Analysis of CASP8 targets, predictions and assessment methods

Shuoyong Shi, Jimin Pei, Ruslan I. Sadreyev, Lisa N. Kinch, Indraneel Majumdar, Jing Tong, Hua Cheng, Bong Hyun Kim, Nick V. Grishin

Research output: Contribution to journalArticle

19 Citations (Scopus)

Abstract

Results of the recent Critical Assessment of Techniques for Protein Structure Prediction, CASP8, present several valuable sources of information. First, CASP targets comprise a realistic sample of currently solved protein structures and exemplify the corresponding challenges for predictors. Second, the plethora of predictions by all possible methods provides an unusually rich material for evolutionary analysis of target proteins. Third, CASP results show the current state of the field and highlight specific problems in both predicting and assessing. Finally, these data can serve as grounds to develop and analyze methods for assessing prediction quality. Here we present results of our analysis in these areas. Our objective is not to duplicate CASP assessment, but to use our unique experience as former CASP5 assessors and CASP8 predictors to (i) offer more insights into CASP targets and predictions based on expert analysis, including invaluable analysis prior to target structure release; and (ii) develop an assessment methodology tailored towards current challenges in the field. Specifically, we discuss preparing target structures for assessment, parsing protein domains, balancing evaluations based on domains and on whole chains, dividing targets into categories and developing new evaluation scores. We also present evolutionary analysis of the most interesting and challenging targets.

Original languageEnglish (US)
Article numberbap003
JournalDatabase
Volume2009
DOIs
StatePublished - 2009

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Proteins
prediction
protein structure
information sources
methodology
proteins
sampling
Protein Domains

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Information Systems

Cite this

Shi, S., Pei, J., Sadreyev, R. I., Kinch, L. N., Majumdar, I., Tong, J., ... Grishin, N. V. (2009). Analysis of CASP8 targets, predictions and assessment methods. Database, 2009, [bap003]. https://doi.org/10.1093/database/bap003

Analysis of CASP8 targets, predictions and assessment methods. / Shi, Shuoyong; Pei, Jimin; Sadreyev, Ruslan I.; Kinch, Lisa N.; Majumdar, Indraneel; Tong, Jing; Cheng, Hua; Kim, Bong Hyun; Grishin, Nick V.

In: Database, Vol. 2009, bap003, 2009.

Research output: Contribution to journalArticle

Shi, S, Pei, J, Sadreyev, RI, Kinch, LN, Majumdar, I, Tong, J, Cheng, H, Kim, BH & Grishin, NV 2009, 'Analysis of CASP8 targets, predictions and assessment methods', Database, vol. 2009, bap003. https://doi.org/10.1093/database/bap003
Shi S, Pei J, Sadreyev RI, Kinch LN, Majumdar I, Tong J et al. Analysis of CASP8 targets, predictions and assessment methods. Database. 2009;2009. bap003. https://doi.org/10.1093/database/bap003
Shi, Shuoyong ; Pei, Jimin ; Sadreyev, Ruslan I. ; Kinch, Lisa N. ; Majumdar, Indraneel ; Tong, Jing ; Cheng, Hua ; Kim, Bong Hyun ; Grishin, Nick V. / Analysis of CASP8 targets, predictions and assessment methods. In: Database. 2009 ; Vol. 2009.
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