The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
AceDRG: a stereochemical description generator for ligands
Open accessAbstract
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 CCP 4.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 REFMAC 5 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.
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Cites
PHENIX : a comprehensive Python-based system for macromolecular structure solution
Adams, P. D., Afonine, P. V., Bunkóczi, G., Chen, V. B., Davis, I. W., Echols, N., Headd, J. J., Hung, L.-W., Kapral, G. J., Grosse-Kunstleve, R. W., et al. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444909052925 · Cited by 23,716
Overview of the CCP 4 suite and current developments
Winn, M. D., Ballard, C. C., Cowtan, K. D., Dodson, E. J., Emsley, P., Evans, P. R., Keegan, R. M., Krissinel, E. B., Leslie, A. G. W., McCoy, A., et al. (2011) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444910045749 · Cited by 12,353
Self-citationThe Cambridge Structural Database
Groom, C. R., Bruno, I. J., Lightfoot, M. P., & Ward, S. C. (2016) · Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials · doi:10.1107/s2052520616003954 · Cited by 10,297
Smart, O. S., Womack, T. O., Flensburg, C., Keller, P., Paciorek, W., Sharff, A., Vonrhein, C., & Bricogne, G. (2012) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444911056058 · Cited by 612
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Metadata
- Authors
- Long, F., Nicholls, R. A., Emsley, P., Gražulis, S., Merkys, A., Vaitkus, A., & Murshudov, G. N.
- Venue
- Acta Crystallographica Section D Structural Biology
- Published
- 2017-02-01
- Volume
- 73
- Issue
- 2
- Pages
- 112-122
- ISSN
- 2059-7983 (ISSN-L)
- OpenAlex
- W2585341756
- Cited by
- 398
- References
- 4
- FWCI
- 8.42
- Type
- journal article
- Language
- en
- Open access
- hybrid
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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