Computer-generated three-dimensional structure

Our algorithms were verified by analyzing images from computer generated three-dimensional structures. 

Three-dimensional structures of small molecules and macromolecules are being generated in record numbers. A database of the X-ray crystal structures of >70,000 small organocarbon compounds and another of several hundred protein and DNA struaures are available to scientists. Furthermore, it is often routine to experimentally determine the three-dimensional structure of a small molecule by single-crystal X-ray diffraction, and it is very easy to build on the computer a three-dimensional structure of a small molecule and to discover most if not all of its low-energy conformations. Finally, there is a... 

Figure 2.27. A computer-generated three-dimensional model of the macromolecular structure of vitrinite in coal showing porosity between coal substance (Marsh, unpublished results).

A computer-generated three-dimensional model of a possible macromolecule of coal is shown in Figure 2.27. It is a structure-less three-dimensional cage-like aggregate of atoms (C, H, O, N, S) with a water density of about 1.3 gcm. The model shows that the sizes of spaces within the macromolecular system approximate to those of the atoms and demonstrates the presence of microporosity within the coals. 

Threading essentially entails comparing the sequence of the polypeptide whose three-dimensional structure you wish to predict with the database sequences known to generate specific fold patterns. Computer programs can then be used to estimate the probability of the target sequence adopting each known folding structure. 

The three dimensional structure was obtained by means of single crystal X-ray diffraction. CuKa radiation, a graphite monochromator, and a photomultiplier tube were used to collect 1825 total reflections on an automated diffractometer. Of these, 1162 were used for the analysis. Figure 2 shows a computer generated drawing of halcinonide. The position of the chlorine atom was not clear from the Patterson map, but the direct method program "MULTAN" gave its position. 

Computer-generated model of the quaternary structure of hemoglobin, a protein consisting of four interlinked polypeptide chains, each shown in a different color. Computers are important tools for the study of biomolecules, as they help scientists visualize complex three-dimensional structures. 

Closely related to the use of models is the corresponding one of stereoviews to illustrate molecular perspective. The increased availability of molecular data and the use of computers to generate stereoviews has made their use routine in journal accounts of structure determinations. Unlike models, no matter how useful, stereo-views have the ability to capture the depth of a three-dimensional structure on a two-dimensional sheet of paper. An increased number of stereoviews has been included in this edition. 

First we show in Fig. 5 a ribbon model of the three-dimensional structure of the PS-II reaction center of Pisum sativam (pea) generated by computer modeling in Fig. 5. This model was constructed by Ruffle, Donnelly, Blundell and Nugent , using information drawn from the crystal structures of the... 

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