Yingkai Zhang

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 45

Top Topics

Molecular Dynamics Simulations

Machine Learning

Top Venues

Journal of chemical information and modeling

Nature communications

Proceedings of the National Academy of Sciences of the United States of America

Journal of chemical theory and computation

This page only lists publications with an associated author ORCID identifier.

Publications

Jianping Li, Ampon Sae Her, Alida Besch, Belen Ramirez-Cordero, Maureen Crames, James R Banigan, Casey Mueller, William M Marsiglia, Yingkai Zhang, Nathaniel J Traaseth
Dynamics underlie the drug recognition mechanism by the efflux transporter EmrE. Nature communications 15 (1) (2024)
Chao Han, Dongdong Zhang, Song Xia, Yingkai Zhang
Accurate Prediction of NMR Chemical Shifts: Integrating DFT Calculations with Three-Dimensional Graph Neural Networks. Journal of chemical theory and computation 20 (12) (2024)
Jianping Li, Ampon Sae Her, Alida Besch, Belen Ramirez-Cordero, Maureen Crames, James R Banigan, Casey Mueller, William M Marsiglia, Yingkai Zhang, Nathaniel J Traaseth
Dynamics underlie the drug recognition mechanism by the efflux transporter EmrE. Nature communications 15 (1) (2024)
Nathan Soper, Isabelle Yardumian, Eric Chen, Chao Yang, Samantha Ciervo, Aaron L Oom, Ludovic Desvignes, Mark J Mulligan, Yingkai Zhang, Tania J Lupoli
A Repurposed Drug Interferes with Nucleic Acid to Inhibit the Dual Activities of Coronavirus Nsp13. ACS chemical biology 19 (7) (2024)
Nathan Soper, Isabelle Yardumian, Eric Chen, Chao Yang, Samantha Ciervo, Aaron L Oom, Ludovic Desvignes, Mark J Mulligan, Yingkai Zhang, Tania J Lupoli
A Repurposed Drug Interferes with Nucleic Acid to Inhibit the Dual Activities of Coronavirus Nsp13. ACS chemical biology (2024)
Chao Han, Dongdong Zhang, Song Xia, Yingkai Zhang
Accurate Prediction of NMR Chemical Shifts: Integrating DFT Calculations with Three-Dimensional Graph Neural Networks. Journal of chemical theory and computation 20 (12) (2024)
Nathan Soper, Isabelle Yardumian, Eric Chen, Chao Yang, Samantha Ciervo, Aaron L Oom, Ludovic Desvignes, Mark J Mulligan, Yingkai Zhang, Tania J Lupoli
A Repurposed Drug Interferes with Nucleic Acid to Inhibit the Dual Activities of Coronavirus Nsp13. ACS chemical biology 19 (7) (2024)
Jianping Li, Ampon Sae Her, Alida Besch, Belen Ramirez-Cordero, Maureen Crames, James R Banigan, Casey Mueller, William M Marsiglia, Yingkai Zhang, Nathaniel J Traaseth
Dynamics underlie the drug recognition mechanism by the efflux transporter EmrE. Nature communications 15 (1) (2024)
Chao Han, Dongdong Zhang, Song Xia, Yingkai Zhang
Accurate Prediction of NMR Chemical Shifts: Integrating DFT Calculations with Three-Dimensional Graph Neural Networks. Journal of chemical theory and computation (2024)
Nathan Soper, Isabelle Yardumian, Eric Chen, Chao Yang, Samantha Ciervo, Aaron L Oom, Ludovic Desvignes, Mark J Mulligan, Yingkai Zhang, Tania J Lupoli
A Repurposed Drug Interferes with Nucleic Acid to Inhibit the Dual Activities of Coronavirus Nsp13. ACS chemical biology 19 (7) (2024)
Jianping Li, Ampon Sae Her, Alida Besch, Belen Ramirez-Cordero, Maureen Crames, James R Banigan, Casey Mueller, William M Marsiglia, Yingkai Zhang, Nathaniel J Traaseth
Dynamics underlie the drug recognition mechanism by the efflux transporter EmrE. Nature communications 15 (1) (2024)
Chao Han, Dongdong Zhang, Song Xia, Yingkai Zhang
Accurate Prediction of NMR Chemical Shifts: Integrating DFT Calculations with Three-Dimensional Graph Neural Networks. Journal of chemical theory and computation 20 (12) (2024)
Angel Dâ Oliviera, Xuhang Dai, Saba Mottaghinia, Evan P Geissler, Lucie Etienne, Yingkai Zhang, Jeffrey S Mugridge
Recognition and Cleavage of Human tRNA Methyltransferase TRMT1 by the SARS-CoV-2 Main Protease. bioRxiv : the preprint server for biology (2023)
