The second round of the community-wide initiative Critical Assessment of automated Structure Determination of Proteins by NMR (CASD-NMR-2013) comprised ten blind target datasets, consisting of unprocessed spectral data, assigned chemical shift lists and unassigned NOESY peak and RDC lists, that were made available in both curated (i.e. manually refined) or un-curated (i.e. automatically generated) form. Ten structure calculation programs, using fully automated protocols only, generated a total of 164 three-dimensional structures (entries) for the ten targets, sometimes using both curated and un-curated lists to generate multiple entries for a single target. The accuracy of the entries could be established by comparing them to the corresponding manually solved structure of each target, which was not available at the time the data were provided. Across the entire data set, 71Â*% of all entries submitted achieved an accuracy relative to the reference NMR structure better than 1.5Â*Ã?. Methods based on NOESY peak lists achieved even better results with up to 100Â*% of the entries within the 1.5Â*Ã? threshold for some programs. However, some methods did not converge for some targets using un-curated NOESY peak lists. Over 90Â*% of the entries achieved an accuracy better than the more relaxed threshold of 2.5Â*Ã? that was used in the previous CASD-NMR-2010 round. Comparisons between entries generated with un-curated versus curated peaks show only marginal improvements for the latter in those cases where both calculations converged.
[NMR paper] Analysis of the structural quality of the CASD-NMR 2013 entries.
Analysis of the structural quality of the CASD-NMR 2013 entries.
Analysis of the structural quality of the CASD-NMR 2013 entries.
J Biomol NMR. 2015 Jun 3;
Authors: Ragan TJ, Fogh RH, Tejero R, Vranken W, Montelione GT, Rosato A, Vuister GW
Abstract
We performed a comprehensive structure validation of both automated and manually generated structures of the 10 targets of the CASD-NMR-2013 effort. We established that automated structure determination protocols are capable of reliably producing structures of comparable accuracy and...
nmrlearner
Journal club
0
06-03-2015 11:04 PM
Analysis of the structural quality of the CASD-NMR 2013 entries
Analysis of the structural quality of the CASD-NMR 2013 entries
Abstract
We performed a comprehensive structure validation of both automated and manually generated structures of the 10 targets of the CASD-NMR-2013 effort. We established that automated structure determination protocols are capable of reliably producing structures of comparable accuracy and quality to those generated by a skilled researcher, at least for small, single domain proteins such as the ten targets tested. The most robust results appear to be obtained when NOESY peak lists are...
nmrlearner
Journal club
0
06-02-2015 05:47 PM
[NMR paper] Analysis of the performance of the CHESHIRE and YAPP methods at CASD-NMR round 3.
Analysis of the performance of the CHESHIRE and YAPP methods at CASD-NMR round 3.
Related Articles Analysis of the performance of the CHESHIRE and YAPP methods at CASD-NMR round 3.
J Biomol NMR. 2015 May 20;
Authors: Cavalli A, Vendruscolo M
Abstract
We present an analysis of the results obtained at CASD-NMR round 3 by the CHESHIRE and the YAPP methods. To determine protein structures, the CHESHIRE method uses solely information provided by NMR chemical shifts, while the YAPP method uses an automated assignment of NOESY spectra....
nmrlearner
Journal club
0
05-21-2015 04:28 PM
Analysis of the performance of the CHESHIRE and YAPP methods at CASD-NMR round 3
Analysis of the performance of the CHESHIRE and YAPP methods at CASD-NMR round 3
Abstract
We present an analysis of the results obtained at CASD-NMR round 3 by the CHESHIRE and the YAPP methods. To determine protein structures, the CHESHIRE method uses solely information provided by NMR chemical shifts, while the YAPP method uses an automated assignment of NOESY spectra. Of the ten targets of CASD-NMR round 3, nine CHESHIRE predictions and eight YAPP ones were submitted. The eight YAPP predictions ranged from 0.7 to 1.9 � Cα accuracy, with an...
nmrlearner
Journal club
0
05-20-2015 10:27 AM
[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...
nmrlearner
Journal club
0
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....
nmrlearner
Journal club
0
03-04-2015 08:56 AM
Exclusively NOESY-based automated NMR assignment and structure determination of proteins
Exclusively NOESY-based automated NMR assignment and structure determination of proteins
Abstract A fully automated method is presented for determining NMR solution structures of proteins using exclusively NOESY spectra as input, obviating the need to measure any spectra only for obtaining resonance assignments but devoid of structural information. Applied to two small proteins, the approach yielded structures that coincided closely with conventionally determined structures.
Content Type Journal Article
Pages 1-10
DOI 10.1007/s10858-011-9502-8
nmrlearner
Journal club
0
04-01-2011 09:31 PM
Exclusively NOESY-based automated NMR assignment and structure determination of proteins.
Exclusively NOESY-based automated NMR assignment and structure determination of proteins.
Exclusively NOESY-based automated NMR assignment and structure determination of proteins.
J Biomol NMR. 2011 Mar 30;
Authors: Ikeya T, Jee JG, Shigemitsu Y, Hamatsu J, Mishima M, Ito Y, Kainosho M, Güntert P
A fully automated method is presented for determining NMR solution structures of proteins using exclusively NOESY spectra as input, obviating the need to measure any spectra only for obtaining resonance assignments but devoid of structural information....
The second round of Critical Assessment of Automated Structure Determination of Proteins by NMR: CASD-NMR-2013
Linear Mode
