CASP9 assessment of free modeling target predictions

Lisa Kinch, Shuo Yong Shi, Qian Cong, Hua Cheng, Yuxing Liao, Nick V. Grishin

Research output: Contribution to journalArticlepeer-review

85 Scopus citations


We present an overview of the ninth round of Critical Assessment of Protein Structure Prediction (CASP9) "Template free modeling" category (FM). Prediction models were evaluated using a combination of established structural and sequence comparison measures and a novel automated method designed to mimic manual inspection by capturing both global and local structural features. These scores were compared to those assigned manually over a diverse subset of target domains. Scores were combined to compare overall performance of participating groups and to estimate rank significance. Moreover, we discuss a few examples of free modeling targets to highlight the progress and bottlenecks of current prediction methods. Notably, a server prediction model for a single target (T0581) improved significantly over the closest structure template (44% GDT increase). This accomplishment represents the "winner" of the CASP9 FM category. A number of human expert groups submitted slight variations of this model, highlighting a trend for human experts to act as "meta predictors" by correctly selecting among models produced by the top-performing automated servers. The details of evaluation are available at.

Original languageEnglish (US)
Pages (from-to)59-73
Number of pages15
JournalProteins: Structure, Function and Bioinformatics
Issue numberSUPPL. 10
StatePublished - 2011


  • Alignment quality
  • CASP9
  • Domain structure
  • Protein-fold prediction
  • Structure comparison
  • ab-initio

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology


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