An automatic method for CASP9 free modeling structure prediction assessment

Qian Cong, Lisa N. Kinch, Jimin Pei, Shuoyong Shi, Vyacheslav N. Grishin, Wenlin Li, Nick V. Grishin

Research output: Contribution to journalArticle

15 Citations (Scopus)

Abstract

Motivation: Manual inspection has been applied to and is well accepted for assessing critical assessment of protein structure prediction (CASP) free modeling (FM) category predictions over the years. Such manual assessment requires expertise and significant time investment, yet has the problems of being subjective and unable to differentiate models of similar quality. It is beneficial to incorporate the ideas behind manual inspection to an automatic score system, which could provide objective and reproducible assessment of structure models.Results: Inspired by our experience in CASP9 FM category assessment, we developed an automatic superimposition independent method named Quality Control Score (QCS) for structure prediction assessment. QCS captures both global and local structural features, with emphasis on global topology. We applied this method to all FM targets from CASP9, and overall the results showed the best agreement with Manual Inspection Scores among automatic prediction assessment methods previously applied in CASPs, such as Global Distance Test Total Score (GDT_TS) and Contact Score (CS). As one of the important components to guide our assessment of CASP9 FM category predictions, this method correlates well with other scoring methods and yet is able to reveal good-quality models that are missed by GDT_TS.

Original languageEnglish (US)
Article numberbtr572
Pages (from-to)3371-3378
Number of pages8
JournalBioinformatics
Volume27
Issue number24
DOIs
StatePublished - Dec 2011

Fingerprint

Structure Prediction
Modeling
Quality Control
Inspection
Quality control
Prediction
Model structures
Research Design
Protein Structure Prediction
Topology
Expertise
Differentiate
Scoring
Proteins
Correlate
Model
Contact
Target

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability
  • Medicine(all)

Cite this

Cong, Q., Kinch, L. N., Pei, J., Shi, S., Grishin, V. N., Li, W., & Grishin, N. V. (2011). An automatic method for CASP9 free modeling structure prediction assessment. Bioinformatics, 27(24), 3371-3378. [btr572]. https://doi.org/10.1093/bioinformatics/btr572

An automatic method for CASP9 free modeling structure prediction assessment. / Cong, Qian; Kinch, Lisa N.; Pei, Jimin; Shi, Shuoyong; Grishin, Vyacheslav N.; Li, Wenlin; Grishin, Nick V.

In: Bioinformatics, Vol. 27, No. 24, btr572, 12.2011, p. 3371-3378.

Research output: Contribution to journalArticle

Cong, Q, Kinch, LN, Pei, J, Shi, S, Grishin, VN, Li, W & Grishin, NV 2011, 'An automatic method for CASP9 free modeling structure prediction assessment', Bioinformatics, vol. 27, no. 24, btr572, pp. 3371-3378. https://doi.org/10.1093/bioinformatics/btr572
Cong Q, Kinch LN, Pei J, Shi S, Grishin VN, Li W et al. An automatic method for CASP9 free modeling structure prediction assessment. Bioinformatics. 2011 Dec;27(24):3371-3378. btr572. https://doi.org/10.1093/bioinformatics/btr572
Cong, Qian ; Kinch, Lisa N. ; Pei, Jimin ; Shi, Shuoyong ; Grishin, Vyacheslav N. ; Li, Wenlin ; Grishin, Nick V. / An automatic method for CASP9 free modeling structure prediction assessment. In: Bioinformatics. 2011 ; Vol. 27, No. 24. pp. 3371-3378.
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