Analysis of the structural quality of the CASD-NMR 2013 entries

Timothy J. Ragan, Rasmus H. Fogh, Roberto Tejero, Wim Vranken, Gaetano Montelione, Antonio Rosato, Geerten W. Vuister

Research output: Contribution to journalArticle

2 Citations (Scopus)

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 used either as the primary input data or to augment chemical shift data without the need to manually filter such lists. A detailed analysis of the long-range NOE restraints generated by the different programs from the same data showed a surprisingly low degree of overlap. Additionally, we found that there was no significant correlation between the extent of the NOE restraint overlap and the accuracy of the structure. This result was surprising given the importance of NOE data in producing good quality structures. We suggest that this could be explained by the information redundancy present in NOEs between atoms contained within a fixed covalent network.

Original languageEnglish (US)
Pages (from-to)527-540
Number of pages14
JournalJournal of biomolecular NMR
Volume62
Issue number4
DOIs
StatePublished - Aug 22 2015

Fingerprint

Chemical shift
Redundancy
Research Personnel
Nuclear magnetic resonance
Atoms
Proteins
Protein Domains

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Spectroscopy

Keywords

  • Blind testing
  • CASD-NMR
  • NMR
  • NOE
  • Protein
  • Quality
  • Structure determination
  • Validation

Cite this

Ragan, T. J., Fogh, R. H., Tejero, R., Vranken, W., Montelione, G., Rosato, A., & Vuister, G. W. (2015). Analysis of the structural quality of the CASD-NMR 2013 entries. Journal of biomolecular NMR, 62(4), 527-540. https://doi.org/10.1007/s10858-015-9949-0
Ragan, Timothy J. ; Fogh, Rasmus H. ; Tejero, Roberto ; Vranken, Wim ; Montelione, Gaetano ; Rosato, Antonio ; Vuister, Geerten W. / Analysis of the structural quality of the CASD-NMR 2013 entries. In: Journal of biomolecular NMR. 2015 ; Vol. 62, No. 4. pp. 527-540.
@article{0f6bc0f686f54837b9012d8dfb7dd936,
title = "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 used either as the primary input data or to augment chemical shift data without the need to manually filter such lists. A detailed analysis of the long-range NOE restraints generated by the different programs from the same data showed a surprisingly low degree of overlap. Additionally, we found that there was no significant correlation between the extent of the NOE restraint overlap and the accuracy of the structure. This result was surprising given the importance of NOE data in producing good quality structures. We suggest that this could be explained by the information redundancy present in NOEs between atoms contained within a fixed covalent network.",
keywords = "Blind testing, CASD-NMR, NMR, NOE, Protein, Quality, Structure determination, Validation",
author = "Ragan, {Timothy J.} and Fogh, {Rasmus H.} and Roberto Tejero and Wim Vranken and Gaetano Montelione and Antonio Rosato and Vuister, {Geerten W.}",
year = "2015",
month = "8",
day = "22",
doi = "10.1007/s10858-015-9949-0",
language = "English (US)",
volume = "62",
pages = "527--540",
journal = "Journal of Biomolecular NMR",
issn = "0925-2738",
publisher = "Springer Netherlands",
number = "4",

}

Ragan, TJ, Fogh, RH, Tejero, R, Vranken, W, Montelione, G, Rosato, A & Vuister, GW 2015, 'Analysis of the structural quality of the CASD-NMR 2013 entries', Journal of biomolecular NMR, vol. 62, no. 4, pp. 527-540. https://doi.org/10.1007/s10858-015-9949-0

Analysis of the structural quality of the CASD-NMR 2013 entries. / Ragan, Timothy J.; Fogh, Rasmus H.; Tejero, Roberto; Vranken, Wim; Montelione, Gaetano; Rosato, Antonio; Vuister, Geerten W.

In: Journal of biomolecular NMR, Vol. 62, No. 4, 22.08.2015, p. 527-540.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Analysis of the structural quality of the CASD-NMR 2013 entries

AU - Ragan, Timothy J.

AU - Fogh, Rasmus H.

AU - Tejero, Roberto

AU - Vranken, Wim

AU - Montelione, Gaetano

AU - Rosato, Antonio

AU - Vuister, Geerten W.

PY - 2015/8/22

Y1 - 2015/8/22

N2 - 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 used either as the primary input data or to augment chemical shift data without the need to manually filter such lists. A detailed analysis of the long-range NOE restraints generated by the different programs from the same data showed a surprisingly low degree of overlap. Additionally, we found that there was no significant correlation between the extent of the NOE restraint overlap and the accuracy of the structure. This result was surprising given the importance of NOE data in producing good quality structures. We suggest that this could be explained by the information redundancy present in NOEs between atoms contained within a fixed covalent network.

AB - 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 used either as the primary input data or to augment chemical shift data without the need to manually filter such lists. A detailed analysis of the long-range NOE restraints generated by the different programs from the same data showed a surprisingly low degree of overlap. Additionally, we found that there was no significant correlation between the extent of the NOE restraint overlap and the accuracy of the structure. This result was surprising given the importance of NOE data in producing good quality structures. We suggest that this could be explained by the information redundancy present in NOEs between atoms contained within a fixed covalent network.

KW - Blind testing

KW - CASD-NMR

KW - NMR

KW - NOE

KW - Protein

KW - Quality

KW - Structure determination

KW - Validation

UR - http://www.scopus.com/inward/record.url?scp=84941992800&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84941992800&partnerID=8YFLogxK

U2 - 10.1007/s10858-015-9949-0

DO - 10.1007/s10858-015-9949-0

M3 - Article

C2 - 26032236

AN - SCOPUS:84941992800

VL - 62

SP - 527

EP - 540

JO - Journal of Biomolecular NMR

JF - Journal of Biomolecular NMR

SN - 0925-2738

IS - 4

ER -