Tong Wang

Ab initio characterization of protein molecular dynamics with AI2BMD

Tong Wang, Xinheng He, Mingyu Li, Yatao Li, Ran Bi, Yusong Wang, Chaoran Cheng, Xiangzhen Shen, Jiawei Meng, He Zhang, Haiguang Liu, Zun Wang, Shaoning Li, Bin Shao, Tie-Yan Liu

Nature | November 2024

Publication

Overcoming the barrier of orbital-free density functional theory for molecular systems using deep learning

He Zhang, Siyuan Liu, Jiacheng You, Chang Liu, Shuxin Zheng, Ziheng Lu, Tong Wang, Nanning Zheng, Bin Shao

Nature Computational Science | March 2024

DOI Publication PDF Preprint

Enhancing geometric representations for molecules with equivariant vector-scalar interactive message passing

Yusong Wang, Tong Wang, Shaoning Li, Xinheng He, Mingyu Li, Zun Wang, Nanning Zheng, Bin Shao, Tie-Yan Liu

Nature Communications | January 2024, Vol 15(313)

Publication

Geometric Transformer with Interatomic Positional Encoding

Yusong Wang, Shaoning Li, Tong Wang, Bin Shao, Nanning Zheng, Tie-Yan Liu

NeurIPS 2023 | October 2023

Publication Publication

Efficiently incorporating quintuple interactions into geometric deep learning force fields

Zun Wang, Guoqing Liu, Yichi Zhou, Tong Wang, Bin Shao

NeurIPS 2023 | October 2023

Publication

AIMD-Chig: Exploring the conformational space of a 166-atom protein Chignolin with ab initio molecular dynamics

Tong Wang, Xinheng He, Mingyu Li, Bin Shao, Tie-Yan Liu

Scientific Data | August 2023

Publication

AI2BMD: efficient characterization of protein dynamics with ab initio accuracy

Tong Wang, Xinheng He, Mingyu Li, Yusong Wang, Zun Wang, Shaoning Li, Bin Shao, Tie-Yan Liu

July 2023

Preprint

Improving machine learning force fields for molecular dynamics simulations with fine-grained force metrics

Zun Wang, Hongfei Wu, Lixin Sun, Xinheng He, Zhirong Liu, Bin Shao, Tong Wang, Tie-Yan Liu

The Journal of Chemical Physics | July 2023, Vol 159(3)

Cover Story

Publication

Long-Short-Range Message-Passing: A Physics-Informed Framework to Capture Non-Local Interaction for Scalable Molecular Dynamics Simulation

Yunyang Li, Yusong Wang, Lin Huang, Han Yang, Xinran wei, Jia Zhang, Tong Wang, Zun Wang, Bin Shao, Tie-Yan Liu

April 2023

Preprint

DSN-DDI: an accurate and generalized framework for drug–drug interaction prediction by dual-view representation learning

Zimeng Li, Shichao Zhu, Bin Shao, Xiangxiang Zeng, Tong Wang, Tie-Yan Liu

Briefings in Bioinformatics | January 2023

Publication

An ensemble of VisNet, Transformer-M, and pretraining models for molecular property prediction in OGB Large-Scale Challenge@ NeurIPS 2022

Yusong Wang, Shaoning Li, Tong Wang, Zun Wang, Xinheng He, Bin Shao, Tie-Yan Liu

MSR-TR-2022-35 | November 2022

Published by Microsoft

Competition Winner

Publication

Stochastic Lag Time Parameterization for Markov State Models of Protein Dynamics

Shiqi Gong, Xinheng He, Qi Meng, Zhiming Ma, Bin Shao, Tong Wang, Tie-Yan Liu

The Journal of Physical Chemistry B | November 2022

Cover Story

Publication

ViSNet: a scalable and accurate geometric deep learning potential for molecular dynamics simulation

