Structures Computer Assisted

After approaches to the solution of the major tasks in chemoinformatics have thus been outlined, these methods are put to work in specific applications. Some of these apphcations, such as structure elucidation on the basis of spectral information, reaction prediction, computer-assisted synthesis design or drug design, are presented in Chapter 10. 

P7] N.A. B. Gray, Computer-Assisted Structure Elucidation, Wiley, New York, 1986. 

Zhang and co-workers worked on the structure-based, computer-assisted search for low molecular weight, non-peptidic protein tyrosine phosphate IB (PTPIB) inhibitors, also using the DOCK methodology [89], They identified several potent and selective PTPIB inhibitors by saeening the ACD. 

However, better use of spectral information for more rapid elucidation of the structure of a reaction product, or of a natural product that has just been isolated, requires the use of computer-assisted structure elucidation (CASE) systems. The CASE systems that exist now are far away from being routinely used by the bench chemist. More work has to go into their development. 

A computer assisted approach of heterocyclic structures (825, 826) predicted a new method of synthesis for the thiazole (826). This method was reported soon after by P. Dubs (807). The same program proposed two other methods not yet experimentally checked (827). 

Visual and computer-assisted identification of the structure of a sample analyzed by a mass spectrometer. 

StiJl, D. R., F. F. Westnim, Jr., and G. C. Sinke, The Chemical Thermodynamics of Organic Compounds, John Wiley and Sons, New York, 1969. Stuper, A. J., W. E. Brugger, and P. C. Jurs, Computer Assisted Studies of Chemical Structur e and Biological Function, John Wiley and Sons, New York, 1979. 

It is our pleasure to thank Dr. Don Nicholson for computational assistance and valuable discussions. The authors benefited from the NATO travel grant No 890816.The research of two of the authors (D.Z. and A.N.A) was partially benefited from collaborations within, and has been partially funded by, the Human Capital and Mobility Network on Ab-Initio (from electronic structure) calculation of complex processes in materials (contract ERBCHRXCT930369). 

Molecular modeling itself can be simply described as the computer-assisted calculation, modulation, and visualization of realistic 3D-molecular structures and their physical-chemical properties using force fields/ molecular mechanics. 

Moreover, molecular modeling is one key method of a wide range of computer-assisted methods to analyze and predict relationships between protein sequence, 3D-molecular structure, and biological function (sequence-structure-function relationships). In molecular pharmacology these methods focus predominantly on analysis of interactions between different proteins, and between ligands (hormones, drugs) and proteins as well gaining information at the amino acid and even to atomic level. 

The constantly increasing amount of data coming from high throughput experimental methods, from genome sequences, from functional- and structural genomics has given a rise to a need for computer-assisted methods to elucidate sequence-structure-function relationships. 

Corey EJ, Wipke WT, Cramer RD HI, Howe WJ. Computer-assisted synthetic analysis. Facile man-machine communication of chemical structure by interactive computer graphics. J Am Chem Soc 1972 94 421-30. 

Downs GM, Willett P. Clustering of chemical structure databases for compound selection. In van de Waterbeemd H, editor, Advanced computer-assisted techniques in drug discovery. Weinheim VCH Verlag, 1994. p. 111-30. 

Rose SL, Jurs PC. Computer-assisted studies of structure-activity relationships of A-nitroso compounds. J Med Chem 1981 25 769-76. 

Stuper, A. J., Brugger, W. E., Jurs, P. C. Computer-Assisted Studies of Chemical Structure and Biological Function, Wiley, New York, 1979. 

Stanton, D. T., Jurs, P. C. Development and use of charged partial surface area structural descriptors in computer-assisted quantitative strucmre-property relationship smdies. Anal. Chem. 1990, 62, 2323-2329. 

Baumann, K., Clerc, J. T. Computer-assisted IR spectra prediction - linked similarity searches for structures and spectra. Anal. Chim. Acta 1997, 348, 327-343. 

The electrochemical cell for the polarographic measurements had a four-electrode configuration equipped with a microsyringe, and was connected to a computer-assisted data-acquisition system [7]. On the other hand, the cyclic voltammetric measurements that are also assisted by a computer data-acquisition system were carried out using a gel electrode that contains the aqueous phase [8]. The cell structure was as follows ... 

Warr WA (1993) Computer-assisted structure elucidation. Anal Chem 65 1045A 1087A... 

Weinstein, H., R. Osman, and J. P. Green. 1979. The Molecular Basis of Structure-Activity Relationships Quantum Chemical Recognition Mechanisms in Drug-Receptor Interactions. In Computer-Assisted Drug Design. E. C. Olson and R. E. Christofferson, eds. American Chemical Society, Washington, D.C. 

CASE (computer-assisted structure elucidation) programs. ... 

Morphometric analysis utilizing computer assisted tomography (CAT) or magnetic resonance imaging (MRI) to reveal brain structure ... 

The early structure-activity studies [69, 70] were limited in the number of compounds studied but showed that reasonable correlations could be drawn between the structure of compounds and their biological activity without a complete understanding of the underlying mechanisms involved. Chou and Jurs [71] expanded the approach to structure-activity relationships by applying computer-assisted mathematical and statistical methods to a large set of N-nitroso compounds. These methods... 

Plant Cells and Tissues Structure-Function Relationships. Methods for the Cytochemical/Histochemical Localization of Plant Cell/Tissue Chemicals. Methods in Light Microscope Radioautography. Some Fluorescence Microscopical Methods for Use with Algal, Fungal, and Plant Cells. Fluorescence Microscopy of Aniline Blue Stained Pistils. A Short Introduction to Immunocytochemistry and a Protocol for Immunovi-sualization of Proteins with Alkaline Phosphatase. The Fixation of Chemical Forms on Nitrocellulose Membranes. Dark-Field Microscopy and Its Application to Pollen Tube Culture. Computer-Assisted Microphotometry. Isolation and Characterization of... 

N.A.B. Gray, A. Buchs, D.H. Smith and C. Djerassi, Application of artificial intelligence for chemical inference. Part XXXVI. Computer assisted structural interpretation of mass spectral data, Helv. Chim. Acta, 64 (1981) 458-470. 

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