Crystal structures model building models

Figure 3 Development of the number of new crystal structures and homology models published over the years. The overall steady increase is clearly visible, as is the increase in homology and pharmacophore models during (temporary) declines in number of crystal structures, illustrating the complementary nature of experimental structure determination and model building. Publication of structures for isoforms that have been extensively used for homology model building are indicated at the top.

Numerous insightful reviews detail the use of the rhodopsin crystal structure as a model building template for other class A GPCRs (Archer et al., 2003 Ballesteros et al., 2001 Becker et al., 2003 FUipek et al, 2003). Modeling studies of GPCR structure have been advanced to such an extent that ab initio structure prediction methods using the minimum possible experimental structural information are underway (Vaidehi et al., 2002). 

A second product is the ICE Solid-State Model Kit, developed by L. A. Mayer and G. C. Lisensky, which makes it possible to build extended three-dimensional structures Using a base with holes, templates for some 60 different structures, rods, and four sizes of spheres in radius ratios, common crystal structures can be assembled in a matter of minutes (3). Furthermore, many structures can be assembled from different perspectives by teams of students For example, the cubic NaCl unit cell can be assembled with its orientation on the face of the cube or on the body diagonal. Natural cleavage planes can be found with the kit Lifting one sphere will separate atomic planes from one another. (Contact ICE for ordering information.)... 

A recently obtained high resolution structure of two crystal forms of the N-lobe of human serum transferrin (at 0.16 and 0.18 nm resolution) shows disorder at the iron-binding sites (MacGillivray et ah, 1998). Model building and refinement show... 

The result is the electron density map of the protein crystal. The final task for the crystallographer is to build the appropriate protein model, i. e., putting amino acid for amino acid into the electron density. Routinely the theoretical amplitudes and phases are calculated from the model and compared to the experimental data in order to check the correctness of model building. The positions of the protein backbone and the amino acid side chains are well defined by X-ray structures at a... 

Model building remains a useful technique for situations where the data are not amenable to solution in any other way, and for which existing related crystal structures can be used as a starting point. This usually happens because of a combination of structural complexity and poor data quality. For recent examples of this in the structure solution of polymethylene chains see Dorset [21] and [22]. It is interesting to note that model building methods for which there is no prior information are usually unsuccessful because the data are too insensitive to the atomic coordinates. This means that the recent advances in structure solution from powder diffraction data (David et al. [23]) in which a model is translated and rotated in a unit cell and in which the torsional degrees of freedom are also sampled by rotating around bonds which are torsionally free will be difficult to apply to structure solution with electron data. 

AutoRickshaw considers crystal structure determination as a multistep process in which each step in structure solution, from substructure determination to model building and validation, requires certain... 

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