Yusong Wang, Shaoning Li, Xinheng He, Mingyu Li, Zun Wang, Nanning Zheng, Bin Shao, Tong Wang, Tie-Yan Liu

October 2022

Preprint

Direct Molecular Conformation Generation

Jinhua Zhu, Yingce Xia, Chang Liu, Lijun Wu, Shufang Xie, Yusong Wang, Tong Wang, Tao Qin, Wengang Zhou, Houqiang Liu, Haiguang Liu, Tie-Yan Liu

Transactions on Machine Learning Research | October 2022

Publication

Tailoring Molecules for Protein Pockets: a Transformer-based Generative Solution for Structured-based Drug Design

Kehan Wu, Yingce Xia, Yang Fan, Pan Deng, Haiguang Liu, Lijun Wu, Shufang Xie, Tong Wang, Tao Qin, Tie-Yan Liu

August 2022

Preprint

Improved Drug-target Interaction Prediction with Intermolecular Graph Transformer

Siyuan Liu, Yusong Wang, Yifan Deng, Liang He, Bin Shao, Jian Yin, Nanning Zheng, Tie-Yan Liu, Tong Wang

Briefings in Bioinformatics | May 2022

Publication

Structural insights into the SARS-CoV-2 Omicron RBD-ACE2 interaction

Jun Lan, Xinheng He, Yifei Ren, Ziyi Wang, Huan Zhou, Shilong Fan, Chenyou Zhu, Dongsheng Liu, Bin Shao, Tie-Yan Liu, Qisheng Wang, Linqi Zhang, Jiwan Ge, Tong Wang, Xinquan Wang

Cell Research | April 2022

Publication

Loss of Spike N370 glycosylation as an important evolutionary event for the enhanced infectivity of SARS-CoV-2

Shuyuan Zhang, Qingtai Liang, Xinheng He, Chongchong Zhao, Wenlin Ren, Ziqing Yang, Ziyi Wang, Qiang Ding, Haiteng Deng, Tong Wang, Linqi Zhang, Xinquan Wang

Cell Research | January 2022

Publication Project

Exploring the Regulatory Function of the N-terminal Domain of SARS-CoV-2 Spike Protein through Molecular Dynamics Simulation

Yao Li, Tong Wang, Juanrong Zhang, Bin Shao, Haipeng Gong, Yusong Wang, Xinheng He, Siyuan Liu, Tie-Yan Liu

Advanced Theory and Simulations | September 2021

"Top Downloaded Article" Award, Cover Story

DOI PDF Project

Complementing sequence-derived features with structural information extracted from fragment libraries for protein structure prediction

Siyuan Liu, Qijiang Xu, Tong Wang, Bin Shao, Jian Yin, Tie-Yan Liu

BMC Bioinformatics | June 2021, Vol 22(1): pp. 351-351

DOI Publication

SAMF: a Self-adaptive Protein Modeling Framework

Wenze Ding, Qijiang Xu, Siyuan Liu, Tong Wang, Bin Shao, Haipeng Gong, Tie-Yan Liu

Bioinformatics | May 2021

DOI Project

Improved fragment sampling for ab initio protein structure prediction using deep neural networks

Tong Wang, Yanhua Qiao, Wenze Ding, Wenzhi Mao, Yaoqi Zhou, Haipeng Gong

Nature Machine Intelligence | August 2019, Vol 1(8): pp. 347-355

DOI Publication Publication

Improved fragment-based movement with LRFragLib for all-atom Ab initio protein folding

Tong Wang, Haipeng Gong, Eugene I. Shakhnovich

arXiv: Quantitative Methods | June 2019

Preprint Preprint

Identification of residue pairing in interacting β-strands from a predicted residue contact map.

