PMID- 28177307 OWN - NLM STAT- MEDLINE DCOM- 20171025 LR - 20171025 IS - 2059-7983 (Electronic) IS - 2059-7983 (Linking) VI - 73 IP - Pt 2 DP - 2017 Feb 1 TI - AceDRG: a stereochemical description generator for ligands. PG - 112-122 LID - 10.1107/S2059798317000067 [doi] AB - The program AceDRG is designed for the derivation of stereochemical information about small molecules. It uses local chemical and topological environment-based atom typing to derive and organize bond lengths and angles from a small-molecule database: the Crystallography Open Database (COD). Information about the hybridization states of atoms, whether they belong to small rings (up to seven-membered rings), ring aromaticity and nearest-neighbour information is encoded in the atom types. All atoms from the COD have been classified according to the generated atom types. All bonds and angles have also been classified according to the atom types and, in a certain sense, bond types. Derived data are tabulated in a machine-readable form that is freely available from CCP4. AceDRG can also generate stereochemical information, provided that the basic bonding pattern of a ligand is known. The basic bonding pattern is perceived from one of the computational chemistry file formats, including SMILES, mmCIF, SDF MOL and SYBYL MOL2 files. Using the bonding chemistry, atom types, and bond and angle tables generated from the COD, AceDRG derives the `ideal' bond lengths, angles, plane groups, aromatic rings and chirality information, and writes them to an mmCIF file that can be used by the refinement program REFMAC5 and the model-building program Coot. Other refinement and model-building programs such as PHENIX and BUSTER can also use these files. AceDRG also generates one or more coordinate sets corresponding to the most favourable conformation(s) of a given ligand. AceDRG employs RDKit for chemistry perception and for initial conformation generation, as well as for the interpretation of SMILES strings, SDF MOL and SYBYL MOL2 files. FAU - Long, Fei AU - Long F AD - Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England. FAU - Nicholls, Robert A AU - Nicholls RA AD - Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England. FAU - Emsley, Paul AU - Emsley P AD - Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England. FAU - Graaeulis, Saulius AU - Graaeulis S AD - Institute of Biotechnology, Sauletekio al. 7, LT-10257 Vilnius, Lithuania. FAU - Merkys, Andrius AU - Merkys A AD - Institute of Biotechnology, Sauletekio al. 7, LT-10257 Vilnius, Lithuania. FAU - Vaitkus, Antanas AU - Vaitkus A AD - Institute of Biotechnology, Sauletekio al. 7, LT-10257 Vilnius, Lithuania. FAU - Murshudov, Garib N AU - Murshudov GN AD - Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England. LA - eng PT - Journal Article DEP - 20170201 PL - United States TA - Acta Crystallogr D Struct Biol JT - Acta crystallographica. Section D, Structural biology JID - 101676043 RN - 0 (Bacterial Proteins) RN - 0 (EthR protein, Mycobacterium tuberculosis) RN - 0 (Ligands) RN - 0 (Repressor Proteins) RN - 0 (Small Molecule Libraries) RN - EC 5.4.- (Intramolecular Transferases) RN - EC 5.4.99.9 (UDP-galactopyranose mutase) SB - IM MH - Bacterial Proteins/chemistry/metabolism MH - Binding Sites MH - Crystallography, X-Ray MH - Databases, Factual MH - Deinococcus/chemistry/metabolism MH - Intramolecular Transferases/chemistry/metabolism MH - Ligands MH - Models, Molecular MH - Molecular Conformation MH - Mycobacterium tuberculosis/chemistry/metabolism MH - Repressor Proteins/chemistry/metabolism MH - Small Molecule Libraries/*chemistry/metabolism MH - *Software MH - Stereoisomerism PMC - PMC5297914 OTO - NOTNLM OT - AceDRG OT - Crystallography Open Database OT - RDKit OT - ligand chemistry OT - refinement EDAT- 2017/02/09 06:00 MHDA- 2017/10/27 06:00 CRDT- 2017/02/09 06:00 PHST- 2016/09/29 00:00 [received] PHST- 2017/01/03 00:00 [accepted] PHST- 2017/02/09 06:00 [entrez] PHST- 2017/02/09 06:00 [pubmed] PHST- 2017/10/27 06:00 [medline] AID - S2059798317000067 [pii] AID - 10.1107/S2059798317000067 [doi] PST - ppublish SO - Acta Crystallogr D Struct Biol. 2017 Feb 1;73(Pt 2):112-122. doi: 10.1107/S2059798317000067. Epub 2017 Feb 1. PMID- 22505262 OWN - NLM STAT- MEDLINE DA - 20120416 DCOM- 20120619 LR - 20141016 IS - 1399-0047 (Electronic) IS - 0907-4449 (Linking) VI - 68 IP - Pt 4 DP - 2012 Apr TI - Handling ligands with Coot. PG - 425-30 LID - 10.1107/S0907444912000200 [doi] AB - Coot is a molecular-graphics application primarily aimed to assist in model building and validation of biological macromolecules. Recently, tools have been added to work with small molecules. The newly incorporated tools for the manipulation and validation of ligands include interaction with PRODRG, subgraph isomorphism-based tools, representation of ligand chemistry, ligand fitting and analysis, and are described here. FAU - Debreczeni, Judit E AU - Debreczeni JE AD - Structure and Biophysics, DS, AstraZeneca, Alderley Park SK10 4TG, England. judit.debreczeni@astrazeneca.com FAU - Emsley, Paul AU - Emsley P LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120316 PL - United States TA - Acta Crystallogr D Biol Crystallogr JT - Acta crystallographica. Section D, Biological crystallography JID - 9305878 RN - 0 (Ligands) SB - IM MH - Crystallography, X-Ray/*methods MH - Ligands MH - Models, Molecular MH - Software PMC - PMC3322601 OID - NLM: PMC3322601 EDAT- 2012/04/17 06:00 MHDA- 2012/06/20 06:00 CRDT- 2012/04/17 06:00 PHST- 2011/08/25 [received] PHST- 2012/01/03 [accepted] PHST- 2012/03/16 [epublish] AID - S0907444912000200 [pii] AID - 10.1107/S0907444912000200 [doi] PST - ppublish SO - Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):425-30. doi: 10.1107/S0907444912000200. Epub 2012 Mar 16.