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Improved protein structure prediction using potentials from deep learning 期刊论文
NATURE, 2020, 577 (7792) : 706-+
作者:  Ma, Runze;  Cao, Duanyun;  Zhu, Chongqin;  Tian, Ye;  Peng, Jinbo;  Guo, Jing;  Chen, Ji;  Li, Xin-Zheng;  Francisco, Joseph S.;  Zeng, Xiao Cheng;  Xu, Li-Mei;  Wang, En-Ge;  Jiang, Ying
收藏  |  浏览/下载：142/0  |  提交时间：2020/07/03

Protein structure prediction can be used to determine the three-dimensional shape of a protein from its amino acid sequence(1). This problem is of fundamental importance as the structure of a protein largely determines its function(2)  however, protein structures can be difficult to determine experimentally. Considerable progress has recently been made by leveraging genetic information. It is possible to infer which amino acid residues are in contact by analysing covariation in homologous sequences, which aids in the prediction of protein structures(3). Here we show that we can train a neural network to make accurate predictions of the distances between pairs of residues, which convey more information about the structure than contact predictions. Using this information, we construct a potential of mean force(4) that can accurately describe the shape of a protein. We find that the resulting potential can be optimized by a simple gradient descent algorithm to generate structures without complex sampling procedures. The resulting system, named AlphaFold, achieves high accuracy, even for sequences with fewer homologous sequences. In the recent Critical Assessment of Protein Structure Prediction(5) (CASP13)-a blind assessment of the state of the field-AlphaFold created high-accuracy structures (with template modelling (TM) scores(6) of 0.7 or higher) for 24 out of 43 free modelling domains, whereas the next best method, which used sampling and contact information, achieved such accuracy for only 14 out of 43 domains. AlphaFold represents a considerable advance in protein-structure prediction. We expect this increased accuracy to enable insights into the function and malfunction of proteins, especially in cases for which no structures for homologous proteins have been experimentally determined(7).


  
Palmitoylation of NOD1 and NOD2 is required for bacterial sensing 期刊论文
SCIENCE, 2019, 366 (6464) : 460-+
作者:  Lu, Yan;  Zheng, Yuping;  Coyaud, Etienne;  Zhang, Chao;  Selvabaskaran, Apiraam;  Yu, Yuyun;  Xu, Zizhen;  Weng, Xialian;  Chen, Ji Shun;  Meng, Ying;  Warner, Neil;  Cheng, Xiawei;  Liu, Yangyang;  Yao, Bingpeng;  Hu, Hu;  Xia, Zonping;  Muise, Aleixo M.;  Klip, Amira;  Brumell, John H.;  Girardin, Stephen E.;  Ying, Songmin;  Fairn, Gregory D.;  Raught, Brian;  Sun, Qiming;  Neculai, Dante
收藏  |  浏览/下载：11/0  |  提交时间：2019/11/27
Differential responses of carbon-degrading enzyme activities to warming: Implications for soil respiration 期刊论文
GLOBAL CHANGE BIOLOGY, 2018, 24 (10) : 4816-4826
作者:  Chen, Ji;  Luo, Yiqi;  Garcia-Palacios, Pablo;  Cao, Junji;  Dacal, Marina;  Zhou, Xuhui;  Li, Jianwei;  Xia, Jianyang;  Niu, Shuli;  Yang, Huiyi;  Shelton, Shelby;  Guo, Wei;  van Groenigen, Kees Jan
收藏  |  浏览/下载：11/0  |  提交时间：2019/04/09
cellulase activity  decomposition  extracellular enzyme activity  global warming  ligninase activity  recalcitrant carbon pool  soil microorganisms  soil respiration  
Characteristics of climate change and its relationship with land use/cover change in Yunnan Province, China 期刊论文
INTERNATIONAL JOURNAL OF CLIMATOLOGY, 2018, 38 (5) : 2520-2537
作者:  Shi, Haiyun;  Chen, Ji
收藏  |  浏览/下载：7/0  |  提交时间：2019/04/09
climate change  temperature  precipitation  extremes  land use/cover change  
土壤有机碳分解对增温和放牧的响应及其胞外酶驱动机制 项目
项目编号：41701292； 经费：240000(CNY)； 起止日期：2018 / dc_date_end
项目负责人:  陈骥
收藏  |  浏览/下载：11/0  |  提交时间：2019/11/27
Enhanced decomposition of stable soil organic carbon and microbial catabolic potentials by long-term field warming 期刊论文
GLOBAL CHANGE BIOLOGY, 2017, 23 (11)
作者:  Feng, Wenting;  Liang, Junyi;  Hale, Lauren E.;  Jung, Chang Gyo;  Chen, Ji;  Zhou, Jizhong;  Xu, Minggang;  Yuan, Mengting;  Wu, Liyou;  Bracho, Rosvel;  Pegoraro, Elaine;  Schuur, Edward A. G.;  Luo, Yiqi
收藏  |  浏览/下载：7/0  |  提交时间：2019/04/09
diversity  Geochip  incubation  inverse modeling  long-term warming  metagenomics  microbial community  soil organic carbon  turnover  
Costimulation of soil glycosidase activity and soil respiration by nitrogen addition 期刊论文
GLOBAL CHANGE BIOLOGY, 2017, 23 (3)
作者:  Chen, Ji;  Luo, Yiqi;  Li, Jianwei;  Zhou, Xuhui;  Cao, Junji;  Wang, Rui-Wu;  Wang, Yunqiang;  Shelton, Shelby;  Jin, Zhao;  Walker, Laura M.;  Feng, Zhaozhong;  Niu, Shuli;  Feng, Wenting;  Jian, Siyang;  Zhou, Lingyan
收藏  |  浏览/下载：6/0  |  提交时间：2019/04/09
glycosidase activity  meta-analysis  nitrogen addition  soil respiration  soil type  vegetation type  
水对过成熟页岩中超临界气体吸附的影响 项目
项目编号：41602132； 经费：200000(CNY)； 起止日期：2017 / dc_date_end
项目负责人:  陈吉
收藏  |  浏览/下载：0/0  |  提交时间：2019/04/11