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J Biomol NMR. 2015 Aug;62(4):413-24. doi: 10.1007/s10858-015-9953-4. Epub 2015 Jun 14.

The second round of Critical Assessment of Automated Structure Determination of Proteins by NMR: CASD-NMR-2013.

Author information

1
Department of Chemistry and Magnetic Resonance Center, University of Florence, 50019, Sesto Fiorentino, Italy.
2
Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.
3
(IB)2 Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Triomflaan, 1050, Brussels, Belgium.
4
Department of Biochemistry, School of Biological Sciences, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, LE1 9HN, UK.
5
Departamento de Química Física, Universidad de Valencia, Avda. Dr. Moliner 50, 46100, Burjassot (Valencia), Spain.
6
Complex Carbohydrate Research Center and Northeast Structural Genomics Consortium, University of Georgia, Athens, GA, 30602, USA.
7
Department of Medical Biophysics, Cancer Genomics and Proteomics, Ontario Cancer Institute, Northeast Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada.
8
Department of Chemistry and Biochemistry, Northeast Structural Genomics Consortium, Miami University, Oxford, OH, 45056, USA.
9
Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA.
10
Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA.
11
Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA. guy@cabm.rutgers.edu.
12
Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA. guy@cabm.rutgers.edu.
13
Department of Biochemistry, School of Biological Sciences, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, LE1 9HN, UK. gv29@le.ac.uk.

Abstract

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, 71 % of all entries submitted achieved an accuracy relative to the reference NMR structure better than 1.5 Å. Methods based on NOESY peak lists achieved even better results with up to 100% of the entries within the 1.5 Å threshold for some programs. However, some methods did not converge for some targets using un-curated NOESY peak lists. Over 90% of the entries achieved an accuracy better than the more relaxed threshold of 2.5 Å 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.

KEYWORDS:

Accuracy; Automation; Blind testing; CASD-NMR; Chemical shift; NMR; NOE; Precision; Protein; Quality; Structure determination; Validation

PMID:
26071966
PMCID:
PMC4569658
DOI:
10.1007/s10858-015-9953-4
[Indexed for MEDLINE]
Free PMC Article

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