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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:143/0  |  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).


  
Multi-model analysis of climate impacts on plant photosynthesis in China during 2000-2015 期刊论文
INTERNATIONAL JOURNAL OF CLIMATOLOGY, 2019, 39 (15) : 5539-5555
作者:  Yan, Hao;  Wang, Shao-Qiang;  Cao, Yun;  Xu, Ling-Ling;  Wu, Men-xin;  Cheng, Lu;  Mao, Liu-Xi;  Zhang, Xian-Zhou;  Liu, Yun-Fen;  Wang, Yan-Fen;  Chen, Shi-Ping;  Li, Ying-Nian;  Han, Shi-Jie;  Zhou, Guo-Yi;  Zhang, Yi-Ping;  Shugart, Herman H.;  Wang, Jun-Bang;  Zhao, Feng-Hua
收藏  |  浏览/下载:13/0  |  提交时间:2020/02/17
climate change  dry/wet climate  Gross primary production  meteorological factors  multi-model analysis  
Ozone enhancement due to the photodissociation of nitrous acid in eastern China 期刊论文
ATMOSPHERIC CHEMISTRY AND PHYSICS, 2019, 19 (17) : 11267-11278
作者:  Tie, Xuexi;  Long, Xin;  Li, Guohui;  Zhao, Shuyu;  Cao, Junji;  Xu, Jianming
收藏  |  浏览/下载:9/0  |  提交时间:2019/11/27
Impact of the Green Light Program on haze in the North China Plain, China 期刊论文
ATMOSPHERIC CHEMISTRY AND PHYSICS, 2019, 19 (17) : 11185-11197
作者:  Long, Xin;  Tie, Xuexi;  Zhou, Jiamao;  Dai, Wenting;  Li, Xueke;  Feng, Tian;  Li, Guohui;  Cao, Junji;  An, Zhisheng
收藏  |  浏览/下载:6/0  |  提交时间:2019/11/27
Stochastic simulations reveal few green wave surfing populations among spring migrating herbivorous waterfowl 期刊论文
NATURE COMMUNICATIONS, 2019, 10
作者:  Wang, Xin;  Cao, Lei;  Fox, Anthony D.;  Fuller, Richard;  Griffin, Larry;  Mitchell, Carl;  Zhao, Yunlin;  Moon, Oun-Kyong;  Cabot, David;  Xu, Zhenggang;  Batbayar, Nyambayar;  Koelzsch, Andrea;  van der Jeugd, Henk P.;  Madsen, Jesper;  Chen, Liding;  Nathan, Ran
收藏  |  浏览/下载:14/0  |  提交时间:2019/11/27
High Contribution of Secondary Brown Carbon to Aerosol Light Absorption in the Southeastern Margin of Tibetan Plateau 期刊论文
GEOPHYSICAL RESEARCH LETTERS, 2019, 46 (9) : 4962-4970
作者:  Wang, Qiyuan;  Han, Yongming;  Ye, Jianhuai;  Liu, Suixin;  Pongpiachan, Siwatt;  Zhang, Ningning;  Han, Yuemei;  Tian, Jie;  Wu, Cheng;  Long, Xin;  Zhang, Qian;  Zhang, Wenyan;  Zhao, Zhuzi;  Cao, Junji
收藏  |  浏览/下载:10/0  |  提交时间:2019/11/26
Pan-cancer genome and transcriptome analyses of 1,699 paediatric leukaemias and solid tumours 期刊论文
NATURE, 2018, 555 (7696) : 371-+
作者:  Ma, Xiaotu;  Liu, Yu;  Liu, Yanling;  Alexandrov, Ludmil B.;  Edmonson, Michael N.;  Gawad, Charles;  Zhou, Xin;  Li, Yongjin;  Rusch, Michael C.;  Easton, John;  Huether, Robert;  Gonzalez-Pena, Veronica;  Wilkinson, Mark R.;  Hermida, Leandro C.;  Davis, Sean;  Sioson, Edgar;  Pounds, Stanley;  Cao, Xueyuan;  Ries, Rhonda E.;  Wang, Zhaoming;  Chen, Xiang;  Dong, Li;  Diskin, Sharon J.;  Smith, Malcolm A.;  Auvil, Jaime M. Guidry;  Meltzer, Paul S.;  Lau, Ching C.;  Perlman, Elizabeth J.;  Maris, John M.;  Meshinchi, Soheil;  Hunger, Stephen P.;  Gerhard, Daniela S.;  Zhang, Jinghui
收藏  |  浏览/下载:15/0  |  提交时间:2019/11/27
Emission Characteristics of Primary Brown Carbon Absorption From Biomass and Coal Burning: Development of an Optical Emission Inventory for China 期刊论文
JOURNAL OF GEOPHYSICAL RESEARCH-ATMOSPHERES, 2019, 124 (3) : 1879-1893
作者:  Tian, Jie;  Wang, Qiyuan;  Ni, Haiyan;  Wang, Meng;  Zhou, Yaqing;  Han, Yongming;  Shen, Zhenxing;  Pongpiachan, Siwatt;  Zhang, Ningning;  Zhao, Zhuzi;  Zhang, Qian;  Zhang, Yue;  Long, Xin;  Cao, Junji
收藏  |  浏览/下载:8/0  |  提交时间:2019/04/09
Sensitivity of EMIC Wave-Driven Scattering Loss of Ring Current Protons to Wave Normal Angle Distribution 期刊论文
GEOPHYSICAL RESEARCH LETTERS, 2019, 46 (2) : 590-598
作者:  Cao, Xing;  Ni, Binbin;  Summers, Danny;  Shprits, Yuri Y.;  Gu, Xudong;  Fu, Song;  Lou, Yuequn;  Zhang, Yang;  Ma, Xin;  Zhang, Wenxun;  Huang, He;  Yi, Juan
收藏  |  浏览/下载:14/0  |  提交时间:2019/04/09
Short-Term Weather Patterns Modulate Air Quality in Eastern China During 2015-2016 Winter 期刊论文
JOURNAL OF GEOPHYSICAL RESEARCH-ATMOSPHERES, 2019, 124 (2) : 986-1002
作者:  Zhao, Shuyu;  Feng, Tian;  Tie, Xuexi;  Dai, Wenting;  Zhou, Jiamao;  Long, Xin;  Li, Guohui;  Cao, Junji
收藏  |  浏览/下载:9/0  |  提交时间:2019/04/09