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Zhejiang University: Hangzhou, Zhejiang, CN

Employment
Source: Self-asserted source
zhe wang

Works (44)

Can molecular dynamics simulations improve predictions of protein-ligand binding affinity with machine learning?

Briefings in bioinformatics
2023-03-01 | Journal article
Contributors: Gu S; Chao Shen; Yu J; Zhao H; Huanxiang Liu; Liu L; Sheng R; Xu L; Wang Z; Tingjun Hou et al.
Source: Self-asserted source
zhe wang

SDEGen: learning to evolve molecular conformations from thermodynamic noise for conformation generation.

Chemical science
2023-01-12 | Journal article
Contributors: Zhang H; Li S; Jintu Zhang; Wang Z; wang jike; Jiang D; Bian Z; Zhang Y; Deng Y; Song J et al.
Source: Self-asserted source
zhe wang

Cooperation of structural motifs controls drug selectivity in cyclin-dependent kinases: an advanced theoretical analysis.

Briefings in bioinformatics
2023-01-01 | Journal article
Contributors: Wang L; Xu L; Wang Z; Tingjun Hou; Hao H; Huiyong Sun
Source: Self-asserted source
zhe wang

Learning with uncertainty to accelerate the discovery of histone lysine-specific demethylase 1A (KDM1A/LSD1) inhibitors.

Briefings in bioinformatics
2023-01-01 | Journal article
Contributors: Wang D; Wu Z; Chao Shen; Bao L; Luo H; Wang Z; Yao H; De-Xin Kong; Luo C; Tingjun Hou
Source: Self-asserted source
zhe wang
grade
Preferred source (of 2)‎

fastDRH: a webserver to predict and analyze protein-ligand complexes based on molecular docking and MM/PB(GB)SA computation.

Briefings in bioinformatics
2022-09-01 | Journal article
Contributors: Wang Z; Pan H; Huiyong Sun; Kang Y; Liu H; Dongsheng Cao; Tingjun Hou
Source: Self-asserted source
zhe wang

Determination of Molecule Category of Ligands Targeting the Ligand-Binding Pocket of Nuclear Receptors with Structural Elucidation and Machine Learning.

Journal of chemical information and modeling
2022-08-30 | Journal article
Contributors: Wang Q; Wang Z; Tian S; Wang L; Tang R; Yu Y; Ge J; Tingjun Hou; Hao H; Huiyong Sun
Source: Self-asserted source
zhe wang
grade
Preferred source (of 2)‎

Predicting the mutation effects of protein-ligand interactions via end-point binding free energy calculations: strategies and analyses.

Journal of cheminformatics
2022-08-20 | Journal article
Contributors: Yu Y; Wang Z; Wang L; Tian S; Hou T; Huiyong Sun
Source: Self-asserted source
zhe wang
grade
Preferred source (of 2)‎

Discovery of novel non-nucleoside inhibitors with high potency and selectivity for DNA methyltransferase 3A.

European journal of medicinal chemistry
2022-08-15 | Journal article
Contributors: Yu J; Chai X; Pang J; Wang Z; Zhao H; Xie T; Xu L; Sheng R; Li D; Zeng S et al.
Source: Self-asserted source
zhe wang

Structure-guided and phage-assisted evolution of a therapeutic anti-EGFR antibody to reverse acquired resistance.

Nature communications
2022-07-30 | Journal article
Contributors: Zhuang X; Wang Z; Fan J; Bai X; Xu Y; James Chou; Tingjun Hou; Shuqing Chen; Liqiang Pan
Source: Self-asserted source
zhe wang

Structural view on the role of the TRD loop in regulating DNMT3A activity: a molecular dynamics study.

Physical chemistry chemical physics : PCCP
2022-07-06 | Journal article
Contributors: hong zhao; Yu J; Gaoqi Weng; Yu J; Wang E; Gao J; Huanxiang Liu; Tingjun Hou; Wang Z; Yu Kang
Source: Self-asserted source
zhe wang

Organic Compound Synthetic Accessibility Prediction Based on the Graph Attention Mechanism.

Journal of chemical information and modeling
2022-06-08 | Journal article
Contributors: Yu J; Wang J; Zhao H; Gao J; Yu Kang; Dongsheng Cao; Wang Z; Tingjun Hou
Source: Self-asserted source
zhe wang
grade
Preferred source (of 2)‎

Kinome-wide polypharmacology profiling of small molecules by multi-task graph isomorphism network approach.

Acta pharmaceutica Sinica. B
2022-05-12 | Journal article
Contributors: Bao L; Wang Z; Wu Z; Luo H; Yu J; Yu Kang; Cao D; Tingjun Hou
Source: Self-asserted source
zhe wang

Characterizing the stabilization effects of stabilizers in protein-protein systems with end-point binding free energy calculations.

