Parin Sripakdeevong

TL;DR: This paper describes the ROSIE server infrastructure, a step-by-step ‘serverification’ protocol for use by Rosetta developers, and the deployment of the first nine ROSIE applications by six separate developer teams.

TL;DR: A first, collective, blind experiment in RNA three-dimensional (3D) structure prediction, encompassing three prediction puzzles, to assess the leading edge of RNA structure prediction techniques; compare existing methods and tools; and evaluate their relative strengths, weaknesses, and limitations.

TL;DR: Enumerative real-space refinement assisted by electron density under Rosetta (ERRASER) coupled to Python-based hierarchical environment for integrated 'xtallography' (PHENIX) diffraction-based refinement of three-dimensional RNA models fitted into crystallographic density maps.

TL;DR: It is demonstrated that integrating 1H NMR chemical shift data with Rosetta de novo modeling can be used to consistently determine high-resolution RNA structures.

TL;DR: A working hypothesis is presented for recursively constructing well-packed atomic-detail models in small steps, enumerating several million conformations for each monomer, and covering all build-up paths, that systematically outperforms existing Monte Carlo and knowledge-based methods for 3D structure prediction.