Computer-assisted molecular modeling

In contrast, quantum mechanical calculations are more time consuming but are not dependent on empirical parameterization (i.e., they are ab initio). These methods have long been used to deduce and rationalize the structures and relative energies not 

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Computer-assisted molecular modeling (CAMM), 16 726 uses of, 16 728-757... 

Computer-assisted molecular modeling package, 10 331-333 Computer-assisted tomography (CAT), sodium iodide in, 22 827 Computer-automated image analysis, as a particle counting method, 18 146-149 Computer-controlled viscometers, 21 732 Computer controller, closed loop fuel metering system, 10 57 Computer control loop, components of, 20 677-678... 

We determined the structure of human PNP by x-ray crystallography and used these results in combination with computer-assisted molecular modeling to design inhibitor candidates. We examined how well the shape and chemical... 

Computational biochemistry and computer-assisted molecular modeling have rapidly become a vital component of biochemical research. Mechanisms of ligand-receptor and enzyme-substrate interactions, protein folding, protein-protein and protein-nucleic acid recognition, and de novo protein engineering are but a few examples of problems that may be addressed and facilitated by this technology. 

Proton nuclei located at different positions within the small molecules and amino adds that were investigated exhibit similar degrees of spin-probe accessibility as shown by the similar values of slope d(l/Ti)/dC for these protons in the presence of the neutral spin-probe IV. This experimental observation is consistent with the theoretical estimation of spin-probe accessibility as studied by computer-assisted molecular modeling of the various amino acid/spin-probe encounter complexes in our study. 

A. M. Jeffery and R. M. J. Liskamp, Proc. Natl. Acad. Sci. USA, 83, 241 (1986). Computer Assisted Molecular Modelling of Tumor Promoters. 

To establish the relative configuration of the newly formed stereocenters of the bridged 1,2-oxazocine 109, obtained from an alkene-aldehyde intermediate, a computer-assisted molecular modeling coupled with I/hh calculations was utilized. 

Although desirable, it is generally difficult to obtain direct experimental evidence on the transition states and detailed pathways of individual elementary steps in a catalytic cycle. It may then be useful to apply the technique of computer-assisted molecular modeling as the next-best alternative, to obtain relevant information on proposed elementary reactions of a catalytic cycle (cf. Section 3.1.2). The results of molecular modeling studies, which we undertook to obtain a more detailed, though qualitative, understanding of some elementary steps in the above mentioned Pd-methoxy cycle for propyne carbonylation, are summarized below. 

Once an enzyme or receptor has been identified, ideally it should be isolated and characterized. A three-dimensional structure is very useful and can be determined from X-ray crystallography, NMR or by some other means which may include computer-assisted molecular modeling. The mechanism for the normal catalytic activity of the enzyme should be understood. This includes knowing the natural substrates, any natural inhibitors, and any coenzyme requirements. An i n vitro assay method must be developed to quantitatively test the effectiveness of potential inhibitors. At this point molecular modeling techniques can be used in the design process. 

Selectivity of the compound for pest and non-pest species can also be designed into the molecule with the aid of computer-assisted molecular modeling techniques. There are several ways to affect this selectivity differential inhibition of the enzyme,... 

The scientist has an innate desire to be able to rationally design a compound with a predicted (biological) activity. Computer-assisted molecular modeling techniques. X-ray crys-... 

It is to be expected that in the near future point mutations in the cloned and expressed 5-HT transporter together with computer assisted molecular modelling techniques wiU probably lead to a greater imderstanding of the exact mode of binding of 5-HT uptake inhibitors of different chemical structures. 

Computer assisted molecular modelling could establish the relative binding orientations of the different drugs and thus offer some insight in the topography of the bindii site on the 5-HT transporter. 

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