Protein Data Bank database generation

Computational results were obtained using Spartan 08 (Wavefunction Inc., Irvine, CA) and software programs from Accelrys Software Inc. with graphical displays generated by the Discovery Studio Visualizer. Where protein structures have been downloaded from the RCSB Protein Data Bank the full references and PDB IDs have been given. I wish to acknowledge the use of the Chemical Database Service at Daresbury for access to other crystal structures. Again, full primary sources can be found in the references. 

Structure retrieval or generation Crystal structures of organic compounds can be found in the Cambridge Crystallographic Data Centre (CCDC) database (http //www.ccdc.cam.ac.uk/). Those that do not exist may be generated by 3D rendering software. The 3D structural coordinates of biomacromolecules can be retrieved from the Protein Data Bank (http //www.rcsb.org/pdb/). 

Ricketts, E.M. Rradshaw, J. Hann, M. Hayes, F. Tanna, N. Ricketts. D.M. 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. 1993, 33. 905-925. 

The IsoStar library contains over 25 000 pre-generated scatter plots, derived principally from the CSD, but also with contributions from the Protein Data Bank (PDB) [2]. The scatter plots are hyperlinked to both databases so that specific interactions... 

E. M. Ricketts,/. Bradshaw, M. Hann,F. Hayes,N.Tanna, and D. M. Ridketts,/. Chem. Inf. Comput. Set., 33, 905 (1993). Comparison of Conformations at Small Molecules from the Protein Data Bank with Those Generated by Concord, Cobra, ChemDBS-3D and Converter, and Those Extracted from die Cambridge Structural Database. 

Cambridge Structural Database De Novo Ligand Design Pharmacophore and Drug Discovery Protein Data Bank (PDB) A Database of 3D Structural Information of Biological Macromolecules Structure Databases Three-dimensional Structure Generation Automation Three-dimensional Structure Searching. 

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