Molecular modeling technique structure

Molecular mechanics is the simplest and the most commonly used molecular modelling technique. It focuses on the low energy structures of molecules which correspond to energy minima in the classical force field used to represent the molecule [44]. A typical molecular mechanics study consists of the following steps [45] ... 

Molecular modeling techniques are a powerful tool to obtain a very detailed insight in the three-dimensional structure of dendrimer molecules at the atomic level. They have been applied to calculate sizes of the polypropylene imine) dendrimers and radial density profiles in order to estimate the free volume inside the dendrimers, as well as to make predictions about de Gennes dense-packed generations. The molecular modeling work by Coussens and co-workers [20] was focused on the generations 1-5 of the DAB-dendr-(CN)n and DAB-dendr-(NH2)n (n = 4, 8, 16,32, 64). 

For quantitative structure-activity relationship (QSAR) studies a three-dimensional model of a DNA-quinoIone complex was built using molecular modeling techniques. It was based on the intercalation of quinolone into the double helix of DNA. It was concluded that the intercalation model is consistent with most available data on the structure of the quinolone complex. This predicted... 

A relatively recent development in QSAR research is molecular reference (MOLREF). This molecular modelling technique is a method that compares the structures of any number of test molecules with a reference molecule, in a quantitative structure-activity relationship study (27). Partial least squares regression analysis was used in molecular reference to analyse the relation between X- and Y-matrices. In this paper, forty-two disubstituted benzene compounds were tested for toxicity to Daphnia... 

Atomistic molecular modeling techniques have proven to be a very useful tool for the investigation of the structure and dynamics of dense amorphous membrane polymers and of transport processes in these materials. By utilizing these methods, information can be obtained that is not accessible by experimental means. 

In the search for new drug candidates, scientists use molecular modeling techniques to identify potentially new structural moieties and screen natural sources or large families of synthetically related compounds, along with modifying exisiting compounds. Once a potentially new drug has been iden-... 

Although crystallographical protein structures are firmly based on experimental data, it must be borne in mind that for resolutions of around 2 A and worse, the electron density maps are not sufficiently detailed to resolve individual atoms. In order to circumvent this problem, molecular modeling techniques are often applied and usually yield reliable structural models that best represent the measured diffraction patterns (25). However, the likelihood of... 

Over the last 40 years, the scientific literature has abounded with examples of the application of quantitative structure-activity relationships (QSARs) and molecular modeling techniques to the problem of predicting biological activity. The application of these techniques to the prediction of pharmacokinetic or toxicokinetic parameters has been, until recently, less intensely researched. 

Masimirembwa, I. Zamora, Structural analysis of CYP2C9 and CYP2C5 and an evaluation of commonly used molecular modeling techniques, Drug Metab. Dispos. 2004, 32, 1218-1229. 

Some attempts to inclnde structural diffusion exist. The mechanism of proton transport in bulk water has been studied by various molecular modeling techniques like the Car-Parinello ab initio molecnlar dynamics simnlations (CPAIMD), mixed quan-tnm and classical mechanics technique (QM/MM), E " ... 

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