3D structure databases

Today, 3D databases, which provide the means for storing and searching for 3D information of compounds, are proven to be useful tools in drug discovery programs. This is well exemplified with the recent discovery of novel nonpeptide HIV-1 protease inhibitors using pharmacophore searches of the National Cancer Institute 3D structural database [13-15]. 

B. D., Hillman, D. Building 3D structural databases experiences with MDDr-3D and FCD-3D. Tetrahedron Comput. Methodol. 1990, 3, 531-536. 

The implementation of efficient and updated 2D and 3D structure databases is one major challenge in molecular diversity management. In addition to the compound design and selection criteria used for the compilation, the quality of the compound storage, manipulation, and logistics systems used for the management of the collection are key factors to yield reproducible results. ... 

Comparative molecular field analysis (CoMFA). 2. Towards its use with 3D-structural databases. Tetrahedron Comput. Methodol. 3, 47-59. 

FIGURE 11.2. The 3D protein structure of fasciculin 1 derived from green mamba (Dendroaspis angusticeps) snake venom. [Image obtained from the public domain at the US National Library of Medicine, National Center for Biotechnology Information, Molecular Modeling Database 3D Structure Database (MMDB)]. 

Clark, M., Cramer, R. D., Ill, Jones, D., Patterson, D., Simeroth, P. Comparative molecular field analysis (CoMFA) 2. Toward its use with 3D structural databases. Tetrahedron Comp. Meth. 1990, 3, 47. 

See also Dynamics of Protein Folding (from chapter 6), Chaperonins, 3D Structural Database... 

There are numerous current trends in the software and methodology of CAMD. Two of the most important are 1) the growing use of 3D structural databases, and 2) the merging of statistical modeling and molecular modeling techniques in finding solutions to CAMD problems. 

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