Target Highlights in CASP9: Experimental Target Structures for the Critical Assessment of Techniques for Protein Structure Prediction

By Andriy Kryshtafovych, John Moult, S. G. Bartual, J. Bazan, Helen M. Berman, Darren E. Casteel, E. Christodoulou, J. Everett, Jens Hausmann, T. Heidebrecht and 20 more. 2011

24 citations recorded by the source corpus.

One goal of the CASP community wide experiment on the critical assessment of techniques for protein structure prediction is to identify the current state of the art in protein structure prediction and modeling. A fundamental principle of CASP is blind prediction on a set of relevant protein targets, that is, the participating computational methods are tested on a common set of experimental target proteins, for which the experimental structures are not known at the time of modeling. Therefore, the CASP experiment would not have been possible without broad support of the experimental protein structural biology community. In this article, several experimental groups discuss the structures of the proteins which they provided as prediction targets for CASP9, highlighting structural and functional peculiarities of these structures: the long tail fiber protein gp37 from bacteriophage T4, the cyclic GMP‐dependent protein kinase Iβ dimerization/docking domain, the ectodomain of the JTB (jumping translocation breakpoint) transmembrane receptor, Autotaxin in complex with an inhibitor, the DNA‐binding J‐binding protein 1 domain essential for biosynthesis and maintenance of DNA base‐J (β‐D‐glucosyl‐hydroxymethyluracil) in Trypanosoma and Leishmania, an so far uncharacterized 73 residue domain from Ruminococcus gnavus with a fold typical for PDZ‐like domains, a domain from the phycobilisome core‐membrane linker phycobiliprotein ApcE from Synechocystis, the heat shock protein 90 activators PFC0360w and PFC0270w from Plasmodium falciparum, and 2‐oxo‐3‐deoxygalactonate kinase from Klebsiella pneumoniae. Proteins 2011; © 2011 Wiley‐Liss, Inc.

Subfields: Cell Biology, Materials Chemistry, Molecular Biology

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Citations in the corpus

Assessment of template based protein structure predictions in CASP9 (2011, background): “Knowing the complete macromolecular assembly is therefore in many cases crucial to understand the functional properties of a protein.9– 11 The community experiment on Critical Assessment of Techniques for Protein Structure Prediction (CASP) is assessing the state of the art in modeling techniques…”
Biological and Functional Relevance of CASP Predictions (2017, methodology): “(3) The fraction of correctly and incorrectly predicted secondary structure as reported by DSSP [Kabsch and Sander 1983].”
CAD‐score: A new contact area difference‐based function for evaluation of protein structural models (2013, methodology): “25 CAD-score is a robust measure for evaluating and ranking single-domain models As a first step, we decided to compare CAD-score with GDT-TS, a standard CASP score that withstood the test of time and is generally recognized as the single most effective reference-based score.”
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 Experiment CASP10 (2014, background): “We hope that this type of manuscript, which was introduced in CASP9, 2 will help the structure prediction community to better understand which features of a structure are important from the point of view of crystal-lographers and NMR spectroscopists and how these features should be taken into accoun”
RNA target highlights in CASP15: Evaluation of predicted models by structure providers (2023, background): “This article follows the tradition of protein CASP target highlight articles, 6 – 11 where each section provides the accounts of the structure providers and their insights into the accuracy of the models submitted.”