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.
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.
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DOI：
10.1002/prot.24489
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发表时间：
2014-02
影响因子：
2.9
通讯作者：
Schwede, Torsten
中科院分区：
文献类型：
--
作者：
Kryshtafovych, Andriy;Moult, John;Bales, Patrick;Bazan, J. Fernando;Biasini, Marco;Burgin, Alex;Chen, Chen;Cochran, Frank V.;Craig, Timothy K.;Das, Rhiju;Fass, Deborah;Garcia-Doval, Carmela;Herzberg, Osnat;Lorimer, Donald;Luecke, Hartmut;Ma, Xiaolei;Nelson, Daniel C.;van Raaij, Mark J.;Rohwer, Forest;Segall, Anca;Seguritan, Victor;Zeth, Kornelius;Schwede, Torsten
在过去的二十年里，CASP评估了蛋白质结构预测技术的最新发展水平，并确定了需要进一步发展的领域。如果没有实验结构生物学社区提供的预测目标，CASP是不可能的。在最新的实验CASP 10中，超过100种结构被建议作为预测目标，其中一些结构似乎非常难以建模。在本文中，一些最具挑战性的目标的作者讨论了哪些特定的科学问题促使靶蛋白的实验结构测定，哪些结构特征从结构或功能的角度特别有趣，以及这些特征在提交给CASP 10的预测中正确再现的程度。具体而言，将提出以下目标：酸门控尿素通道，一个难以预测的跨膜蛋白从重要的人类病原体幽门螺杆菌;人白细胞介素IL-34的结构，最近发现的螺旋细胞因子;的结构的功能不明的酶OrfY从Thermoproteus tenax形成的基因复制和一个新的折叠;拟病毒巯基氧化酶R596的ORFan结构域;来自噬菌体T7的纤维蛋白gp 17;噬菌体CBA-120尾钉蛋白;来自海洋环境宏基因组样本的病毒外壳蛋白;最后是前所未有的一类结构预测目标基于工程化的富含二硫键的小蛋白。
For the last two decades, CASP has assessed the state of the art in techniques for protein structure prediction and identified areas which required further development. CASP would not have been possible without the prediction targets provided by the experimental structural biology community. In the latest experiment, CASP10, over 100 structures were suggested as prediction targets, some of which appeared to be extraordinarily difficult for modeling. In this paper, authors of some of the most challenging targets discuss which specific scientific question motivated the experimental structure determination of the target protein, which structural features were especially interesting from a structural or functional perspective, and to what extent these features were correctly reproduced in the predictions submitted to CASP10. Specifically, the following targets will be presented: the acid-gated urea channel, a difficult to predict trans-membrane protein from the important human pathogen Helicobacter pylori; the structure of human interleukin IL-34, a recently discovered helical cytokine; the structure of a functionally uncharacterized enzyme OrfY from Thermoproteus tenax formed by a gene duplication and a novel fold; an ORFan domain of mimivirus sulfhydryl oxidase R596; the fibre protein gp17 from bacteriophage T7; the Bacteriophage CBA-120 tailspike protein; a virus coat protein from metagenomic samples of the marine environment; and finally an unprecedented class of structure prediction targets based on engineered disulfide-rich small proteins.
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DOI：
10.1126/science.1231887
发表时间：
2013-02-01
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Hu B;Margolin W;Molineux IJ;Liu J
通讯作者：
Liu J
影响因子：
2.9
作者：
Kimura RH;Levin AM;Cochran FV;Cochran JR
通讯作者：
Cochran JR
影响因子：
3.7
作者：
Das R
通讯作者：
Das R
影响因子：
2.9
作者：
Huang, Yuanpeng J.;Mao, Binchen;Aramini, James M.;Montelione, Gaetano T.
通讯作者：
Montelione, Gaetano T.
影响因子：
2.9
作者：
Heineman, Richard H.;Springman, Rachael;Bull, James J.
通讯作者：
Bull, James J.