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High-Grade Ore for Data Mining in 3D Structures

The 3-dimensional structures of proteins, nucleic acids, and complexes are becoming an increasingly important part of bioinformatics, with the advent of structural genomics, protein-protein interaction analysis, and largescale functional genomics. Although not approaching the extent of sequence data, the 3D database is huge, complex, and growing rapidly. The quality of 3D data is very good but varies increasingly widely as more protein crystal structures are being done at atomic resolution, while ever-larger molecular machinery can be successfully tackled at meaningful but quite low resolution. NMR (nuclear magnetic resonance) methodology for determining 3D structures is currently changing even more rapidly than crystallography. As in any data analysis effort, an understanding and assessment of possible errors is a crucial aspect of doing structural bioinformatics. After a brief review of the traditional criteria for assessing structural quality, this chapter will concentrate on a new validation method that is especially powerful yet quite accessible to non-experts. This method, called