Alida Besch, William M Marsiglia, Moosa Mohammadi, Yingkai Zhang, Nathaniel J Traaseth
Gatekeeper mutations activate FGF receptor tyrosine kinases by destabilizing the autoinhibited state. Proceedings of the National Academy of Sciences of the United States of America 120 (8) (2023)
Alida Besch, William M Marsiglia, Moosa Mohammadi, Yingkai Zhang, Nathaniel J Traaseth
Gatekeeper mutations activate FGF receptor tyrosine kinases by destabilizing the autoinhibited state. Proceedings of the National Academy of Sciences of the United States of America 120 (8) (2023)
Alida Besch, William M Marsiglia, Moosa Mohammadi, Yingkai Zhang, Nathaniel J Traaseth
Gatekeeper mutations activate FGF receptor tyrosine kinases by destabilizing the autoinhibited state. Proceedings of the National Academy of Sciences of the United States of America 120 (8) (2023)
Song Xia, Dongdong Zhang, Yingkai Zhang
Multitask Deep Ensemble Prediction of Molecular Energetics in Solution: From Quantum Mechanics to Experimental Properties. Journal of chemical theory and computation (2023)
Alida Besch, William M Marsiglia, Moosa Mohammadi, Yingkai Zhang, Nathaniel J Traaseth
Gatekeeper mutations activate FGF receptor tyrosine kinases by destabilizing the autoinhibited state. Proceedings of the National Academy of Sciences of the United States of America 120 (8) (2023)
Angel Dâ Oliviera, Xuhang Dai, Saba Mottaghinia, Evan P Geissler, Lucie Etienne, Yingkai Zhang, Jeffrey S Mugridge
Recognition and Cleavage of Human tRNA Methyltransferase TRMT1 by the SARS-CoV-2 Main Protease. bioRxiv : the preprint server for biology (2023)
Song Xia, Eric Chen, Yingkai Zhang
Integrated Molecular Modeling and Machine Learning for Drug Design. Journal of chemical theory and computation (2023)
Alida Besch, William M Marsiglia, Moosa Mohammadi, Yingkai Zhang, Nathaniel J Traaseth
Gatekeeper mutations activate FGF receptor tyrosine kinases by destabilizing the autoinhibited state. Proceedings of the National Academy of Sciences of the United States of America 120 (8) (2023)
Alida Besch, William M Marsiglia, Moosa Mohammadi, Yingkai Zhang, Nathaniel J Traaseth
Gatekeeper mutations activate FGF receptor tyrosine kinases by destabilizing the autoinhibited state. Proceedings of the National Academy of Sciences of the United States of America 120 (8) (2023)
Zhiyuan Zhao, Jintong Du, Yu Du, Yuan Gao, Mingxuan Yu, Yingkai Zhang, Hao Fang, Xuben Hou
Deciphering the Allosteric Activation Mechanism of SIRT6 Using Molecular Dynamics Simulations. Journal of chemical information and modeling (2023)
Alida Besch, William M Marsiglia, Moosa Mohammadi, Yingkai Zhang, Nathaniel J Traaseth
Gatekeeper mutations activate FGF receptor tyrosine kinases by destabilizing the autoinhibited state. Proceedings of the National Academy of Sciences of the United States of America 120 (8) (2023)
Chao Yang, Yingkai Zhang
Delta Machine Learning to Improve Scoring-Ranking-Screening Performances of Protein-Ligand Scoring Functions. Journal of chemical information and modeling 62 (11) (2022)
Xiao-Kang Guo, Yingkai Zhang
CovBinderInPDB: A Structure-Based Covalent Binder Database. Journal of chemical information and modeling (2022)
Ashley E Modell, Frank Marrone, Nihar R Panigrahi, Yingkai Zhang, Paramjit S Arora
Peptide Tethering: Pocket-Directed Fragment Screening for Peptidomimetic Inhibitor Discovery. Journal of the American Chemical Society 144 (3) (2022)
Jieyu Lu, Yingkai Zhang
Unified Deep Learning Model for Multitask Reaction Predictions with Explanation. Journal of chemical information and modeling 62 (6) (2022)
Dongdong Zhang, Song Xia, Yingkai Zhang
Accurate Prediction of Aqueous Free Solvation Energies Using 3D Atomic Feature-Based Graph Neural Network with Transfer Learning. Journal of chemical information and modeling 62 (8) (2022)
Chao Yang, Eric Anthony Chen, Yingkai Zhang
