CHEM-X/MODEL

Figure 7. Chem-X model for a (WC>3)4 cubane-cluster encapsulated in an a-cage of zeolite Y, projected down a 3-fold axis of the host structure, displaying tungsten-dioxo anchoring to extraffamework site II Na+ cation six-ring binding sites.

A module of the CHEM-X modelling system (see modelling section). Storage and retrieval of two- and three-dimensional structures with substructure-search capability. Available databases include Chapman Hall Dictionary of Drugs (15,000 compounds). Chapman Hall Dictionary of Fine Chemicals (120,000 small organics). Chapman Hall Dictionary of Natural Products (54,000), Derwent Standard Drug File (31,000 biologically active compounds), ChemReact (370,000 reaction types) and others. 

Chem/Model, developed and distributed as part the Chem-X modeling package by Chemical Design Ltd., Chipping Norton, Oxon, U.K. 

The further processing of the results is fully integrated into the Chem-X modelling suite and in particular ChemStat. This allows the automatic calculation of a wide variety of properties, either conformationally dependant or not, such as complex geometry variables which might involve vectors, spatial or even quantum mechanical properties and their subsequent analysis using statistics which can also be presented graphically in the form of scatter plots. 

Chem-X Molecular modeling software suites (workstation) Chemical Design, Ltd. 

Hou, T. J., Xu, X. J. ADME evaluation in drug discovery. 3. Modeling blood-brain barrier partitioning using simple molecular descriptors. /. Chem. Inf. Model. 2003, 43, 2137-2152. 

A. V., Yao, X., Doucet, J. P., Fan, B., Hoonakker, F., Fourches, D., Jost, P., Lachiche, N., Vamek, A. Benchmarking of linear and nonlinear approaches for quanfitafive structure-property relafionship studies of metal complexafion with ionophores. J. Chem. Inf. Model. 2006, 46, 808-819. 

Our efforts were supported by three divisions of the American Qiem-ical Society Carbohydrate Qiemistry Cellulose, Paper, and Textiles and Computers in Chemistry. Additional financial support was provided by Polygen Corporation, suppliers of the Quanta Modeling System, and Chemical Design, developers and distributors of CHEM-X. 

Wang, J.M., Krudy, G., Xie, X.Q., Wu, C.D., Holland, G. Genetic algorithm-optimized QSPR models for bioavailability, protein binding, and urinary excretion. J. Chem. Inf. Model. 2006, 46, 2674-83. 

Some of the more approximate or specialized FFs encountered in the literature include CFF, CHEM-X, COSMIC, CYFF, DREIDING, MMX, SHAPES, TRIPOS, VALBOND, and UFF. Well-known FFs for modeling proteins and nucleic acids include AMBER, CHARMM, ECEPP, GROMOS, OPLS and their variants. Some of these latter FFs compromise the quality of reproducing subtle intramolecular electronic effects for the sake of being fast enough to treat biomacromolecules in long molecular simulations. 

The effective size of 1,1,2,2-tetrabromoethane was determined using CHEM-X molecular modeling. 

The validation process enabled the Danish EPA to state that, the (QSAR) models used here are now so reliable that they are able to predict whether a given substance has one or more of the properties selected with an accuracy of approximately 70-85%. In addition to the use described above, the Danish EPA has developed a QSAR database that contains predicted data on more than 166,000 substances (OSPAR Commission, 2000). The Danish EPA used a suite of commercially available and proprietary QSARs for environmental and human health endpoints (see those listed in Table 19.5). The predictions were made off-line and were stored in a database (derived from the CHEM-X software). The database was searchable by Chemical Abstract Service (CAS) number or chemical name. Only discrete organic chemicals can be stored in the database. 

Ma, X.H. et al. 2008. Evaluation of virtual screening performance of support vector machines trained by sparsely distributed active compounds. J. Chem. Inf. Model. 48, 1227-1237. 

Many of the aforementioned features are combined in integrated molecular modeling software such as SYBYL, Chem-X, COSMIC,80 Quanta and CHARMm, BIOGRAF, Insight and Discover, Chemlab, and MOLIDEA. These packages are available on a variety of hardware platforms ranging from personal computers (PCs) to mainframe computers. 

Chem-X Molecular Modeling Program. Chemical Design Ltd., Oxford, 1991. 

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