YARIA: An improved
automated iterative assignment
With the goal in mind to bring the quality of protein NMR structures to the level of high resolution X-ray structures, we newly integrated two components of structure calculations: ARIA for iterative NOE assignment, and YASARA for structure calculation. The resulting integration is termed YARIA, which consists of a set of YASARA macros that control the molecular dynamics protocols needed for good performance with highly ambiguous data sets.
The YARIA integration was tested on 12 data sets, including 10 data sets of the latest CASD-NMR challenge. The results show that the YARIA integration yields structures that score much better in several important structure validation checks, whereas closeness to the deposited structures is similar to those calculated with ARIA/CNS. The YARIA protocols build on YASARA's knowledge-based force fields and form the basis of further improvements in the quality of NMR structure calculation protocols.
YARIA is not only for ARIA users: The state of the art explicit solvent refinement protocols with log normal potentials also work for CYANA and CNS structures.
YARIA was developed by Dr. Chris Spronk
and Dr. Benjamin Bardiaux, it is sold separately and
YASARA Structure and
the YASARA NMR Module.
R E F E R E N C E S
 YARIA: An improved automated iterative assignment and NMR structure calculation protocol
Bardiaux B, Krieger E, Vranken WF, Nilges M, Vriend G, Vuister GW, Karlsson BG and Spronk CAEM (2017) Prepared for submission
 Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8
Krieger E, Joo K, Lee J, Lee J, Raman S, Thompson J, Tyka M, Baker D, Karplus K (2009) Proteins 77 Suppl 9, 114-122
Figure 3: The 12 proteins used to validate the YARIA structure determination protocol, PDB IDs are shown.