Wenzhi Mao, Tong Wang, Wenxuan Zhang, Haipeng Gong

BMC Bioinformatics | April 2018, Vol 19(1): pp. 146-146

DOI PDF Publication Publication Publication Publication Publication

Ab initio characterization of protein molecular dynamics with AI2BMD

Tong Wang, Xinheng He, Mingyu Li, Yatao Li, Ran Bi, Yusong Wang, Chaoran Cheng, Xiangzhen Shen, Jiawei Meng, He Zhang, Haiguang Liu, Zun Wang, Shaoning Li, Bin Shao, Tie-Yan Liu

Nature | November 2024

Publication

Overcoming the barrier of orbital-free density functional theory for molecular systems using deep learning

He Zhang, Siyuan Liu, Jiacheng You, Chang Liu, Shuxin Zheng, Ziheng Lu, Tong Wang, Nanning Zheng, Bin Shao

Nature Computational Science | March 2024

DOI Publication PDF Preprint

Enhancing geometric representations for molecules with equivariant vector-scalar interactive message passing

Yusong Wang, Tong Wang, Shaoning Li, Xinheng He, Mingyu Li, Zun Wang, Nanning Zheng, Bin Shao, Tie-Yan Liu

Nature Communications | January 2024, Vol 15(313)

Publication

Geometric Transformer with Interatomic Positional Encoding

Yusong Wang, Shaoning Li, Tong Wang, Bin Shao, Nanning Zheng, Tie-Yan Liu

NeurIPS 2023 | October 2023

Publication Publication

Efficiently incorporating quintuple interactions into geometric deep learning force fields

Zun Wang, Guoqing Liu, Yichi Zhou, Tong Wang, Bin Shao

NeurIPS 2023 | October 2023

Publication

AI2BMD: efficient characterization of protein dynamics with ab initio accuracy

Tong Wang, Xinheng He, Mingyu Li, Yusong Wang, Zun Wang, Shaoning Li, Bin Shao, Tie-Yan Liu

July 2023

Preprint

Improving machine learning force fields for molecular dynamics simulations with fine-grained force metrics

Zun Wang, Hongfei Wu, Lixin Sun, Xinheng He, Zhirong Liu, Bin Shao, Tong Wang, Tie-Yan Liu

The Journal of Chemical Physics | July 2023, Vol 159(3)

Cover Story

Publication

Long-Short-Range Message-Passing: A Physics-Informed Framework to Capture Non-Local Interaction for Scalable Molecular Dynamics Simulation

Yunyang Li, Yusong Wang, Lin Huang, Han Yang, Xinran wei, Jia Zhang, Tong Wang, Zun Wang, Bin Shao, Tie-Yan Liu

April 2023

Preprint

DSN-DDI: an accurate and generalized framework for drug–drug interaction prediction by dual-view representation learning

Zimeng Li, Shichao Zhu, Bin Shao, Xiangxiang Zeng, Tong Wang, Tie-Yan Liu

Briefings in Bioinformatics | January 2023

Publication

An ensemble of VisNet, Transformer-M, and pretraining models for molecular property prediction in OGB Large-Scale Challenge@ NeurIPS 2022

Yusong Wang, Shaoning Li, Tong Wang, Zun Wang, Xinheng He, Bin Shao, Tie-Yan Liu

MSR-TR-2022-35 | November 2022

Published by Microsoft

Competition Winner

Publication

ViSNet: a scalable and accurate geometric deep learning potential for molecular dynamics simulation

Yusong Wang, Shaoning Li, Xinheng He, Mingyu Li, Zun Wang, Nanning Zheng, Bin Shao, Tong Wang, Tie-Yan Liu

October 2022

Preprint

Direct Molecular Conformation Generation

Jinhua Zhu, Yingce Xia, Chang Liu, Lijun Wu, Shufang Xie, Yusong Wang, Tong Wang, Tao Qin, Wengang Zhou, Houqiang Liu, Haiguang Liu, Tie-Yan Liu

Transactions on Machine Learning Research | October 2022

Publication

Improved Drug-target Interaction Prediction with Intermolecular Graph Transformer

