Challenging the state-of-the-art in protein structure prediction: Highlights of experimental target structures for the 10th Critical Assessment of Techniques for Protein Structure Prediction…

By Andriy Kryshtafovych, John Moult, Patrick M. Bales, J. Bazan, Marco Biasini, A. Burgin, Chen Chen, F. V. Cochran, T. Craig, Rhiju Das and 13 more. 2014

55 citations recorded by the source corpus.

For the last two decades, CASP has assessed the state of the art in techniques for protein structure prediction and identified areas which required further development. CASP would not have been possible without the prediction targets provided by the experimental structural biology community. In the latest experiment, CASP10, more than 100 structures were suggested as prediction targets, some of which appeared to be extraordinarily difficult for modeling. In this article, authors of some of the most challenging targets discuss which specific scientific question motivated the experimental structure determination of the target protein, which structural features were especially interesting from a structural or functional perspective, and to what extent these features were correctly reproduced in the predictions submitted to CASP10. Specifically, the following targets will be presented: the acid‐gated urea channel, a difficult to predict transmembrane protein from the important human pathogen Helicobacter pylori; the structure of human interleukin (IL)−34, a recently discovered helical cytokine; the structure of a functionally uncharacterized enzyme OrfY from Thermoproteus tenax formed by a gene duplication and a novel fold; an ORFan domain of mimivirus sulfhydryl oxidase R596; the fiber protein gene product 17 from bacteriophage T7; the bacteriophage CBA‐120 tailspike protein; a virus coat protein from metagenomic samples of the marine environment; and finally, an unprecedented class of structure prediction targets based on engineered disulfide‐rich small proteins. Proteins 2014; 82(Suppl 2):26–42. © 2013 Wiley Periodicals, Inc.

Subfields: Ecology, Materials Chemistry, Molecular Biology

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Citations in the corpus

Critical assessment of methods of protein structure prediction (CASP) — round x (2013, background): “Then there is a paper highlighting some of the most challenging CASP10 targets from the perspective of members of the experimental community who submitted targets.26 As is standard for four CASPs now, targets are divided into two categories of difficulty.”
Biological and Functional Relevance of CASP Predictions (2017, methodology): “We aim to provide two references for users who are considering structural models for functional annotation: (1) Can model-1 (the best in terms of their structure feature) provide robust functional insights? (2) Can the server (the average of all models) provide models with good functional features? ”
Assessment of ligand binding site predictions in CASP10 (2014, background): “17,23,25,29,32 Some types of this domain use zinc, others use iron or form salt-bridges to create the correct fold, which often does not change conformation upon binding the target.”