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Structural Bioinformatics, 2nd Edition by Philip E. Bourne, Jenny Gu

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14

STRUCTURAL QUALITY ASSURANCE

Roman A. Laskowski

INTRODUCTION

The experimentally determined 3D structures of proteins and nucleic acids represent a key knowledge base from which a vast understanding of biological processes has been derived over the past half century. Individual structures have provided explanations of specific biochemical functions and mechanisms, while comparisons of structures have given insights into general principles governing these complex molecules, the interactions they make, their biological roles, and their evolutionary relationships. The 3D structures are held and looked after by the Worldwide Protein Data Bank (wwPDB) that, as of August 2007, held over 45,000 entries.

These structures form the foundation of Structural Bioinformatics; all structural analyses depend on them and would be impossible without them. Therefore, it is crucial to bear in mind two important truths about them, both of which result from the fact that they have been determined experimentally. The first is that the result of any experiment is merely a “model” that aims to give as good an explanation for the experimental data as possible. The term “structure” is commonly used, but you should realize that this should be correctly read as “model.” As such, the model may be an accurate and meaningful representation of the molecule, or it may be a poor one. The quality of the data and the care with which the experiment has been performed will determine which it is. Independently performed ...

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