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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).


  
Numerical Simulation of the Irrigation Effects on Surface Fluxes and Local Climate in Typical Mountain-Oasis-Desert Systems in the Central Asia Arid Area 期刊论文
JOURNAL OF GEOPHYSICAL RESEARCH-ATMOSPHERES, 2019, 124 (23) : 12485-12506
作者:  Zhang, Miao;  Luo, Geping;  Cao, Xiaoshu;  Hamdi, Rafiq;  Li, Tao;  Cai, Peng;  Ye, Hui;  He, Huili
收藏  |  浏览/下载:8/0  |  提交时间:2020/02/17
Numerical Simulation of the Irrigation Effects on Surface Fluxes and Local Climate in Typical Mountain-Oasis-Desert Systems in the Central Asia Arid Area 期刊论文
JOURNAL OF GEOPHYSICAL RESEARCH-ATMOSPHERES, 2019
作者:  Zhang, Miao;  Luo, Geping;  Cao, Xiaoshu;  Hamdi, Rafiq;  Li, Tao;  Cai, Peng;  Ye, Hui;  He, Huili
收藏  |  浏览/下载:10/0  |  提交时间:2020/02/17
Flood and drip irrigations  Irrigation effects  Water-heat interactions  Modified WRF-Noah  
Chemical and optical properties of carbonaceous aerosols in Nanjing, eastern China: regionally transported biomass burning contribution 期刊论文
ATMOSPHERIC CHEMISTRY AND PHYSICS, 2019, 19 (17) : 11213-11233
作者:  Liu, Xiaoyan;  Zhang, Yan-Lin;  Peng, Yiran;  Xu, Lulu;  Zhu, Chunmao;  Cao, Fang;  Zhai, Xiaoyao;  Haque, M. Mozammel;  Yang, Chi;  Chang, Yunhua;  Huang, Tong;  Xu, Zufei;  Bao, Mengying;  Zhang, Wenqi;  Fan, Meiyi;  Lee, Xuhui
收藏  |  浏览/下载:6/0  |  提交时间:2019/11/27
Impact of particle number and mass size distributions of major chemical components on particle mass scattering efficiency in urban Guangzhou in southern China 期刊论文
ATMOSPHERIC CHEMISTRY AND PHYSICS, 2019, 19 (13) : 8471-8490
作者:  Tao, Jun;  Zhang, Zhisheng;  Wu, Yunfei;  Zhang, Leiming;  Wu, Zhijun;  Cheng, Peng;  Li, Mei;  Chen, Laiguo;  Zhang, Renjian;  Cao, Junji
收藏  |  浏览/下载:7/0  |  提交时间:2019/11/27
MiR-497 similar to 195 cluster regulates angiogenesis during coupling with osteogenesis by maintaining endothelial Notch and HIF-1 alpha activity 期刊论文
NATURE COMMUNICATIONS, 2017, 8
作者:  Yang, Mi;  Li, Chang-Jun;  Sun, Xi;  Guo, Qi;  Xiao, Ye;  Su, Tian;  Tu, Man-Li;  Peng, Hui;  Lu, Qiong;  Liu, Qing;  He, Hong-Bo;  Jiang, Tie-Jian;  Lei, Min-Xiang;  Wan, Mei;  Cao, Xu;  Luo, Xiang-Hang
收藏  |  浏览/下载:20/0  |  提交时间:2019/11/27
Raman enhancement on ultra-clean graphene quantum dots produced by quasi-equilibrium plasma-enhanced chemical vapor deposition 期刊论文
NATURE COMMUNICATIONS, 2018, 9
作者:  Liu, Donghua;  Chen, Xiaosong;  Hu, Yibin;  Sun, Tai;  Song, Zhibo;  Zheng, Yujie;  Cao, Yongbin;  Cai, Zhi;  Cao, Min;  Peng, Lan;  Huang, Yuli;  Du, Lei;  Yang, Wuli;  Chen, Gang;  Wei, Dapeng;  Shen, Andrew Thye;  Wei, Dacheng
收藏  |  浏览/下载:6/0  |  提交时间:2019/11/27
Characterization of urban amine-containing particles in southwestern China: seasonal variation, source, and processing 期刊论文
ATMOSPHERIC CHEMISTRY AND PHYSICS, 2019, 19 (5) : 3245-3255
作者:  Chen, Yang;  Tian, Mi;  Huang, Ru-Jin;  Shi, Guangming;  Wang, Huanbo;  Peng, Chao;  Cao, Junji;  Wang, Qiyuan;  Zhang, Shumin;  Guo, Dongmei;  Zhang, Leiming;  Yang, Fumo
收藏  |  浏览/下载:14/0  |  提交时间:2019/04/09
Intensified variability of the El Nino-Southern Oscillation enhances its modulations on tree growths in southeastern China over the past 218 years 期刊论文
INTERNATIONAL JOURNAL OF CLIMATOLOGY, 2018, 38 (14) : 5293-5304
作者:  Wang, Lei;  Fang, Keyan;  Chen, Dai;  Dong, Zhipeng;  Zhou, Feifei;  Li, Yingjun;  Zhang, Peng;  Ou, Tinghai;  Guo, Guoyang;  Cao, Xinguang;  Yu, Mingtong
收藏  |  浏览/下载:13/0  |  提交时间:2019/04/09
ENSO  inter-annual variability  southeast China  tree rings  
Evidence for Majorana bound states in an iron-based superconductor 期刊论文
SCIENCE, 2018, 362 (6412) : 333-335
作者:  Wang, Dongfei;  Kong, Lingyuan;  Fan, Peng;  Chen, Hui;  Zhu, Shiyu;  Liu, Wenyao;  Cao, Lu;  Sun, Yujie;  Du, Shixuan;  Schneeloch, John;  Zhong, Ruidan;  Gu, Genda;  Fu, Liang;  Ding, Hong;  Gao, Hong-Jun
收藏  |  浏览/下载:7/0  |  提交时间:2019/11/27