Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction

Abstract

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, i.e. 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 manuscript, 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 fibre protein gp37 from bacteriophage T4, the cyclic GMP-dependent protein kinase Iβ (PKGIβ) dimerization/docking domain, the ectodomain of the JTB (Jumping Translocation Breakpoint) transmembrane receptor, Autotaxin (ATX) in complex with an inhibitor, the DNA-Binding J-Binding Protein 1 (JBP1) 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 (PBS) core-membrane linker (LCM) phycobiliprotein ApcE from Synechocystis, the Heat shock protein 90 (Hsp90) activators PFC0360w and PFC0270w from Plasmodium falciparum, and 2-oxo-3-deoxygalactonate kinase from Klebsiella pneumoniae.

CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction

“…the better average performance of comparative methods than the single-sequence methods) are similar to those observed in the CASP experiments focused on protein structure prediction (12). We hope that the results of CompaRNA benchmarks will stimulate the community of developers of RNA structure prediction methods to try new solutions (or combinations of the existing solutions) that will eliminate the current bottlenecks and will contribute to the improvement of useful tools available for the wide research community.…”

“…The ability of human experts to predict 3D structures of proteins has been assessed in the course of the Critical Assessment of protein Structure Prediction (CASP) experiment (12), which now has a counterpart in the RNA Puzzles experiment (13). On the other hand, the performance of fully automated methods (without human intervention) was evaluated and prompted important improvements in the context of continuous and automated benchmarks Livebench (14) and EVA (15).…”

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

“…In this article, the experimentalists providing targets for CASP10 present selected target highlights and discuss which aspects of the targets were specifically interesting and to what extent they were correctly reproduced in the predictions. We hope that this type of manuscript, which was introduced in CASP9, will help the structure prediction community to better understand which features of a structure are important from the point of view of crystallographers and NMR spectroscopists and how these features should be taken into account to develop better prediction tools. The article can also be of interest for future CASP assessors to decide which additional aspects of a structure require special attention in the assessment.…”

Critical assessment of methods of protein structure prediction (CASP)—round IX

“…This paper outlines the structure and conduct of the experiment. It is followed by a paper highlighting the most interesting CASP9 targets from the perspective of the members of the experimental community submitting targets to CASP 10 . Next is the paper 11 describing the CASP9 target proteins, guidelines for splitting them into domains (evaluation units) and general principles for assigning the relative difficulty of constructing an accurate model in each case.…”