Protein-Ligand Docking in the Machine-Learning Era. Molecules (Basel, Switzerland) 27 (14) (2022)
Jing Zhao, Alan J Blayney, Xiaorong Liu, Lauren Gandy, Weihua Jin, Lufeng Yan, Jeung-Hoi Ha, Ashley J Canning, Michael Connelly, Chao Yang, Xinyue Liu, Yuanyuan Xiao, Michael S Cosgrove, Sozanne R Solmaz, Yingkai Zhang, David Ban, Jianhan Chen, Stewart N Loh, Chunyu Wang
EGCG binds intrinsically disordered N-terminal domain of p53 and disrupts p53-MDM2 interaction. Nature communications 12 (1) (2021)
Yong Xia, Yan Liu, Chao Yang, Diane M Simeone, Tung-Tien Sun, David J DeGraff, Moon-Shong Tang, Yingkai Zhang, Xue-Ru Wu
Dominant role of CDKN2B/p15INK4B of 9p21.3 tumor suppressor hub in inhibition of cell-cycle and glycolysis. Nature communications 12 (1) (2021)
Justin M Torner, Yuwei Yang, David Rooklin, Yingkai Zhang, Paramjit S Arora
Identification of Secondary Binding Sites on Protein Surfaces for Rational Elaboration of Synthetic Protein Mimics. ACS chemical biology 16 (7) (2021)
Chao Yang, Yingkai Zhang
Lin_F9: A Linear Empirical Scoring Function for Protein-Ligand Docking. Journal of chemical information and modeling 61 (9) (2021)
Kai Wen Teng, Steven T Tsai, Takamitsu Hattori, Carmine Fedele, Akiko Koide, Chao Yang, Xuben Hou, Yingkai Zhang, Benjamin G Neel, John P O'Bryan, Shohei Koide
Selective and noncovalent targeting of RAS mutants for inhibition and degradation. Nature communications 12 (1) (2021)
Jianing Lu, Song Xia, Jieyu Lu, Yingkai Zhang
Dataset Construction to Explore Chemical Space with 3D Geometry and Deep Learning. Journal of chemical information and modeling 61 (3) (2021)
Lingfeng Chen, William M Marsiglia, Huaibin Chen, Joseph Katigbak, Hediye Erdjument-Bromage, David J Kemble, Lili Fu, Jinghong Ma, Gongqin Sun, Yingkai Zhang, Guang Liang, Thomas A Neubert, Xiaokun Li, Nathaniel J Traaseth, Moosa Mohammadi
Molecular basis for receptor tyrosine kinase A-loop tyrosine transphosphorylation. Nature chemical biology 16 (3) (2020)
Joseph Katigbak, Haotian Li, David Rooklin, Yingkai Zhang
AlphaSpace 2.0: Representing Concave Biomolecular Surfaces Using β-Clusters. Journal of chemical information and modeling 60 (3) (2020)
Jouliana Sadek, Michael G Wuo, David Rooklin, Arthur Hauenstein, Seong Ho Hong, Archana Gautam, Hao Wu, Yingkai Zhang, Ethel Cesarman, Paramjit S Arora
Modulation of virus-induced NF-κB signaling by NEMO coiled coil mimics. Nature communications 11 (1) (2020)
Jianing Lu, Xuben Hou, Cheng Wang, Yingkai Zhang
Incorporating Explicit Water Molecules and Ligand Conformation Stability in Machine-Learning Scoring Functions. Journal of chemical information and modeling 59 (11) (2019)
Yuwei Yang, Jianing Lu, Chao Yang, Yingkai Zhang
Exploring fragment-based target-specific ranking protocol with machine learning on cathepsin S. Journal of computer-aided molecular design 33 (12) (2019)
Jianing Lu, Cheng Wang, Yingkai Zhang
Predicting Molecular Energy Using Force-Field Optimized Geometries and Atomic Vector Representations Learned from an Improved Deep Tensor Neural Network. Journal of chemical theory and computation 15 (7) (2019)
Xuben Hou, David Rooklin, Duxiao Yang, Xiao Liang, Kangshuai Li, Jianing Lu, Cheng Wang, Peng Xiao, Yingkai Zhang, Jin-Peng Sun, Hao Fang
Computational Strategy for Bound State Structure Prediction in Structure-Based Virtual Screening: A Case Study of Protein Tyrosine Phosphatase Receptor Type O Inhibitors. Journal of chemical information and modeling 58 (11) (2018)
Hong Mu, Yingkai Zhang, Nicholas E Geacintov, Suse Broyde
Lesion Sensing during Initial Binding by Yeast XPC/Rad4: Toward Predicting Resistance to Nucleotide Excision Repair. Chemical research in toxicology 31 (11) (2018)
David Rooklin, Ashley E Modell, Haotian Li, Viktoriya Berdan, Paramjit S Arora, Yingkai Zhang
Targeting Unoccupied Surfaces on Protein-Protein Interfaces. Journal of the American Chemical Society 139 (44) (2017)