A complete small molecule dataset from the protein data bank

FEBS Letters

Volumn 580, Issue 6, 2006, Pages 1649-1653

  Feldman, Howard J ^a   Snyder, Kevin A ^a   Ticoll, Amy ^a   Pintilie, Greg ^a   Hogue, Christopher W V ^a,b  

^a Blueprint Initiative   (Canada)

^b MOUNT SINAI HOSPITAL   (Canada)

Author keywords

Docking; Heterogen; Molecular perception; Polysaccharide; Small molecule

Indexed keywords

CARBOHYDRATE DERIVATIVE; CYCLOPEPTIDE; MONOMER; POLYMER; POLYSACCHARIDE;

ALGORITHM; ARTICLE; DATA BASE; MOLECULAR MODEL; MOLECULAR SIZE; NOMENCLATURE; PRIORITY JOURNAL; PROTEIN DATA BANK; PROTEIN STRUCTURE;

DATABASES, PROTEIN; LIGANDS; MOLECULAR STRUCTURE; PROTEINS;

EID: 33344474627     PISSN: 00145793     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.febslet.2006.02.003     Document Type: Article

References (16)

1. N. Deshpande The RCSB protein data bank: a redesigned query system and relational database based on the mmCIF schema Nucleic Acids Res. 33 2005 D233 D237
2. Sayle, R.A. (2001) PDB: Cruft to content (perception of molecular connectivity from 3D coordinates). In: Daylight User Group Meeting, Santa Fe, NM.
3. A.W. Schuttelkopf, and D.M. van Aalten PRODRG: a tool for high-throughput crystallography of protein-ligand complexes Acta Crystallogr. D: Biol. Crystallogr. 60 2004 1355 1363
4. J.C. Baber, and E.E. Hodgkin Automatic assignment of chemical connectivity to organic molecules in the Cambridge structural database J. Chem. Inf. Comput. Sci. 32 1992 401 406
5. P. Labute On the perception of molecules from 3D atomic coordinates J. Chem. Inf. Model. 45 2005 215 221
6. R.A. Laskowski, V.V. Chistyakov, and J.M. Thornton PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids Nucleic Acids Res. 33 2005 D266 D268
7. G.J. Kleywegt, and T.A. Jones Databases in protein crystallography Acta Crystallogr. D54 1998 1119 1131
8. S. Velankar, P. McNeil, V. Mittard-Runte, A. Suarez, D. Barrell, R. Apweiler, and K. Henrick E-MSD: an integrated data resource for bioinformatics Nucleic Acids Res. 33 2005 D262 D265
9. M. Hendlich, F. Rippmann, and G. Barnickel BALI: automatic assignment of bond and atom types for protein ligands in the Brookhaven protein databank J. Chem. Inf. Comput. Sci. 37 1997 774 778
10. M. Hendlich, A. Bergner, J. Gunther, and G. Klebe Relibase: design and development of a database for comprehensive analysis of protein-ligand interactions J. Mol. Biol. 326 2003 607 620
11. C. Alfarano The biomolecular interaction network database and related tools 2005 update Nucleic Acids Res. 33 2005 D418 D424
12. J. Chen MMDB: Entrez's 3D-structure database Nucleic Acids Res. 31 2003 474 477
13. A. Dalby, J.G. Nourse, W.D. Hounshell, A.K.I. Gushurst, D.L. Grier, B.A. Leland, and J. Laufer Description of several chemical structure file formats used by computer programs developed at Molecular Design Limited J. Chem. Inf. Comput. Sci. 32 1992 244 255
14. D. Weininger SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules J. Chem. Inf. Comput. Sci. 28 1988 31 36
15. Gabow, H. (1973) Implementation of Algorithms for Maximum Matching on Nonbipartite Graphs. PhD thesis, Department of Computer Science, Stanford University.
16. E.M. Ricketts, J. Bradshaw, M. Hann, F. Hayes, and N. Tanna Comparison of conformations of small molecule structures from the protein data bank with those generated by Concord, Cobra, ChemDBS-3D and Converter and those extracted from the Cambridge structural database J. Chem. Inf. Comput. Sci. 33 1993 905 925