Siyuan Liu, Yusong Wang, Yifan Deng, Liang He, Bin Shao, Jian Yin, Nanning Zheng, Tie-Yan Liu, Tong Wang

Briefings in Bioinformatics | May 2022

Publication

Structural insights into the SARS-CoV-2 Omicron RBD-ACE2 interaction

Jun Lan, Xinheng He, Yifei Ren, Ziyi Wang, Huan Zhou, Shilong Fan, Chenyou Zhu, Dongsheng Liu, Bin Shao, Tie-Yan Liu, Qisheng Wang, Linqi Zhang, Jiwan Ge, Tong Wang, Xinquan Wang

Cell Research | April 2022

Publication

Exploring the Regulatory Function of the N-terminal Domain of SARS-CoV-2 Spike Protein through Molecular Dynamics Simulation

Yao Li, Tong Wang, Juanrong Zhang, Bin Shao, Haipeng Gong, Yusong Wang, Xinheng He, Siyuan Liu, Tie-Yan Liu

Advanced Theory and Simulations | September 2021

"Top Downloaded Article" Award, Cover Story

DOI PDF Project

Complementing sequence-derived features with structural information extracted from fragment libraries for protein structure prediction

Siyuan Liu, Qijiang Xu, Tong Wang, Bin Shao, Jian Yin, Tie-Yan Liu

BMC Bioinformatics | June 2021, Vol 22(1): pp. 351-351

DOI Publication

SAMF: a Self-adaptive Protein Modeling Framework

Wenze Ding, Qijiang Xu, Siyuan Liu, Tong Wang, Bin Shao, Haipeng Gong, Tie-Yan Liu

Bioinformatics | May 2021

DOI Project

Improved fragment sampling for ab initio protein structure prediction using deep neural networks

Tong Wang, Yanhua Qiao, Wenze Ding, Wenzhi Mao, Yaoqi Zhou, Haipeng Gong

Nature Machine Intelligence | August 2019, Vol 1(8): pp. 347-355

DOI Publication Publication

Improved fragment-based movement with LRFragLib for all-atom Ab initio protein folding

Tong Wang, Haipeng Gong, Eugene I. Shakhnovich

arXiv: Quantitative Methods | June 2019

Preprint Preprint

Ab initio characterization of protein molecular dynamics with AI2BMD

Tong Wang, Xinheng He, Mingyu Li, Yatao Li, Ran Bi, Yusong Wang, Chaoran Cheng, Xiangzhen Shen, Jiawei Meng, He Zhang, Haiguang Liu, Zun Wang, Shaoning Li, Bin Shao, Tie-Yan Liu

Nature | November 2024

Publication

AIMD-Chig: Exploring the conformational space of a 166-atom protein Chignolin with ab initio molecular dynamics

Tong Wang, Xinheng He, Mingyu Li, Bin Shao, Tie-Yan Liu

Scientific Data | August 2023

Publication

AI2BMD: efficient characterization of protein dynamics with ab initio accuracy

Tong Wang, Xinheng He, Mingyu Li, Yusong Wang, Zun Wang, Shaoning Li, Bin Shao, Tie-Yan Liu

July 2023

Preprint

Improving machine learning force fields for molecular dynamics simulations with fine-grained force metrics

Zun Wang, Hongfei Wu, Lixin Sun, Xinheng He, Zhirong Liu, Bin Shao, Tong Wang, Tie-Yan Liu

The Journal of Chemical Physics | July 2023, Vol 159(3)

Cover Story

Publication

Long-Short-Range Message-Passing: A Physics-Informed Framework to Capture Non-Local Interaction for Scalable Molecular Dynamics Simulation

Yunyang Li, Yusong Wang, Lin Huang, Han Yang, Xinran wei, Jia Zhang, Tong Wang, Zun Wang, Bin Shao, Tie-Yan Liu

April 2023

Preprint

DSN-DDI: an accurate and generalized framework for drug–drug interaction prediction by dual-view representation learning

