Docking in CAPRI
Docking in CAPRI
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停靠在卡普里岛
DOI：
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发表时间：
2003
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通讯作者：
J. Janin
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作者：
J. Janin
本期《蛋白质》带您来到那不勒斯湾，地中海上方明亮的蓝天和维苏威火山作为背景。不久我们将在卡普里岛登陆，该岛以其悬崖、悠久的历史以及所有访问或居住过那里的艺术家、作家和诗人而闻名。或者我们一起去？也不完全是今天的卡普里不是一个海上度假胜地，而是预测相互作用实验的关键评估，我们对接蛋白质而不是游艇。卡普里实验旨在测试对接方法的能力：如果我们知道蛋白质-蛋白质复合物的组成，我们能否预测其结构？就像CASP（Critical Assessment of methods for Structure Prediction）中的蛋白质折叠预测一样，卡普里预测必须在独立评估员与未发表的实验结构进行比较之前进行盲测。邀请世界各地开发分析蛋白质-蛋白质相互作用和预测复合物结构的方法的所有团体参加。虽然CASP已经有10年的历史了，但卡普里实验始于2001年，并于2001年7月和2002年1月进行了两轮预测。第三轮于2003年1月开始，其他人将遵循提供合适的targets.here我们报告的结果在前两轮卡普里的约20组作出预测的7个目标：7蛋白质-蛋白质复合物，晶体学家提出了新的X射线结构提供给我们。R. Mendez，S.沃达克和他在布鲁塞尔的合作者面临着一项艰巨的任务，即根据晶体学原子坐标来评估这些预测。Kim Henrick在Hinxton（英国）的欧洲生物信息学研究所建立并维护了卡普里网站（http：capri.ebi.ac.uk），所有预测都在该网站上提交，初步结果也在该网站上公布。这项实验首先依赖于我在伊夫河畔、马赛（法国）和罗克维尔（马里兰州）的同事们的慷慨，他们提供了目标的X射线结构，然后是预测小组的专业知识和智慧，最后是评估人员和卡普里网站管理员的辛勤工作。无论第一轮还是第二轮是成功的，你都可以通过浏览卡普里的网站和这里提供的报告来判断。我们希望这次参观能够鼓舞人心，并通过提供目标或做出预测来吸引游客参与未来的实验。
This issue of Proteins takes you to the Gulf of Naples, with a bright blue sky above the Mediterranean sea and Mount Vesuvius in the background. Soon we shall be landing on the Isle of Capri, famous for its cliffs, its long history, and all the artists, writers, and poets who visited or lived there. Or shall we? Well, not quite. Today’s CAPRI is not a sea resort, but the Critical Assessment of PRedicted Interaction experiment, and we are docking proteins instead of a yacht. The CAPRI experiment aims to test the capacity of docking methods: can we predict the structure of a protein–protein complex if we know that of its components? Like protein fold predictions in CASP (Critical Assessment of methods for Structure Prediction), a similar experiment which is well known to the readers of Proteins, a CAPRI prediction must be made blindly before being compared by independent assessors to an unpublished experimental structure. All groups worldwide that develop methods to analyze protein–protein interaction and predict the structure of complexes are invited to participate. Although CASP is 10 years old, the CAPRI experiment began in 2001, and two rounds of predictions were held in July 2001 and January 2002. A third round began in January 2003; others will follow provided suitable targets are found. Here we report results obtained during the first two rounds of CAPRI by some 20 groups making predictions on seven targets: seven protein– protein complexes for which crystallographers had made new X-ray structures available to us. R. Mendez, S. Wodak, and collaborators in Brussels had the difficult task of assessing the predictions against the crystallographic atomic coordinates. Kim Henrick set up and maintained the CAPRI Web site (http://capri.ebi.ac.uk) at the European Bioinformatics Institute of Hinxton (UK), where all predictions were submitted and preliminary results disclosed. The experiment relied first on the generosity of my colleagues in Gif-sur-Yvette and Marseille (France) and in Rockville (MD) who provided the X-ray structures of the targets, then on the expertise and sagacity of the predictor groups, and finally on the hard work of the assessors and the CAPRI webmaster. Whether rounds 1 or 2 were successful, you will judge by touring CAPRI by means of its Web site and of the reports presented here. We hope the tour will be inspiring and that it will entice the visitors to participate in future rounds of the experiment by providing targets or by making predictions.