I am doing drug - DNA interaction studies. For that I am in need of pdb files for di, tetra, hexa and oligo nucleotides (NMR structures are preferential). I didn't get some of the sequence of nucleotides. Can you please suggest any websites besides the protein data bank?
Dear Radhika,
maybe you can find what you search on the NDB, Nucleic Acid Database:
http://ndbserver.rutgers.edu/
that contains about 7000 structures of DNA, RNA and complex assemblies.
I think that it could be very useful for your purposes.
Federico
Dear Federico,
Thanks for your help..The website was really so useful.
Sincerely
R. Radhika
I radhika,
In RCSB the advance search option can be used to derive all the drug bound DNA solved by NMR data. NDB is a mirror of PDB website ,except for few old fibre models pdb files that are of historic importance. If u r looking specifically for NMR data, be careful to use only the best model from the ensemble structure
Federico, if you are looking for custom oligonucleotides, the nucleic acid builder (NAB) module of AmberTools13 (free from http://ambermd.org/). It is really simple to use and their manuals and tutorials are very detailed and helpful. Good luck!
- Badges
- Science topic
- Similar topics
- Bioinformatics
- Bioinformatics and Computational Biology