CASP9 Target Classification

By Lisa N. Kinch, Shuoyong Shi, Hua Cheng, Qian Cong, Jimin Pei, Valerio Mariani, Torsten Schwede, Nick V. Grishin. 2011

66 citations recorded by the source corpus.

The Critical assessment of protein structure prediction round 9 (CASP9) aimed to evaluate predictions for 129 experimentally determined protein structures. To assess tertiary structure predictions, these target structures were divided into domain‐based evaluation units that were then classified into two assessment categories: template based modeling (TBM) and template free modeling (FM). CASP9 targets were split into domains of structurally compact evolutionary modules. For the targets with more than one defined domain, the decision to split structures into domains for evaluation was based on server performance. Target domains were categorized based on their evolutionary relatedness to existing templates as well as their difficulty levels indicated by server performance. Those target domains with sequence‐related templates and high server prediction performance were classified as TMB, whereas those targets without identifiable templates and low server performance were classified as FM. However, using these generalizations for classification resulted in a blurred boundary between CASP9 assessment categories. Thus, the FM category included those domains without sequence detectable templates (25 target domains) as well as some domains with difficult to detect templates whose predictions were as poor as those without templates (five target domains). Several interesting examples are discussed, including targets with sequence related templates that exhibit unusual structural differences, targets with homologous or analogous structure templates that are not detectable by sequence, and targets with new folds. Proteins 2011; © 2011 Wiley‐Liss, Inc.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests (2013, methodology): “Here, stereochemical violations in the model are defined as bond lengths and angles with values that diverge from the respective average reference value derived from high-resolution experimental structures (Engh and Huber, 1991, 2006) by more than a predefined number of standard deviations (12 (cid”
CASP10 results compared to those of previous CASP experiments (2013, methodology): “…used more lenient criteria that included a subjective reasoning on whether the template for the domain was clearly findable by sequence methods at the time of the experiment,13 and, as a result, the FM set included a number of targets with quite good models (with the GDT_TS scores over 50).”
Evaluation of residue-residue contact predictions in CASP9 (2011, neutral): “43 Similarly to previous CASPs, targets for residue contact prediction were limited to the FM and TBM/FM domains, because in the case of closer homology, contacts can easily be derived from templates.”
Evaluation of model quality predictions in CASP9 (2011, unknown): “Thirteentargetswerecancelledbythe organizersandtheassessorsfortertiarystructurepredic-tion,22andthosewerealsoexcludedfromtheQAassess-ment,leaving116targetstobeassessed.”
Evaluation of free modeling targets in CASP11 and ROLL (2016, background): “9,10 This dearth of targets tended to cause difficulty in assigning statistical significance to assessments of FM techniques and prompted the introduction of CASP ROLL into the CASP10 evaluation.”
Assessment of template based protein structure predictions in CASP9 (2011, methodology): “As in previous CASPs, most of the participating groups in the TBM category failed to assign realistic confidence estimates to their predictions, and only a very small fraction of the assessed methods were able to provide accurate models and realistic error estimates at the same time.”
Evaluation of disorder predictions in CASP9 (2011, background): “Structure data for five of these targets (T0533, T0536, T0600, T0612, and T0637) were compromised in the period between the corresponding server and human prediction deadlines,27 and therefore only the server predictions were evaluated on these targets.”
CASP9 Assessment of Free Modeling Target Predictions (2011, background): “See target classification paper in this issue for details.10”
CAMEO - Perspectives on the future of fully automated evaluation of structure prediction methods (2021, unknown): “In addition, as CAMEO is a fully automated workflow without human intervention, we have been focusing on superposition-free scores which alleviate the need to manually split proteins into evaluation units 20,21 to account for domain movements.”
The Expanded FindCore Method for Identification of a Core Atom Set for Assessment of Protein Structure Prediction (2014, methodology): “10 FindCore1 is a superimposition independent method for isolating a core atom set and partitioning that set into domains.”