Pan Deng

TamGen: drug design with target-aware molecule generation through a chemical language model

Kehan Wu, Yingce Xia, Pan Deng, Renhe Liu, Yuan Zhang, Han Guo, Yumeng Cui, Qizhi Pei, Lijun Wu, Shufang Xie, Si Chen, Xi Lu, Song Hu, Jinzhi Wu, C. Chan, Shawn Chen, Liangliang Zhou, Nenghai Yu, Enhong Chen, Haiguang Liu, Jinjiang Guo, Tao Qin, Tie-Yan Liu

Nature Communications | October 2024, Vol 15

DOI Publication Github

Target-aware Molecule Generation for Drug Design Using a Chemical Language Model

Yingce Xia, Kehan Wu, Pan Deng, Renhe Liu, Yuan Zhang, Han Guo, Yumeng Cui, Qizhi Pei, Lijun Wu, Shufang Xie, Si Chen, Xi Lu, Song Hu, Jinzhi Wu, Chi-Kin Chan, Shuo Chen, Liangliang Zhou, Nenghai Yu, Haiguang Liu, Jinjiang Guo, Tao Qin, Tie-Yan Liu

January 2024

Publication Vidéo

CREaTor: zero-shot cis-regulatory pattern modeling with attention mechanisms. Genome Biology

Yongge Li, Fusong Ju, Zhiyuan Chen, Yiming Qu, Huanhuan Xia, Liang He, Jianwei Zhu, Lijun Wu, Bin Shao, Pan Deng

Genome biology | November 2023

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

Pre-training Co-evolutionary Protein Representation via A Pairwise Masked Language Model

Liang He, Shizhuo Zhang, Lijun Wu, Huanhuan Xia, Fusong Ju, He Zhang, Siyuan Liu, Yingce Xia, Jianwei Zhu, Pan Deng, Bin Shao, Tao Qin, Tie-Yan Liu

October 2021

Publication

TamGen: drug design with target-aware molecule generation through a chemical language model

Kehan Wu, Yingce Xia, Pan Deng, Renhe Liu, Yuan Zhang, Han Guo, Yumeng Cui, Qizhi Pei, Lijun Wu, Shufang Xie, Si Chen, Xi Lu, Song Hu, Jinzhi Wu, C. Chan, Shawn Chen, Liangliang Zhou, Nenghai Yu, Enhong Chen, Haiguang Liu, Jinjiang Guo, Tao Qin, Tie-Yan Liu

Nature Communications | October 2024, Vol 15

DOI Publication Github

CREaTor: zero-shot cis-regulatory pattern modeling with attention mechanisms. Genome Biology

Yongge Li, Fusong Ju, Zhiyuan Chen, Yiming Qu, Huanhuan Xia, Liang He, Jianwei Zhu, Lijun Wu, Bin Shao, Pan Deng

Genome biology | November 2023

Publication

Pre-training Co-evolutionary Protein Representation via A Pairwise Masked Language Model

Liang He, Shizhuo Zhang, Lijun Wu, Huanhuan Xia, Fusong Ju, He Zhang, Siyuan Liu, Yingce Xia, Jianwei Zhu, Pan Deng, Bin Shao, Tao Qin, Tie-Yan Liu

October 2021

Publication

Target-aware Molecule Generation for Drug Design Using a Chemical Language Model

Yingce Xia, Kehan Wu, Pan Deng, Renhe Liu, Yuan Zhang, Han Guo, Yumeng Cui, Qizhi Pei, Lijun Wu, Shufang Xie, Si Chen, Xi Lu, Song Hu, Jinzhi Wu, Chi-Kin Chan, Shuo Chen, Liangliang Zhou, Nenghai Yu, Haiguang Liu, Jinjiang Guo, Tao Qin, Tie-Yan Liu

January 2024

Publication Vidéo

CREaTor: zero-shot cis-regulatory pattern modeling with attention mechanisms. Genome Biology

Yongge Li, Fusong Ju, Zhiyuan Chen, Yiming Qu, Huanhuan Xia, Liang He, Jianwei Zhu, Lijun Wu, Bin Shao, Pan Deng

Genome biology | November 2023

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

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

TamGen: drug design with target-aware molecule generation through a chemical language model

Kehan Wu, Yingce Xia, Pan Deng, Renhe Liu, Yuan Zhang, Han Guo, Yumeng Cui, Qizhi Pei, Lijun Wu, Shufang Xie, Si Chen, Xi Lu, Song Hu, Jinzhi Wu, C. Chan, Shawn Chen, Liangliang Zhou, Nenghai Yu, Enhong Chen, Haiguang Liu, Jinjiang Guo, Tao Qin, Tie-Yan Liu

Nature Communications | October 2024, Vol 15

DOI Publication Github

CREaTor: zero-shot cis-regulatory pattern modeling with attention mechanisms. Genome Biology

Yongge Li, Fusong Ju, Zhiyuan Chen, Yiming Qu, Huanhuan Xia, Liang He, Jianwei Zhu, Lijun Wu, Bin Shao, Pan Deng

Genome biology | November 2023

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

Pre-training Co-evolutionary Protein Representation via A Pairwise Masked Language Model

Liang He, Shizhuo Zhang, Lijun Wu, Huanhuan Xia, Fusong Ju, He Zhang, Siyuan Liu, Yingce Xia, Jianwei Zhu, Pan Deng, Bin Shao, Tao Qin, Tie-Yan Liu

October 2021

Publication

Target-aware Molecule Generation for Drug Design Using a Chemical Language Model

Yingce Xia, Kehan Wu, Pan Deng, Renhe Liu, Yuan Zhang, Han Guo, Yumeng Cui, Qizhi Pei, Lijun Wu, Shufang Xie, Si Chen, Xi Lu, Song Hu, Jinzhi Wu, Chi-Kin Chan, Shuo Chen, Liangliang Zhou, Nenghai Yu, Haiguang Liu, Jinjiang Guo, Tao Qin, Tie-Yan Liu

January 2024

Publication Vidéo