The MRS server at the CMBI (http://mrs.cmbi.umcn.nl/) is very quick. It
is not a dedicated ligand searcher, but it finds 23 files with
tetraethylene glycol. It is just a Google-like text-search engine, but
much smarter than grep; for example "tetraetylene glycol" suggests that
you might want to use it with the h... It does this in 0.3 second, so,
if it doesn't solve your problem, it certainly won't waste much of your
time.
MRS is open source, so you can install your in-house version (see
github). But we will keep the cmbi site up and running for a while...
Gert
On 2-10-2018 7:17, Murpholino Peligro wrote:
Hi all.
I was searching for ligands/molecules at
www.rcsb.org/pdb/ligand/chemAdvSearch.do
<http://www.rcsb.org/pdb/ligand/chemAdvSearch.do> (middle tab in
blue). If I try to search with the third option, i.e. "name" of the
ligand/molecule, it never works. I tried tetraethylene glycol, nitric
oxide, cisplatin and even the example provided biotin. Fortunately
specifying the identifier (i.e. 3 letters..2 in some cases)... works.
The problem is...what if I do not know the identifier?
I was wondering if you know another database that might work better
for me? (or you, if your brain works better with chemical names
instead of identifiers)
Ps If there is some sort of coordinate file, preferably pdb or xyz, to
download that will be better.
* Pubchem works with sdf files which I do not like because if I open
the sdf file for biotin with pymol and then save it as pdb, and then
open this on coot it looks strange... (png attached)
(not sure if this is pymol's or coot's fault...but that's another
thread I guess)
Thanks
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