Biomolecules graphics

Akiyoshi Wada, Haruki Nakamura, and Akira Suyama, Computer Graphics of Biomolecules, Tokyo Kagaku Dojin Co., Ltd., Tokyo, 1988. 

The 3D space requirements of most molecules can be represented to a good approximation by such Van der Waals surfaces. Fused sphere VDWS s are used extensively in molecular modeling, especially in the interpretation of biochemical processes and computer aided drug design. These approximate molecular surfaces are conceptually simple, their computation and graphical display on a computer screen take relatively short time, even for large biomolecules. 

The emergence of molecular modeling and computational into a discipline has been closely associated with advances in computer hardware, computer graphics, and software. The availability of more sophisticated number-crunching power has allowed scientists to calculate the properties oflarger and larger molecules. With the advent of supercomputers, dynamics calculations on biomolecules surrounded by an environment of water are becoming common. 

See WWW graphical abstract that represent biomolecules within H3Sb3P30i4sheets... 

The presence of the CVFF force field in a graphical modeling package (Insightll, Discover) has facilitated its application to several classes of biomolecules including oligosaccharides, despite its lack of specific parameters for carbohydrates. ... 

There are numerous force fields and parameter sets available for modeling carbohydrates. Some focus specifically on carbohydrates, while others aim at treating biomolecules in general, and yet others profess to be appropriate for virtually any molecular class. Direct comparisons between force fields are rare and validation of any of the force fields requires extensive and critical comparison with experimental data. Consequently, carbohydrate force fields ate frequently selected on the basis of past familiarity. The advent of convenient graphical modeling interfaces provides a tremendous opportunity to extend carbohydrate modeling to both new users and new molecular systems. Ease of access is not, however, a guarantee of force field suitability. 

---