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WeFold:蛋白质结构预测的一种合作竞争方式

WeFold: a coopetition for protein structure prediction.

作者信息

Khoury George A, Liwo Adam, Khatib Firas, Zhou Hongyi, Chopra Gaurav, Bacardit Jaume, Bortot Leandro O, Faccioli Rodrigo A, Deng Xin, He Yi, Krupa Pawel, Li Jilong, Mozolewska Magdalena A, Sieradzan Adam K, Smadbeck James, Wirecki Tomasz, Cooper Seth, Flatten Jeff, Xu Kefan, Baker David, Cheng Jianlin, Delbem Alexandre C B, Floudas Christodoulos A, Keasar Chen, Levitt Michael, Popović Zoran, Scheraga Harold A, Skolnick Jeffrey, Crivelli Silvia N

机构信息

Department of Chemical and Biological Engineering, Princeton University, Princeton.

出版信息

Proteins. 2014 Sep;82(9):1850-68. doi: 10.1002/prot.24538. Epub 2014 Jul 8.

Abstract

The protein structure prediction problem continues to elude scientists. Despite the introduction of many methods, only modest gains were made over the last decade for certain classes of prediction targets. To address this challenge, a social-media based worldwide collaborative effort, named WeFold, was undertaken by 13 labs. During the collaboration, the laboratories were simultaneously competing with each other. Here, we present the first attempt at "coopetition" in scientific research applied to the protein structure prediction and refinement problems. The coopetition was possible by allowing the participating labs to contribute different components of their protein structure prediction pipelines and create new hybrid pipelines that they tested during CASP10. This manuscript describes both successes and areas needing improvement as identified throughout the first WeFold experiment and discusses the efforts that are underway to advance this initiative. A footprint of all contributions and structures are publicly accessible at http://www.wefold.org.

摘要

蛋白质结构预测问题仍然困扰着科学家们。尽管已经引入了许多方法,但在过去十年中,对于某些类别的预测目标,进展仍然有限。为应对这一挑战,13个实验室开展了一项名为WeFold的基于社交媒体的全球合作项目。在合作过程中,各实验室同时相互竞争。在此,我们展示了将“竞合”应用于蛋白质结构预测和优化问题的首次尝试。通过允许参与的实验室贡献其蛋白质结构预测流程的不同组件,并创建新的混合流程,并在CASP10期间进行测试,竞合得以实现。本手稿描述了整个首次WeFold实验中所取得的成功以及需要改进的领域,并讨论了推进这一计划的正在进行的工作。所有贡献和结构的记录可在http://www.wefold.org上公开获取。

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