Molecular databases

Sequence and molecular databases http //helix.nih.gov/science/databases.html... 

NEW Spartan Model Electronic Modeling Kit, A set of easy-to-use builders allow for the construction and 3-D manipulation of molecules of any size or complexity— from a hydrogen atom to DNA and everything in between. This kit includes the SpartanModel software on CD-ROM, an extensive molecular database, 3-D glasses, and a Tutorial and Users Guide that includes a wealth of activities to help you get the most out of your course. (0-495-01793-0)... 

Jorissen RN, Gilson MK. Virtual screening of molecular databases using a Support Vector Machine. J Chem Inf Model 2005 45 549-61. 

One method of choosing a diverse set of compounds from a molecular database is to first cluster them (see, for example ref. 12) and then select one molecule from each cluster. Clustering ideally groups the molecules into well-separated, compact groups with respect to the descriptor variables. If this is the case, then each cluster or group can be represented by one of its members. This method of choosing a diverse set of objects goes back at least to Zemroch (13) in the statistics literature and has been widely used for chemical databases (14,15). 

The method can also be used to assess the diversity of an existing molecular database by asking how many cells are represented (17). 

The above findings relate to one assay and one data set built up over time, possibly with many analogs of active compounds, and the findings might be different for commercial molecular databases. More benchmarking along these lines is needed. 

However, in recent years the term "in silica expanded its meaning to any type of modeling performed with the use of a computer. This includes the use of experimentally measured in vitra and/or in viva data for the prediction of in viva pharmacokinetics, as well as the construction and analysis of molecular databases. 

Koppenhoefer, B., Nothdurft, A., Pierrot-Sanders, J., Piras, P.,Popescu, P, Roussel, C., Stiebler, M., and Trettin, U. 1993. CHIRBASE A graphical molecular database on the separation of enantiomers by liquid, supercritical fluid, and gas chromatography. Chirality 5 213-219. 

Roussel, C. and Piras, P. 1993. CHIRBASE, a molecular database for storage and retrieval of chro-... 

CHIRBASE, A Molecular Database for Chiral Chromatography. 1992. http //chirbase. u-3mrs.fr/. 

The tools have recently been compared and evaluated in the context of molecule mining.1111 Worlein el al. reimplemented all four methods (same code base, programming expertise and optimization effort). Benchmarks were carried out on a comprehensive set of graph databases, including molecular databases. The molecular databases used were the IC93 (1283 compounds),1121 the HIV assays 1999 (42 689 compounds)1131 and the NCI (237 771 compounds).1141... 

Molecular databases and the associated data banks require the development of a conceptual structure for the information stored about the molecules, descriptive language representing the data, and methods for analysis enabling molecular modeling, similarity searches, classification, visualization, or other uses of the database.320 Currendy, the Protein Data Bank (PDB http 7www.rcsb.org/pdb/) is one of the best known examples of a molecular database. The PDB is a worldwide archive of three-dimensional structural data of biological macromolecules.321 The PDB is a common accentor to many structural databases.322 The success of... 

These pages provide links to larger resource categories such as GenBank, Molecular databases, Genomes and Maps, Tools, Software engineering, and FTP sites. There is also a table with a comprehensive alphabetical index of Web resources. 

Molecular Database Nucleotide Sequences Protein Sequences Structures... 

NIFS databases are widely used directly and through IAEA Genie (only for excitation and ionization cross-sections). New molecular databases will be open soon. A new database for dielectronic satellite lines has been created. In order to store your data in our databases, we are grateful if you send us your numerical data which have been published in a Journal. Organized international collaboration for database would be more efficient for data evaluation and data compilation. 

The Lipinski Rule-of-Five almost certainly represents the first real attempt to identify a drug-like filter for molecular databases. Lipinski analysed the compounds within the World Drag Index that had progressed to Phase II clinical trials or better and discovered a simple set of rales that have been used extensively since their publication in 1997. The LRoF states that a compound may have lower membrane permeability or poorer absorption if two or more of the rules are violated. These rules are a compound should have no more than 5 hydrogen-bond donors, no more than... 

The general aim of VS methods is to retrieve from a molecular database a fraction of true positives that is significantly larger than that of a random compound selection. If a VS method selects n molecules from a database with N entries, the selected hit list consists of active compounds (true positive compounds, TP) and decoys (false positive compounds, FP). Active molecules that are not retrieved by the VS method are defined false negatives FN), whereas the unselected database decoys represent the true negatives TN) (Figure 3.3). 

The TAE/RECON method, developed by Breneman and co-workers based on Bader s quantum theory of Atoms In Molecules (AIM). The TAB method of molecular electron density reconstruction utilizes a library of integrated atomic basins , as defined by the AIM theory, to rapidly reconstruct representations of molecular electron density distributions and van der Waals electronic surface properties. RECON is capable of rapidly generating 6-31-I-G level electron densities and electronic properties of large molecules, proteins or molecular databases, using TAB reconstruction. A library of atomic charge density fragments has been assembled in a form that allows for the rapid retrieval of the fragments, followed by rapid molecular assembly. Additional details of the method are described elsewhere. ... 

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