Zimeng Li, Shichao Zhu, Bin Shao, Xiangxiang Zeng, Tong Wang, Tie-Yan Liu

Briefings in Bioinformatics | January 2023

Publication

Stochastic Lag Time Parameterization for Markov State Models of Protein Dynamics

Shiqi Gong, Xinheng He, Qi Meng, Zhiming Ma, Bin Shao, Tong Wang, Tie-Yan Liu

The Journal of Physical Chemistry B | November 2022

Cover Story

Publication

ViSNet: a scalable and accurate geometric deep learning potential for molecular dynamics simulation

Yusong Wang, Shaoning Li, Xinheng He, Mingyu Li, Zun Wang, Nanning Zheng, Bin Shao, Tong Wang, Tie-Yan Liu

October 2022

Preprint

Direct Molecular Conformation Generation

Jinhua Zhu, Yingce Xia, Chang Liu, Lijun Wu, Shufang Xie, Yusong Wang, Tong Wang, Tao Qin, Wengang Zhou, Houqiang Liu, Haiguang Liu, Tie-Yan Liu

Transactions on Machine Learning Research | October 2022

Publication

Tailoring Molecules for Protein Pockets: a Transformer-based Generative Solution for Structured-based Drug Design

Kehan Wu, Yingce Xia, Yang Fan, Pan Deng, Haiguang Liu, Lijun Wu, Shufang Xie, Tong Wang, Tao Qin, Tie-Yan Liu

August 2022

Preprint

Improved Drug-target Interaction Prediction with Intermolecular Graph Transformer

Siyuan Liu, Yusong Wang, Yifan Deng, Liang He, Bin Shao, Jian Yin, Nanning Zheng, Tie-Yan Liu, Tong Wang

Briefings in Bioinformatics | May 2022

Publication

Structural insights into the SARS-CoV-2 Omicron RBD-ACE2 interaction

Jun Lan, Xinheng He, Yifei Ren, Ziyi Wang, Huan Zhou, Shilong Fan, Chenyou Zhu, Dongsheng Liu, Bin Shao, Tie-Yan Liu, Qisheng Wang, Linqi Zhang, Jiwan Ge, Tong Wang, Xinquan Wang

Cell Research | April 2022

Publication

Loss of Spike N370 glycosylation as an important evolutionary event for the enhanced infectivity of SARS-CoV-2

Shuyuan Zhang, Qingtai Liang, Xinheng He, Chongchong Zhao, Wenlin Ren, Ziqing Yang, Ziyi Wang, Qiang Ding, Haiteng Deng, Tong Wang, Linqi Zhang, Xinquan Wang

Cell Research | January 2022

Publication Project

Exploring the Regulatory Function of the N-terminal Domain of SARS-CoV-2 Spike Protein through Molecular Dynamics Simulation

Yao Li, Tong Wang, Juanrong Zhang, Bin Shao, Haipeng Gong, Yusong Wang, Xinheng He, Siyuan Liu, Tie-Yan Liu

Advanced Theory and Simulations | September 2021

"Top Downloaded Article" Award, Cover Story

DOI PDF Project

Complementing sequence-derived features with structural information extracted from fragment libraries for protein structure prediction

Siyuan Liu, Qijiang Xu, Tong Wang, Bin Shao, Jian Yin, Tie-Yan Liu

BMC Bioinformatics | June 2021, Vol 22(1): pp. 351-351

DOI Publication

SAMF: a Self-adaptive Protein Modeling Framework

Wenze Ding, Qijiang Xu, Siyuan Liu, Tong Wang, Bin Shao, Haipeng Gong, Tie-Yan Liu

Bioinformatics | May 2021

DOI Project

Improved fragment sampling for ab initio protein structure prediction using deep neural networks

Tong Wang, Yanhua Qiao, Wenze Ding, Wenzhi Mao, Yaoqi Zhou, Haipeng Gong

Nature Machine Intelligence | August 2019, Vol 1(8): pp. 347-355

DOI Publication Publication

Improved fragment-based movement with LRFragLib for all-atom Ab initio protein folding

Tong Wang, Haipeng Gong, Eugene I. Shakhnovich

arXiv: Quantitative Methods | June 2019

Preprint Preprint

Identification of residue pairing in interacting β-strands from a predicted residue contact map.

