Rosetta and the Journey to Predict Proteins’ Structures, 20 Years on

Abstract

For two decades, Rosetta has consistently been at the forefront of protein structure prediction. While it has become a very large package comprising programs, scripts, and tools, for different types of macromolecular modelling such as ligand docking, protein-protein docking, protein design, and loop modelling, it started as the implementation of an algorithm for ab initio protein structure prediction. The term ’Rosetta’ appeared for the first time twenty years ago in the literature to describe that algorithm and its contribution to the third edition of the community wide Critical Assessment of techniques for protein Structure Prediction (CASP3). Similar to the Rosetta stone that allowed deciphering the ancient Egyptian civilisation, David Baker and his co-workers have been contributing to deciphering ’the second half of the genetic code’. Although the focus of Baker’s team has expended to de novo protein design in the past few years, Rosetta’s ‘fame’ is associated with its fragment-assembly protein structure prediction approach. Following a presentation of the main concepts underpinning its foundation, especially sequence-structure correlation and usage of fragments, we review the main stages of its developments and highlight the milestones it has achieved in terms of protein structure prediction, particularly in CASP.