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A complete macromolecule modeling package must be able to solve the simpleststructure prediction problems. Despite recent successes in high resolutionstructure modeling and design, the Rosetta software suite fares poorly ondeceptively small protein and RNA puzzles, some as small as four residues. Toillustrate these problems, this manuscript presents extensive Rosetta resultsfor four well-defined test cases: the 20-residue mini-protein Trp cage, an evensmaller disulfide-stabilized conotoxin, the reactive loop of a serine proteaseinhibitor, and a UUCG RNA tetraloop. In contrast to previous Rosetta studies,several lines of evidence indicate that conformational sampling is not themajor bottleneck in modeling these small systems. Instead, approximations andomissions in the Rosetta all-atom energy function currently precludediscriminating experimentally observed conformations from de novo models atatomic resolution. These molecular "puzzles" should serve as useful modelsystems for developers wishing to make foundational improvements to thispowerful modeling suite.

Four small puzzles that Rosetta doesn't solve