Wenzhi Mao, Tong Wang, Wenxuan Zhang, Haipeng Gong

BMC Bioinformatics | April 2018, Vol 19(1): pp. 146-146

DOI PDF Publication Publication Publication Publication Publication

AI2BMD: efficient characterization of protein dynamics with ab initio accuracy

Tong Wang, Xinheng He, Mingyu Li, Yusong Wang, Zun Wang, Shaoning Li, Bin Shao, Tie-Yan Liu

July 2023

Preprint

Long-Short-Range Message-Passing: A Physics-Informed Framework to Capture Non-Local Interaction for Scalable Molecular Dynamics Simulation

Yunyang Li, Yusong Wang, Lin Huang, Han Yang, Xinran wei, Jia Zhang, Tong Wang, Zun Wang, Bin Shao, Tie-Yan Liu

April 2023

Preprint

DSN-DDI: an accurate and generalized framework for drug–drug interaction prediction by dual-view representation learning

Zimeng Li, Shichao Zhu, Bin Shao, Xiangxiang Zeng, Tong Wang, Tie-Yan Liu

Briefings in Bioinformatics | January 2023

Publication

An ensemble of VisNet, Transformer-M, and pretraining models for molecular property prediction in OGB Large-Scale Challenge@ NeurIPS 2022

Yusong Wang, Shaoning Li, Tong Wang, Zun Wang, Xinheng He, Bin Shao, Tie-Yan Liu

MSR-TR-2022-35 | November 2022

Published by Microsoft

Competition Winner

Publication

Stochastic Lag Time Parameterization for Markov State Models of Protein Dynamics

Shiqi Gong, Xinheng He, Qi Meng, Zhiming Ma, Bin Shao, Tong Wang, Tie-Yan Liu

The Journal of Physical Chemistry B | November 2022

Cover Story

Publication

ViSNet: a scalable and accurate geometric deep learning potential for molecular dynamics simulation

Yusong Wang, Shaoning Li, Xinheng He, Mingyu Li, Zun Wang, Nanning Zheng, Bin Shao, Tong Wang, Tie-Yan Liu

October 2022

Preprint

Tailoring Molecules for Protein Pockets: a Transformer-based Generative Solution for Structured-based Drug Design

Kehan Wu, Yingce Xia, Yang Fan, Pan Deng, Haiguang Liu, Lijun Wu, Shufang Xie, Tong Wang, Tao Qin, Tie-Yan Liu

August 2022

Preprint

Improved fragment sampling for ab initio protein structure prediction using deep neural networks

Tong Wang, Yanhua Qiao, Wenze Ding, Wenzhi Mao, Yaoqi Zhou, Haipeng Gong

Nature Machine Intelligence | August 2019, Vol 1(8): pp. 347-355

DOI Publication Publication

Improved fragment-based movement with LRFragLib for all-atom Ab initio protein folding

Tong Wang, Haipeng Gong, Eugene I. Shakhnovich

arXiv: Quantitative Methods | June 2019

Preprint Preprint

Identification of residue pairing in interacting β-strands from a predicted residue contact map.

