Three-dimensional molecular database

THREE-DIMENSIONAL MOLECULAR DATABASES AND PHARMACOPHORE SEARCHING... 

Nikolovska-Coleska Z, Xu L, Hu Z, et al. Discovery of embelin as a cell-permeable, small-molecular weight inhibitor of XIAP through structure-based computational screening of a traditional herbal medicine three-dimensional structure database. J Med Chem 2004 47 2430-2440. 

Martin, Y.C., Danaher, E.B., May, C.S., and Weininger, D. MENTHOR, a database system for the storage and retrieval of three-dimensional molecular structures and associated data searchable by sub structural, biologic, physical, or geometric properties./. Comput.-Aided Mol. Des. 1998, 1, 15-29. 

D. MACCS-3D a new database system for three-dimensional molecular models. Chem. Inf. Syst. 1990, 42-49. 

Lysozyme and Antibodies To fully appreciate how proteins function in a cell, it is helpful to have a three-dimensional view of how proteins interact with other cellular components. Fortunately, this is possible using on-line protein databases and the three-dimensional molecular viewing utilities Chime and Protein Explorer. If you have not yet installed the Chime plug-in on your computer, go to www.mdlchime.com/chime and follow the instructions for your operating system and browser. Once chime is installed, go to the Protein Data Bank (www.rcsb.org/pdb). 

Matter H, Selecting optimally diverse compounds from structural databases A validation study of two-dimensional and three-dimensional molecular descriptors, J. Med. Chem., 40 1219-1229, 1997. 

Another simple approach to finding new inhibitors based on SAR data is to search for compounds that are similar to existing inhibitors. Either two-or three-dimensional molecular descriptors can be calculated for each molecule, and a search is performed on a database to find compounds whose descriptors are most similar to the known inhibitors. Two-dimensional descriptors can be calculated very rapidly, allowing hundreds of thousands of structures to be processed in an hour. Three-dimensional descriptors are more challenging, since they require a time-consuming three-dimensional... 

Matter, H. (1997). Selecting Optimally Diverse Compounds from Structure Databases. A Validation Study of Two-Dimensional and Three-Dimensional Molecular Descriptors. J.Med.Chem., 40,1219-1229. 

New SQL functions and data types can be used to extend a relational database. This is explained in Chapter 10 using PostgreSQL as an example. Ways in which three-dimensional molecular structures can be stored are examined in Chapter 11. This chapter also advocates using an RDBMS instead of molecular structure files and shows how this transition might be accomplished. 

MENTHOR, A Database System for the Storage and Retrieval of Three-Dimensional Molecular Structures and Associated Data Searchable by Substructural, Biological, Physical, or Geometric Properties. 

Molecular graphics visualization software performs an elaborate connect-the-dots process to make the wonderful pictures of protein structure we see in textbooks of biomolecular structure, like the structure for insulin (SINS Isaccs and Agarwa, 1978) shown in Figure 5.1. The connections used are, of course, the chemical bonds between all the atoms. In current use, three-dimensional molecular structure database records employ two different minimalist approaches regarding the storage of bond data. 

A complete application programming interface is available for MMDB as part of the NCBI toolkit, containing a wide variety of C code libraries and applications. Both an ASN.l input/output programming interface layer and a molecular computing layer (MMDB-API) are present in the NCBI toolkit. The NCBI toolkit supports x86 and alpha-based Windows platforms, Macintosh 68K and PowerPC CPUs, and a wide variety of UNIX platforms. The three-dimensional structure database viewer (Cn3D) is an MMDB-API-based application with soince code included in the NCBI toolkit. 

Biomolecular three-dimensional structure database records are cmrently not compatible with macroscopic software tools such as those based on CAD software. Computer-aided design software represents a mature, robust technology, generally superior to the available molecular structure software. However, CAD software and file formats in general are ill-suited to examine the molecular world, owing to the lack of certain specialty views and analytical functions built in for the examination of details of protein structures. 

The classic database of three-dimensional molecular struaures is the Cambridge Structural Database. It contains evaluated small-molecule and polymer X-ray and neutron diffraction data for more than 70,000 compounds. The database grows at the rate of 10% per year. It contains the connection table of each structure (frequently a complex or solvate), the bibliographic... 

Y. C. Martin, E. A. Danaher, C. S. May, and D. Weininger,/. Comput.-AidedMol. Design, 2, 15 (1988). MENTHOR, a Database System for the Storage and Retrieval of Three-Dimensional Molecular Structures and Associated Data Searchable by Substructural, Biologic, Physical, or Geometric Properties. 

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