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Eight large chemical databases have been analyzed and compared to each other. Central to this comparison is the open National Cancer Institute (NCI) database, consisting of approximately 250 000 structures. The other databases analyzed are the Available Chemicals Directory ("ACD," from MDL, release 1.99, 3D-version); the ChemACX ("ACX," from CamSoft,(More)
A Web-based, graphical user interface has been developed to conduct rapid searches by numerous criteria in the more than 250,000 structures of the Open NCI Database. It is based on the chemistry information toolkit CACTVS. Nearly all structures and anticancer and anti-HIV screening data provided by NCI's Developmental Therapeutics Program have been(More)
A number of inexpensive computers were benchmarked with the ab initio program Gaussian 94, using both small standard test jobs and larger density functional (DFT) calculations. Several varieties of Pentium (x86) and Alpha CPU based systems were tested. Most of them were running under the open source code operating system Linux. They were compared with(More)
BACKGROUND A molecule editor, i.e. a program facilitating graphical input and interactive editing of molecules, is an indispensable part of every cheminformatics or molecular processing system. Today, when a web browser has become the universal scientific user interface, a tool to edit molecules directly within the web browser is essential. One of the most(More)
A data set of 379 drugs and drug analogs that are metabolized by human cytochrome P450 (CYP) isoforms 3A4, 2D6, and 2C9, respectively, was studied. A series of descriptor sets directly calculable from the constitution of these drugs was systematically investigated as to their power into classifying a compound into the CYP isoform that metabolizes it. In a(More)
Chemotypes are a new approach for representing molecules, chemical substructures and patterns, reaction rules, and reactions. Chemotypes are capable of integrating types of information beyond what is possible using current representation methods (e.g., SMARTS patterns) or reaction transformations (e.g., SMIRKS, reaction SMILES). Chemotypes are expressed in(More)
The incompleteness of genome-scale metabolic models is a major bottleneck for systems biology approaches, which are based on large numbers of metabolites as identified and quantified by metabolomics. Many of the revealed secondary metabolites and/or their derivatives, such as flavor compounds, are non-essential in metabolism, and many of their synthesis(More)
The pharmacophore-guided approach used in the first phase of the design of novel protein kinase C (PKC) ligands was based on the study of the geometry of bioequivalent pharmacophores present in diacylglycerol (DAG) and in the more potent phorbol ester tumor promoters. A number of potent DAG lactones were generated by this approach, in which the glycerol(More)
The synthesis of new compounds is a quite time consuming and cost expensive task. The need to search and evaluate alternative synthetic paths is a mandatory step before going to the lab. Searching in reaction databases may provide some information about how a compound can be synthesized but often fails if the target is not present in the database. The(More)