Wenzhi Mao, Tong Wang, Wenxuan Zhang, Haipeng Gong

BMC Bioinformatics | April 2018, Vol 19(1): pp. 146-146

DOI PDF Publication Publication Publication Publication Publication

Stochastic Lag Time Parameterization for Markov State Models of Protein Dynamics

Shiqi Gong, Xinheng He, Qi Meng, Zhiming Ma, Bin Shao, Tong Wang, Tie-Yan Liu

The Journal of Physical Chemistry B | November 2022

Cover Story

Publication

Ab initio characterization of protein molecular dynamics with AI2BMD

Tong Wang, Xinheng He, Mingyu Li, Yatao Li, Ran Bi, Yusong Wang, Chaoran Cheng, Xiangzhen Shen, Jiawei Meng, He Zhang, Haiguang Liu, Zun Wang, Shaoning Li, Bin Shao, Tie-Yan Liu

Nature | November 2024

Publication

Overcoming the barrier of orbital-free density functional theory for molecular systems using deep learning

He Zhang, Siyuan Liu, Jiacheng You, Chang Liu, Shuxin Zheng, Ziheng Lu, Tong Wang, Nanning Zheng, Bin Shao

Nature Computational Science | March 2024

DOI Publication PDF Preprint

Enhancing geometric representations for molecules with equivariant vector-scalar interactive message passing

Yusong Wang, Tong Wang, Shaoning Li, Xinheng He, Mingyu Li, Zun Wang, Nanning Zheng, Bin Shao, Tie-Yan Liu

Nature Communications | January 2024, Vol 15(313)

Publication

AIMD-Chig: Exploring the conformational space of a 166-atom protein Chignolin with ab initio molecular dynamics

Tong Wang, Xinheng He, Mingyu Li, Bin Shao, Tie-Yan Liu

Scientific Data | August 2023

Publication

AI2BMD: efficient characterization of protein dynamics with ab initio accuracy

Tong Wang, Xinheng He, Mingyu Li, Yusong Wang, Zun Wang, Shaoning Li, Bin Shao, Tie-Yan Liu

July 2023

Preprint

Improving machine learning force fields for molecular dynamics simulations with fine-grained force metrics

Zun Wang, Hongfei Wu, Lixin Sun, Xinheng He, Zhirong Liu, Bin Shao, Tong Wang, Tie-Yan Liu

The Journal of Chemical Physics | July 2023, Vol 159(3)

Cover Story

Publication

Long-Short-Range Message-Passing: A Physics-Informed Framework to Capture Non-Local Interaction for Scalable Molecular Dynamics Simulation

Yunyang Li, Yusong Wang, Lin Huang, Han Yang, Xinran wei, Jia Zhang, Tong Wang, Zun Wang, Bin Shao, Tie-Yan Liu

April 2023

Preprint

DSN-DDI: an accurate and generalized framework for drug–drug interaction prediction by dual-view representation learning

Zimeng Li, Shichao Zhu, Bin Shao, Xiangxiang Zeng, Tong Wang, Tie-Yan Liu

Briefings in Bioinformatics | January 2023

Publication

Stochastic Lag Time Parameterization for Markov State Models of Protein Dynamics

Shiqi Gong, Xinheng He, Qi Meng, Zhiming Ma, Bin Shao, Tong Wang, Tie-Yan Liu

The Journal of Physical Chemistry B | November 2022

Cover Story

Publication

ViSNet: a scalable and accurate geometric deep learning potential for molecular dynamics simulation

Yusong Wang, Shaoning Li, Xinheng He, Mingyu Li, Zun Wang, Nanning Zheng, Bin Shao, Tong Wang, Tie-Yan Liu

October 2022

Preprint

Direct Molecular Conformation Generation

Jinhua Zhu, Yingce Xia, Chang Liu, Lijun Wu, Shufang Xie, Yusong Wang, Tong Wang, Tao Qin, Wengang Zhou, Houqiang Liu, Haiguang Liu, Tie-Yan Liu

Transactions on Machine Learning Research | October 2022

Publication

Tailoring Molecules for Protein Pockets: a Transformer-based Generative Solution for Structured-based Drug Design

Kehan Wu, Yingce Xia, Yang Fan, Pan Deng, Haiguang Liu, Lijun Wu, Shufang Xie, Tong Wang, Tao Qin, Tie-Yan Liu

