Protein Structure Prediction: From Recognition of Matches with Known Structures to Recombination of Fragments

Abstract

The field of protein structure prediction has been revolutionized by the application of “mix-and-match” methods both in template-based homology modeling, as well as in template-free, “de novo” folding. Automated generation of models that are closer to the native structure of the target protein than the structure of its closest homolog is currently possible by recombination of fragments copied from known protein structures or extracted from alternative starting models. It is also the most successful approach in the cases where the target protein exhibits a novel three-dimensional fold. This chapter is an update of a review article published earlier [Bujnicki JM, Chem Bio Chem 7(1):19–27, 2006 Jan 9, Copyright Wiley-VCH Verlag GmbH & Co. KGaA. Reproduced with permission]. It summarizes the recent developments in both template-based and template-free protein structure modeling and compares the available methods for protein structure prediction by recombination of fragments.