Molecular modeling methods

Computer graphics has had a dramatic impact upon molecular modelling. It should always be remembered, however, that there is much more to molecular modelling than computer graphics. It is the interaction between molecular graphics and the imderlying theoretical methods that has enhanced the accessibility of molecular modelling methods and assisted the analysis and interpretation of such calculations. 

In conclusion, we can say that molecular orbital methods, sometimes in conjunction with molecular modeling methods, are a precious tool in the investigation of anti-tumor drugs. 

Tian, J. et al., Probing the binding of scutellarin to human serum albumin by circular dichroism, fluorescence spectroscopy, FTIR, and molecular modeling method. Biomacromolecules, 5, 1956, 2004. 

The committee recognizes that the design and synthesis of molecules or structures that exhibit useful chemical recognition properties is extremely difficult, with a high risk of failure. Advanced molecular modeling methods are beginning to be applied to this area, but preliminary results are... 

Affinity and recognition may be analysed along such qualitative or semi-quantitative considerations [1.27, 2.3, 2.4]. These are translated into quantitative factors through the interaction parameters and functions employed in molecular modelling methods [1.38-1.49]. 

Over the last 15 years particularly atomistic molecular modeling methods have found widespread application in the investigation of small-molecule permeation [2-15]. 

Zsila, F., Bikadi, Z., and Simony, M. 2002. Retinoic acid binding properties of the lipocalin member (3-lactoglobulin studied by circular dichroism, electronic absorption spectroscopy and molecular modeling methods. Biochem. Pharmacol. 64, 1651-1660. 

Different scales presented in Figure 3-1 are related to different approximation levels. For an overview of conventional molecular modelling methods, (see e.g.1-3). Bridging the above mentioned disparate time scales for the description of biologically relevant collective motions requires hierarchical, multi-scale approaches. In practice, to describe real complex (bio)molecular or material systems and processes various models have to be coupled to each other. Selected coupling mechanisms will be briefly reviewed. 

Lesyng B, McCammon JA (1993) Molecular Modeling Methods, Basic Techniques and Challenging Problems. Pharmac. Ther 60(149) 167... 

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