Endonuclease PvuII (1PVI) DNA - GATTACAGATTACA
CAP - Catabolite gene Activating Protein (1BER)
DNA - GATTACAGATTACAGATTACA Endonuclease PvuII bound to palindromic DNA recognition site CAGCTG (1PVI) DNA - GATTACAGATTACAGATTACA TBP - TATA box Binding Protein (1C9B)
CAP - Catabolite gene Activating Protein (1BER)
GCN4 - leucine zipper transcription factor bound to palindromic DNA recognition site ATGAC(G)TCAT (1YSA)
GCN4 - leucine zipper transcription factor bound to palindromic DNA recognition site ATGAC(G)TCAT (1YSA)
GCN4 - leucine zipper transcription factor bound to palindromic DNA recognition site ATGAC(G)TCAT (1YSA)
GCN4 - leucine zipper transcription factor bound to palindromic DNA recognition site ATGAC(G)TCAT (1YSA)
GCN4 - leucine zipper transcription factor bound to palindromic DNA recognition site ATGAC(G)TCAT (1YSA)
GCN4 - leucine zipper transcription factor bound to palindromic DNA recognition site ATGAC(G)TCAT (1YSA)
TBP - TATA box Binding Protein (1C9B)
 

YARIA: An improved automated iterative assignment
NMR structure calculation protocol


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[1]. The YARIA protocols build on YASARA's knowledge-based force fields[2] 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 requires ARIA, YASARA Structure and the YASARA NMR Module.
For questions, pricing, support, feedback and feature requests you can
1. send an email: if you heard about YARIA somewhere else contact spronk3dnmr at icloud.com, if you just read about YARIA on this page contact spronk at yasara.org
2. Join the YARIA group on facebook


R E F E R E N C E S

[1] 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
[2] 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



YARIA Circle

Figure 1: The YARIA structure determination cycle. After peak assignment by ARIA, YASARA uses the restraints to determine the structure in four phases. The final phase 4 uses log normal potentials, the resulting structure is returned to ARIA for another round of improved peak assignment.


YARIA results

Figure 2: Average structure validation results obtained for 12 NMR structures (see Figure 3 at the bottom). For the Molprobity clashscore lower is better, for all others higher is better. The NMR structures are obtained in four different ways (left to right): 1) The original structure deposited in the PDB, 2) The structure recalculated with ARIA/CNS using the original NMR data, 3) The structure from 2) additionally refined with YASARA. 4) The structure recalculated with ARIA/YASARA (=YARIA) using the original NMR data.



YARIA Datasets

Figure 3: The 12 proteins used to validate the YARIA structure determination protocol, PDB IDs are shown.