Target highlights In CASP3: Experimental target structures for the critical assessment of techniquea for protein structure prediction

摘要

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 bacteriophagc T4, the cyclic GMP-dependcnt protein kinase Ibeta dimeriza-tion/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 (beta-D-glucosy]-hydroxymethyluracil) in Tryp-anosoma and Leishmania, an so far uncharacterized 73 residue domain from Rumitiococcus gnavus with a fold typical for PDZ-like domains, a domain from the phycobilisome core-membrane linker phy-cobiliprotein ApcE from Synechocyslis, the heat shock protein 90 activators PFC0360w and PFC0270w from Plasmodium falciparum, and 2-oxo-3-deoxygalactonate kinase from Klebsiella