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

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TitleTarget highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction.
Publication TypeJournal Article
Year of Publication2011
AuthorsKryshtafovych, A, Moult, J, Bartual, SG, J Bazan, F, Berman, H, Casteel, DE, Christodoulou, E, Everett, JK, Hausmann, J, Heidebrecht, T, Hills, T, Hui, R, Hunt, JF, Seetharaman, J, Joachimiak, A, Kennedy, MA, Kim, C, Lingel, A, Michalska, K, Montelione, GT, Otero, JM, Perrakis, A, Pizarro, JC, van Raaij, MJ, Ramelot, TA, Rousseau, F, Tong, L, Wernimont, AK, Young, J, Schwede, T
JournalProteins
Volume79 Suppl 10
Pagination6-20
Date Published2011
ISSN1097-0134
KeywordsAmino Acid Sequence, Animals, Bacteriophage T4, Computational Biology, Cyclic GMP-Dependent Protein Kinases, DNA-Binding Proteins, Humans, Klebsiella pneumoniae, Leishmania, Models, Molecular, Molecular Sequence Data, Phosphoric Diester Hydrolases, Phosphotransferases (Alcohol Group Acceptor), Plasmodium falciparum, Protein Conformation, Protein Folding, Proteins, Protozoan Proteins, Trypanosoma, Viral Proteins
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.

DOI10.1002/prot.23196
Alternate JournalProteins
PubMed ID22020785
PubMed Central IDPMC3692002
Grant ListK22 CA124517-03 / CA / NCI NIH HHS / United States
P41 LM007085 / LM / NLM NIH HHS / United States
P41 LM007085-01 / LM / NLM NIH HHS / United States
R01 GM090161-03 / GM / NIGMS NIH HHS / United States
R01 GM100482 / GM / NIGMS NIH HHS / United States
U54 GM074942 / GM / NIGMS NIH HHS / United States
U54 GM074942-01 / GM / NIGMS NIH HHS / United States
U54 GM094585 / GM / NIGMS NIH HHS / United States
U54 GM094585-01 / GM / NIGMS NIH HHS / United States