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DeePMD-kit v2: A software package for deep potential models 期刊论文
JOURNAL OF CHEMICAL PHYSICS, 2023, 卷号: 159, 期号: 5, 页码: 24
作者:  Zeng, Jinzhe;  Zhang, Duo;  Lu, Denghui;  Mo, Pinghui;  Li, Zeyu;  Chen, Yixiao;  Rynik, Marian;  Huang, Li'ang;  Li, Ziyao;  Shi, Shaochen;  Wang, Yingze;  Ye, Haotian;  Tuo, Ping;  Yang, Jiabin;  Ding, Ye;  Li, Yifan;  Tisi, Davide;  Zeng, Qiyu;  Bao, Han;  Xia, Yu;  Huang, Jiameng;  Muraoka, Koki;  Wang, Yibo;  Chang, Junhan;  Yuan, Fengbo;  Bore, Sigbjorn Loland;  Cai, Chun;  Lin, Yinnian;  Wang, Bo;  Xu, Jiayan;  Zhu, Jia-Xin;  Luo, Chenxing;  Zhang, Yuzhi;  Goodall, Rhys E. A.;  Liang, Wenshuo;  Singh, Anurag Kumar;  Yao, Sikai;  Zhang, Jingchao;  Wentzcovitch, Renata;  Han, Jiequn;  Liu, Jie;  Jia, Weile;  York, Darrin M.;  E, Weinan;  Car, Roberto;  Zhang, Linfeng;  Wang, Han
收藏  |  浏览/下载：11/0  |  提交时间：2023/12/04
DeepBindBC: A practical deep learning method for identifying native-like protein-ligand complexes in virtual screening 期刊论文
METHODS, 2022, 卷号: 205, 页码: 247-262
作者:  Zhang, Haiping;  Zhang, Tingting;  Saravanan, Konda Mani;  Liao, Linbu;  Wu, Hao;  Zhang, Haishan;  Zhang, Huiling;  Pan, Yi;  Wu, Xuli;  Wei, Yanjie
收藏  |  浏览/下载：14/0  |  提交时间：2023/07/12
Native like protein-ligand  Drug virtual screening  ResNet  Deep learning  Human pancreatic alpha amylase inhibitor  
An Efficient Modern Strategy to Screen Drug Candidates Targeting RdRp of SARS-CoV-2 With Potentially High Selectivity and Specificity 期刊论文
FRONTIERS IN CHEMISTRY, 2022, 卷号: 10, 页码: 13
作者:  Zhang, Haiping;  Gong, Xiaohua;  Peng, Yun;  Saravanan, Konda Mani;  Bian, Hengwei;  Zhang, John Z. H.;  Wei, Yanjie;  Pan, Yi;  Yang, Yang
收藏  |  浏览/下载：24/0  |  提交时间：2022/12/07
antiviral agent  RdRp  compound specificity estimation  virtual screening  tubeimoside III  
An Integrated Deep Learning and Molecular Dynamics Simulation-Based Screening Pipeline Identifies Inhibitors of a New Cancer Drug Target TIPE2 期刊论文
FRONTIERS IN PHARMACOLOGY, 2021, 卷号: 12, 页码: 13
作者:  Zhang, Haiping;  Li, Junxin;  Saravanan, Konda Mani;  Wu, Hao;  Wang, Zhichao;  Wu, Du;  Wei, Yanjie;  Lu, Zhen;  Chen, Youhai H.;  Wan, Xiaochun;  Pan, Yi
收藏  |  浏览/下载：29/0  |  提交时间：2022/06/21
TIPE2  UM-164  virtual screening  deep learning  molecular dynamics simulation  
Long-term behavior of vacancy defects in Pu-Ga alloy: Effects of temperature and Ga concentration 期刊论文
COMPUTATIONAL AND THEORETICAL CHEMISTRY, 2021, 卷号: 1204, 页码: 10
作者:  Xu, Lei;  Wang, Li-Fang;  Chen, Xin;  Gao, Xing-Yu;  Shang, Hong-Hui;  Liu, Hai-Feng;  Song, Hai-Feng
收藏  |  浏览/下载：37/0  |  提交时间：2021/12/01
Vacancy defects  Dynamical evolution  Pu-Ga alloy  Actinide metals  Atomistic kinetic Monte Carlo  Molecular dynamics  
A novel virtual screening procedure identifies Pralatrexate as inhibitor of SARS-CoV-2 RdRp and it reduces viral replication in vitro 期刊论文
PLOS COMPUTATIONAL BIOLOGY, 2020, 卷号: 16, 期号: 12, 页码: 20
作者:  Zhang, Haiping;  Yang, Yang;  Li, Junxin;  Wang, Min;  Saravanan, Konda Mani;  Wei, Jinli;  Ng, Justin Tze-Yang;  Hossain, Md Tofazzal;  Liu, Maoxuan;  Zhang, Huiling;  Ren, Xiaohu;  Pan, Yi;  Peng, Yin;  Shi, Yi;  Wan, Xiaochun;  Liu, Yingxia;  Wei, Yanjie
收藏  |  浏览/下载：39/0  |  提交时间：2021/12/01
Transcriptomic analysis of glioblastoma multiforme providing new insights into GPR17 signaling communication 期刊论文
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 2020, 页码: 14
作者:  Mutharasu, Gnanavel;  Murugesan, Akshaya;  Konda Mani, Saravanan;  Yli-Harja, Olli;  Kandhavelu, Meenakshisundaram
收藏  |  浏览/下载：48/0  |  提交时间：2020/12/10
GPR17  signaling networks  glioblastoma multiforme  RNA-Seq  protein–  protein interface  kinases  
Structural basis for the inhibition of SARS-CoV2 main protease by Indian medicinal plant-derived antiviral compounds 期刊论文
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 2020, 页码: 9
作者:  Saravanan, Konda Mani;  Zhang, Haiping;  Senthil, Renganathan;  Vijayakumar, Kevin Kumar;  Sounderrajan, Vignesh;  Wei, Yanjie;  Shakila, Harshavardhan
收藏  |  浏览/下载：97/0  |  提交时间：2020/12/10
SARS-CoV2  main protease  medicinal plants  molecular docking and dynamics  drug design  
Live-SIMBA: an ImageJ plug-in for the universal and accelerated single molecule-guided Bayesian localization super resolution microscopy (SIMBA) method 期刊论文
BIOMEDICAL OPTICS EXPRESS, 2020, 卷号: 11, 期号: 10, 页码: 5842-5859
作者:  Li, Hongjia;  Xu, Fan;  Gao, Shan;  Zhang, Mingshu;  Xue, Fudong;  Xu, Pingyong;  Zhang, Fa
收藏  |  浏览/下载：48/0  |  提交时间：2020/12/10
FastNBL: fast neighbor lists establishment for molecular dynamics simulation based on bitwise operations 期刊论文
JOURNAL OF SUPERCOMPUTING, 2020, 卷号: 76, 期号: 7, 页码: 5501-5520
作者:  Li, Kun;  Li, Shigang;  Huang, Shan;  Chen, Yifeng;  Zhang, Yunquan
收藏  |  浏览/下载：49/0  |  提交时间：2020/12/10
Neighbor list  Bitwise operations  SIMD  Molecular dynamics