Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction
- 1 January 2011
- journal article
- research article
- Published by Wiley in Proteins-Structure Function and Bioinformatics
- Vol. 79 (S10), 6-20
- https://doi.org/10.1002/prot.23196
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, 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;Keywords
This publication has 61 references indexed in Scilit:
- Structural basis of substrate discrimination and integrin binding by autotaxinNature Structural & Molecular Biology, 2011
- CASP9 target classificationProteins-Structure Function and Bioinformatics, 2011
- Structure of the bacteriophage T4 long tail fiber receptor-binding tipProceedings of the National Academy of Sciences, 2010
- A Crystal Structure of the Cyclic GMP-dependent Protein Kinase Iβ Dimerization/Docking Domain Reveals Molecular Details of Isoform-specific Anchoring*Journal of Biological Chemistry, 2010
- Boronic acid-based inhibitor of autotaxin reveals rapid turnover of LPA in the circulationProceedings of the National Academy of Sciences, 2010
- PSI-2: Structural Genomics to Cover Protein Domain Family SpaceStructure, 2009
- PDBsum new thingsNucleic Acids Research, 2009
- Structural specificity in coiled-coil interactionsCurrent Opinion in Structural Biology, 2008
- High blood pressure arising from a defect in vascular functionProceedings of the National Academy of Sciences, 2008
- The Protein Data BankNucleic Acids Research, 2000