Computer Modeling with a Protein Data Base
The widespread use of computer graphics in the last 10 years has contributed to the spread and ease with which crystallographers can solve and refine macromolecular structures. In particular computer graphics modeling programs have been used to construct the initial model in electron density maps, and to remove model errors during crystallo- graphic refinement (see Jones 1987, for a short review). In much of this interactive work, the experience of the modeler has played an important (sometimes critical) role. This manifests itself in an ability to recognize and use structural features. An intimate knowledge of protein stereochemistry can be of great use in constructing and modifying a known structure. The modeling program, Frodo (Jones 1978, 1982) provided a set of tools to construct and manipulate fragments into maps in a straightforward general way. These fragments could be α- helices, β-strands or various types of turns, for example. In our recent work (Jones and Thirup 1986) we have generalized these concepts so that the fragments come directly from a data base of well refined protein structures.
KeywordsPeptide Plane Graphic Refinement Branch Side Chain Side Chain Rotamers Modeling Homologous Protein
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