Stefano Forli wrote > Hi, > I don't know if it can be useful for this specific problem, but the PDB > has an advanced > search interface which allows to use chemical information to query > structures: > > http://www.rcsb.org/pdb/search/advSearch.do?search=new > Choose a Query Type -> Chemical component: ... > > You can use SMILES, InChi descriptors, or chemical component type, which > include > saccharide groups with various degrees of connections, and you can do > substructure or > similarity searches. > > For the records, each chemical compound that is deposited must have a > unique ID, which > will be in both the PDB and mmCIF files. > > Cheers, > > S > > On 11/20/2015 03:11 AM, Alexandre Fassio wrote: >> Dimitri Maziuk wrote >>> On 11/19/2015 05:07 PM, Alexandre Fassio wrote: >>> >>> ... Apparently, they don't have a >>>> ligand defined on the Chemical Component Dictionary that would >>>> represent >>>> these assembled ligands. >>> >>> As I understand it, they'll make a separate "compound" ligand for things >>> that they see often, like in drugs -- I can't provide an example off the >>> top of my head I'm afraid. For most "one-off" cases they will have them >>> as separate ligands. But there should still be information in the >>> struct_conn table in mmCIF for the macro structure. >>> >>> There's also chem_comp_atom.leaving_atom_flag in the ligand mmCIF, but >>> that one's an even worse mess. :( >>> >>> -- >>> Dimitri Maziuk >>> Programmer/sysadmin >>> BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu >>> >>> >>> ------------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> OpenBabel-discuss mailing list >> >>> OpenBabel-discuss@.sourceforge >> >>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >>> >>> >>> signature.asc (197 bytes) >>> <http://forums.openbabel.org/attachment/4659058/0/signature.asc> >> >> Hi Dimitri, >> >> I got it. Maybe the ligands was assembled to form only one and instead to >> create a new id to this ligand they prefer to represent the used >> compounds >> to represent it. I guess that they create IDs only when the compound is >> seen >> often as you said. >> >> Thanks. >> >> >> >> >> -- >> View this message in context: >> http://forums.openbabel.org/Problem-in-converting-a-PDB-file-to-MOL2-tp4659035p4659061.html >> Sent from the General discussion mailing list archive at Nabble.com. >> >> ------------------------------------------------------------------------------ >> _______________________________________________ >> OpenBabel-discuss mailing list >>
> OpenBabel-discuss@.sourceforge >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >> >> > > -- > > Stefano Forli, PhD > > Assistant Professor of Integrative > Structural and Computational Biology, > Molecular Graphics Laboratory > > Dept. of Integrative Structural > and Computational Biology, MB-112F > The Scripps Research Institute > 10550 North Torrey Pines Road > La Jolla, CA 92037-1000, USA. > > tel: +1 (858)784-2055 > fax: +1 (858)784-2860 > email: > forli@ > http://www.scripps.edu/~forli/ > > ------------------------------------------------------------------------------ > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@.sourceforge > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss Hi Stefano, Thanks for the reply. However, my problem is a bit different. It's more related to how to convert a PDB to Mol2 considering the covalent bonds between the ligands and/or how to get a SDF that represents a set of ligands covalently bonded. Anyway, thank you. best wishes. -- View this message in context: http://forums.openbabel.org/Problem-in-converting-a-PDB-file-to-MOL2-tp4659035p4659063.html Sent from the General discussion mailing list archive at Nabble.com. ------------------------------------------------------------------------------ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
