enough, depending on how it was done, but the VnD also does their own structure modeling analysis on how the variation affects the protein structure and drug/ligand binding.
This tip movie isn’t long enough to really show you the breadth of what is available from the VnD, but I hope it will be enough to encourage you to read the NAR article (listed below), and to check out VnD. One thing to note: don’t expect to find every dbSNP rs# over there – one that I’ve been using in our tutorial isn’t over there. They are specifically interested in variations within genes that might effect drug binding. But hey, you can’t query DrugBank with rs#s, and I’ve never seen the structure modeling done like VnD, so it is a worthy resource that you may want to investigate if you are interested in how genetic variations connect with disease and drug therapies.
VnD: Variations and Drugs resource - http://vnd.kobic.re.kr:8080/VnD/index.jsp
Korean Bioinformation Center (KOBIC) – http://www.kobic.re.kr/
RCSB PDB – http://www.pdb.org
OpenHelix Tutorial on the RCSB PDB – http://www.openhelix.com/pdb
dbSNP: Short Genetic Variations, from NCBI - http://www.ncbi.nlm.nih.gov/projects/SNP/
OpenHelix Tutorial on NCBI’s dbSNP – http://www.openhelix.com/cgi/tutorialInfo.cgi?id=39
For links to other resources and OpenHelix tutorials mentioned in this post, please see our catalog of resources – http://www.openhelix.com/cgi/tutorials.cgi
Yang, J., Oh, S., Ko, G., Park, S., Kim, W., Lee, B., & Lee, S. (2010). VnD: a structure-centric database of disease-related SNPs and drugs Nucleic Acids Research, 39 (Database) DOI: 10.1093/nar/gkq957