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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).


  
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
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
Structure of the maize photosystem I supercomplex with light-harvesting complexes I and II 期刊论文
SCIENCE, 2018, 360 (6393) : 1109-1112
作者:  Pan, Xiaowei;  Ma, Jun;  Su, Xiaodong;  Cao, Peng;  Chang, Wenrui;  Liu, Zhenfeng;  Zhang, Xinzheng;  Li, Mei
收藏  |  浏览/下载:5/0  |  提交时间:2019/11/27
Weakly perturbative imaging of interfacial water with submolecular resolution by atomic force microscopy 期刊论文
NATURE COMMUNICATIONS, 2018, 9
作者:  Peng, Jinbo;  Guo, Jing;  Hapala, Prokop;  Cao, Duanyun;  Ma, Runze;  Cheng, Bowei;  Xu, Limei;  Ondracek, Martin;  Jelinek, Pavel;  Wang, Enge;  Jiang, Ying
收藏  |  浏览/下载:4/0  |  提交时间:2019/11/27
PAF1 regulation of promoter-proximal pause release via enhancer activation 期刊论文
SCIENCE, 2017, 357 (6357) : 1294-1298
作者:  Chen, Fei Xavier;  Xie, Peng;  Collings, Clayton K.;  Cao, Kaixiang;  Aoi, Yuki;  Marshall, Stacy A.;  Rendleman, Emily J.;  Ugarenko, Michal;  Ozark, Patrick A.;  Zhang, Anda;  Shiekhattar, Ramin;  Smith, Edwin R.;  Zhang, Michael Q.;  Shilatifard, Ali
收藏  |  浏览/下载:8/0  |  提交时间:2019/11/27
Structure and assembly mechanism of plant C2S2M2-type PSII-LHCII supercomplex 期刊论文
SCIENCE, 2017, 357 (6353) : 816-+
作者:  Su, Xiaodong;  Ma, Jun;  Wei, Xuepeng;  Cao, Peng;  Zhu, Dongjie;  Chang, Wenrui;  Liu, Zhenfeng;  Zhang, Xinzheng;  Li, Mei
收藏  |  浏览/下载:7/0  |  提交时间:2019/11/27
Satellite-based entanglement distribution over 1200 kilometers 期刊论文
SCIENCE, 2017, 356 (6343) : 1180-1184
作者:  Yin, Juan;  Cao, Yuan;  Li, Yu-Huai;  Liao, Sheng-Kai;  Zhang, Liang;  Ren, Ji-Gang;  Cai, Wen-Qi;  Liu, Wei-Yue;  Li, Bo;  Dai, Hui;  Li, Guang-Bing;  Lu, Qi-Ming;  Gong, Yun-Hong;  Xu, Yu;  Li, Shuang-Lin;  Li, Feng-Zhi;  Yin, Ya-Yun;  Jiang, Zi-Qing;  Li, Ming;  Jia, Jian-Jun;  Ren, Ge;  He, Dong;  Zhou, Yi-Lin;  Zhang, Xiao-Xiang;  Wang, Na;  Chang, Xiang;  Zhu, Zhen-Cai;  Liu, Nai-Le;  Chen, Yu-Ao;  Lu, Chao-Yang;  Shu, Rong;  Peng, Cheng-Zhi;  Wang, Jian-Yu;  Pan, Jian-Wei
收藏  |  浏览/下载:17/0  |  提交时间:2019/11/27