Hi all,
Non redundant dataset of proteins can be prepared by many available methods. Can I do the same for DNA, RNA or protein-DNA complex.
Any information regarding the Server or procedure will be very helpful to me.
Thanx in advance
The NDB had a tool to obtain a list of non-redundant RNA-contained structures in the archive. http://rna.bgsu.edu/rna3dhub/nrlist/. Unfortunately, it hasn't been updated since the end of the year- which .. is .. strange - and I will look into that.
As you said, RCSB PDB does keep clusters for proteins, but doing it for DNA is tough because we have so many short oligo segments, incompletely resolved parts, and whatnot in the structures.
source: I work for the RCSB.
Dear prasun,
you can download 3D structures of nucleic acid from NDB instead of PDB. NDB structural database is updated and it contains 7430 nucleic acid structures still 1 april 2015. PLZ REFER
http://ndbserver.rutgers.edu/
for protein-nucleic acid complexes you can download it from PDB or MMDB.
- Badges
- Science topic