August 2022

Preprint

Improved Drug-target Interaction Prediction with Intermolecular Graph Transformer

Siyuan Liu, Yusong Wang, Yifan Deng, Liang He, Bin Shao, Jian Yin, Nanning Zheng, Tie-Yan Liu, Tong Wang

Briefings in Bioinformatics | May 2022

Publication

Structural insights into the SARS-CoV-2 Omicron RBD-ACE2 interaction

Jun Lan, Xinheng He, Yifei Ren, Ziyi Wang, Huan Zhou, Shilong Fan, Chenyou Zhu, Dongsheng Liu, Bin Shao, Tie-Yan Liu, Qisheng Wang, Linqi Zhang, Jiwan Ge, Tong Wang, Xinquan Wang

Cell Research | April 2022

Publication

Loss of Spike N370 glycosylation as an important evolutionary event for the enhanced infectivity of SARS-CoV-2

Shuyuan Zhang, Qingtai Liang, Xinheng He, Chongchong Zhao, Wenlin Ren, Ziqing Yang, Ziyi Wang, Qiang Ding, Haiteng Deng, Tong Wang, Linqi Zhang, Xinquan Wang

Cell Research | January 2022

Publication Project

Exploring the Regulatory Function of the N-terminal Domain of SARS-CoV-2 Spike Protein through Molecular Dynamics Simulation

Yao Li, Tong Wang, Juanrong Zhang, Bin Shao, Haipeng Gong, Yusong Wang, Xinheng He, Siyuan Liu, Tie-Yan Liu

Advanced Theory and Simulations | September 2021

"Top Downloaded Article" Award, Cover Story

DOI PDF Project

Complementing sequence-derived features with structural information extracted from fragment libraries for protein structure prediction

Siyuan Liu, Qijiang Xu, Tong Wang, Bin Shao, Jian Yin, Tie-Yan Liu

BMC Bioinformatics | June 2021, Vol 22(1): pp. 351-351

DOI Publication

SAMF: a Self-adaptive Protein Modeling Framework

Wenze Ding, Qijiang Xu, Siyuan Liu, Tong Wang, Bin Shao, Haipeng Gong, Tie-Yan Liu

Bioinformatics | May 2021

DOI Project

Improved fragment sampling for ab initio protein structure prediction using deep neural networks

Tong Wang, Yanhua Qiao, Wenze Ding, Wenzhi Mao, Yaoqi Zhou, Haipeng Gong

Nature Machine Intelligence | August 2019, Vol 1(8): pp. 347-355

DOI Publication Publication

Improved fragment-based movement with LRFragLib for all-atom Ab initio protein folding

Tong Wang, Haipeng Gong, Eugene I. Shakhnovich

arXiv: Quantitative Methods | June 2019

Preprint Preprint

Identification of residue pairing in interacting β-strands from a predicted residue contact map.

Wenzhi Mao, Tong Wang, Wenxuan Zhang, Haipeng Gong

BMC Bioinformatics | April 2018, Vol 19(1): pp. 146-146

DOI PDF Publication Publication Publication Publication Publication

Geometric Transformer with Interatomic Positional Encoding

Yusong Wang, Shaoning Li, Tong Wang, Bin Shao, Nanning Zheng, Tie-Yan Liu

NeurIPS 2023 | October 2023

Publication Publication

Efficiently incorporating quintuple interactions into geometric deep learning force fields

Zun Wang, Guoqing Liu, Yichi Zhou, Tong Wang, Bin Shao

NeurIPS 2023 | October 2023

Publication

An ensemble of VisNet, Transformer-M, and pretraining models for molecular property prediction in OGB Large-Scale Challenge@ NeurIPS 2022

Yusong Wang, Shaoning Li, Tong Wang, Zun Wang, Xinheng He, Bin Shao, Tie-Yan Liu

MSR-TR-2022-35 | November 2022

Published by Microsoft

Competition Winner

Publication