UNIO is a comprehensive software suite for protein NMR structure determination that enables full automation of all NMR data analysis steps involvedâ??including signal identification in NMR spectra, sequence-specific backbone and side-chain resonance assignment, NOE assignment and structure calculation. Within the framework of the second round of the community-wide stringent blind NMR structure determination challenge (CASD-NMR 2), we participated in two categories of CASD-NMR 2, namely using either raw NMR spectra or unrefined NOE peak lists as input. A total of 15 resulting NMR structure bundles were submitted for 9 out of 10 blind protein targets. All submitted UNIO structures accurately coincided with the corresponding blind targets as documented by an average backbone root mean-square deviation to the reference proteins of only 1.2Â*Ã?. Also, the precision of the UNIO structure bundles was virtually identical to the ensemble of reference structures. By assessing the quality of all UNIO structures submitted to the two categories, we find throughout that only the UNIOâ??ATNOS/CANDID approach using raw NMR spectra consistently yielded structure bundles of high quality for direct deposition in the Protein Data Bank. In conclusion, the results obtained in CASD-NMR 2 are another vital proof for robust, accurate and unsupervised NMR data analysis by UNIO for real-world applications.
[NMR paper] NMR data-driven structure determination using NMR-I-TASSER in the CASD-NMR experiment.
NMR data-driven structure determination using NMR-I-TASSER in the CASD-NMR experiment.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--production.springer.de-OnlineResources-Logos-springerlink.gif Related Articles NMR data-driven structure determination using NMR-I-TASSER in the CASD-NMR experiment.
J Biomol NMR. 2015 Mar 4;
Authors: Jang R, Wang Y, Xue Z, Zhang Y
Abstract
NMR-I-TASSER, an adaption of the I-TASSER algorithm combining NMR data for protein structure determination, recently joined the second...
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03-06-2015 12:45 AM
NMR data-driven structure determination using NMR-I-TASSER in the CASD-NMR experiment
NMR data-driven structure determination using NMR-I-TASSER in the CASD-NMR experiment
Abstract
NMR-I-TASSER, an adaption of the I-TASSER algorithm combining NMR data for protein structure determination, recently joined the second round of the CASD-NMR experiment. Unlike many molecular dynamics-based methods, NMR-I-TASSER takes a molecular replacement-like approach to the problem by first threading the target through the PDB to identify structural templates which are then used for iterative NOE assignments and fragment structure assembly refinements....
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03-04-2015 08:56 AM
[NMR paper] J-UNIO protocol used for NMR structure determination of the 206-residue protein NP_346487.1 from Streptococcus pneumoniae TIGR4.
J-UNIO protocol used for NMR structure determination of the 206-residue protein NP_346487.1 from Streptococcus pneumoniae TIGR4.
J-UNIO protocol used for NMR structure determination of the 206-residue protein NP_346487.1 from Streptococcus pneumoniae TIGR4.
J Biomol NMR. 2014 Nov 27;
Authors: Jaudzems K, Pedrini B, Geralt M, Serrano P, Wüthrich K
Abstract
The NMR structure of the 206-residue protein NP_346487.1 was determined with the J-UNIO protocol, which includes extensive automation of the structure determination. With input...
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11-28-2014 11:37 AM
J-UNIO protocol used for NMR structure determination of the 206-residue protein NP_346487.1 from Streptococcus pneumoniae TIGR4
J-UNIO protocol used for NMR structure determination of the 206-residue protein NP_346487.1 from Streptococcus pneumoniae TIGR4
Abstract
The NMR structure of the 206-residue protein NP_346487.1 was determined with the J-UNIO protocol, which includes extensive automation of the structure determination. With input from three APSY-NMR experiments, UNIO-MATCH automatically yielded 77Â*% of the backbone assignments, which were interactively validated and extended to 97Â*%. With an input of the near-complete backbone assignments and three 3D...
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11-26-2014 10:50 PM
Automated robust and accurate assignment of protein resonances for solid state NMR
Automated robust and accurate assignment of protein resonances for solid state NMR
Abstract
The process of resonance assignment represents a time-consuming and potentially error-prone bottleneck in structural studies of proteins by solid-state NMR (ssNMR). Software for the automation of this process is therefore of high interest. Procedures developed through the last decades for solution-state NMR are not directly applicable for ssNMR due to the inherently lower data quality caused by lower sensitivity and broader lines, leading to overlap between...
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06-19-2014 10:21 PM
Robust and highly accurate automatic NOESY assignment and structure determination with Rosetta
Robust and highly accurate automatic NOESY assignment and structure determination with Rosetta
Abstract
We have developed a novel and robust approach for automatic and unsupervised simultaneous nuclear Overhauser effect (NOE) assignment and structure determination within the CS-Rosetta framework. Starting from unassigned peak lists and chemical shift assignments, autoNOE-Rosetta determines NOE cross-peak assignments and generates structural models. The approach tolerates incomplete and raw NOE peak lists as well as incomplete or partially...
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06-19-2014 10:21 PM
[NMR paper] Automated robust and accurate assignment of protein resonances for solid state NMR.
Automated robust and accurate assignment of protein resonances for solid state NMR.
Automated robust and accurate assignment of protein resonances for solid state NMR.
J Biomol NMR. 2014 May 10;
Authors: Nielsen JT, Kulminskaya N, Bjerring M, Nielsen NC
Abstract
The process of resonance assignment represents a time-consuming and potentially error-prone bottleneck in structural studies of proteins by solid-state NMR (ssNMR). Software for the automation of this process is therefore of high interest. Procedures developed through...
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05-13-2014 03:11 PM
The J-UNIO protocol for automated protein structure determination by NMR in solution
The J-UNIO protocol for automated protein structure determination by NMR in solution
Abstract The J-UNIO (JCSG protocol using the software UNIO) procedure for automated protein structure determination by NMR in solution is introduced. In the present implementation, J-UNIO makes use of APSY-NMR spectroscopy, 3D heteronuclear-resolved -NOESY experiments, and the software UNIO. Applications with proteins from the JCSG target list with sizes up to 150 residues showed that the procedure is highly robust and efficient. In all instances the correct polypeptide fold was obtained in the first...
CASD-NMR 2: robust and accurate unsupervised analysis of raw NOESY spectra and protein structure determination with UNIO
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