Introduction to Protein Structure Prediction

This chapter gives a graceful introduction to problem of protein threedimensional structure prediction, and focuses on how to make structural sense out of a single input sequence with unknown structure, the ‘query’ or ‘target’ sequence. We give an overview of the different classes of modelling techniques, notably template-based and template free. We also discuss the way in which structural predictions are validated within the global community, and elaborate on the extent to which predicted structures may be trusted and used in practice. Finally we discuss whether the concept of a single fold pertaining to a protein structure is sustainable given recent insights. In short, we conclude that the general protein three-dimensional structure prediction problem remains unsolved, especially if we desire quantitative predictions. However, if a homologous structural template is available in the PDB model or reasonable to high accuracy may be generated. Structural Bioinformatics c © Abeln & Feenstra, 2014-2017