Four small puzzles that Rosetta doesn't solve

TL;DR

This paper demonstrates that Rosetta struggles with small protein and RNA puzzles due to limitations in its energy function, highlighting areas for fundamental improvements in modeling accuracy.

Contribution

It identifies the core reason for Rosetta's failure on small puzzles as energy function inaccuracies rather than sampling issues, providing a basis for future enhancements.

Findings

Rosetta cannot reliably discriminate native conformations in small systems

Sampling is not the main bottleneck in small system modeling

Energy function approximations hinder accurate structure prediction

Abstract

A complete macromolecule modeling package must be able to solve the simplest structure prediction problems. Despite recent successes in high resolution structure modeling and design, the Rosetta software suite fares poorly on deceptively small protein and RNA puzzles, some as small as four residues. To illustrate these problems, this manuscript presents extensive Rosetta results for four well-defined test cases: the 20-residue mini-protein Trp cage, an even smaller disulfide-stabilized conotoxin, the reactive loop of a serine protease inhibitor, and a UUCG RNA tetraloop. In contrast to previous Rosetta studies, several lines of evidence indicate that conformational sampling is not the major bottleneck in modeling these small systems. Instead, approximations and omissions in the Rosetta all-atom energy function currently preclude discriminating experimentally observed conformations from de novo models at atomic resolution. These molecular "puzzles" should serve as useful model systems for developers wishing to make foundational improvements to this powerful modeling suite.