Briefings in bioinformatics
2022-05-01 | Journal article
Contributors: Tang R; Chen P; Wang Z; Wang L; Hao H; Tingjun Hou; Huiyong Sun
Source: Self-asserted source
zhe wang

Deep learning approaches for de novo drug design: An overview.

Current opinion in structural biology
2021-11-22 | Journal article
Contributors: Wang M; Wang Z; Huiyong Sun; Wang J; Shen C; Weng G; Chai X; Li H; Cao D; Tingjun Hou
Source: Self-asserted source
zhe wang

DeepChargePredictor: a web server for predicting QM-based atomic charges via state-of-the-art machine-learning algorithms.

Bioinformatics (Oxford, England)
2021-11-01 | Journal article
Contributors: Wang J; Huiyong Sun; Chen J; Jiang D; Wang Z; Wu Z; Chen X; Cao D; Tingjun Hou
Source: Self-asserted source
zhe wang

Discovery of novel DprE1 inhibitors via computational bioactivity fingerprints and structure-based virtual screening.

Acta pharmacologica Sinica
2021-10-19 | Journal article
Contributors: Xueping Hu; Yang L; Chai X; Lei YX; Alam MS; Liu L; Shen C; Jiang DJ; Wang Z; Liu ZY et al.
Source: Self-asserted source
zhe wang

The impact of cross-docked poses on performance of machine learning classifier for protein-ligand binding pose prediction.

Journal of cheminformatics
2021-10-16 | Journal article
Contributors: Shen C; Xueping Hu; Gao J; Zhang X; Zhong H; Wang Z; Xu L; Kang Y; Cao D; Tingjun Hou
Source: Self-asserted source
zhe wang
grade
Preferred source (of 2)‎

Do we need different machine learning algorithms for QSAR modeling? A comprehensive assessment of 16 machine learning algorithms on 14 QSAR data sets.

Briefings in bioinformatics
2021-07-01 | Journal article
Contributors: Wu Z; Zhu M; Kang Y; Leung EL; Tailong Lei; Shen C; Jiang D; Wang Z; Cao D; Hou T
Source: Self-asserted source
zhe wang

Beware of the generic machine learning-based scoring functions in structure-based virtual screening.

Briefings in bioinformatics
2021-05-01 | Journal article
Contributors: Shen C; Hu Y; Wang Z; Zhang X; Pang J; Wang G; Zhong H; Xu L; Cao D; Hou T
Source: Self-asserted source
zhe wang

Discovery of novel HBV capsid assembly modulators by structure-based virtual screening and bioassays.

Bioorganic & medicinal chemistry
2021-03-04 | Journal article
Contributors: Wang Y; Wang Z; Liu J; Wang Y; Wu R; Sheng R; Hou T
Source: Self-asserted source
zhe wang

Could graph neural networks learn better molecular representation for drug discovery? A comparison study of descriptor-based and graph-based models.

Journal of cheminformatics
2021-02-17 | Journal article
Contributors: Jiang D; Wu Z; Hsieh CY; Chen G; Liao B; Wang Z; Shen C; Cao D; Wu J; Tingjun Hou
Source: Self-asserted source
zhe wang

ASFP (Artificial Intelligence based Scoring Function Platform): a web server for the development of customized scoring functions.

Journal of cheminformatics
2021-02-04 | Journal article
Contributors: Zhang X; Shen C; Guo X; Wang Z; Weng G; Ye Q; Wang G; He Q; Yang B; Cao D et al.
Source: Self-asserted source
zhe wang
grade
Preferred source (of 2)‎

Can machine learning consistently improve the scoring power of classical scoring functions? Insights into the role of machine learning in scoring functions.

Briefings in bioinformatics
2021-01-01 | Journal article
Contributors: Shen C; Hu Y; Wang Z; Zhang X; Zhong H; Wang G; Yao X; Xu L; Cao D; Hou T
Source: Self-asserted source
zhe wang

Comprehensive Evaluation of Fourteen Docking Programs on Protein-Peptide Complexes.

Journal of chemical theory and computation
2020-05-06 | Journal article
Contributors: Weng G; Gao J; Wang Z; Wang E; Hu X; Yao X; Dongsheng Cao; Tingjun Hou
Source: Self-asserted source
zhe wang

Development and Evaluation of MM/GBSA Based on a Variable Dielectric GB Model for Predicting Protein-Ligand Binding Affinities.

Journal of chemical information and modeling
2020-03-20 | Journal article
Contributors: Wang E; Hui Liu; Wang J; Weng G; Huiyong Sun; Wang Z; Kang Y; Tingjun Hou
Source: Self-asserted source
zhe wang
grade
Preferred source (of 2)‎

ADMET evaluation in drug discovery. 20. Prediction of breast cancer resistance protein inhibition through machine learning.

Journal of cheminformatics
2020-03-05 | Journal article
Contributors: Jiang D; Lei T; Wang Z; Shen C; Cao D; Tingjun Hou
Source: Self-asserted source
zhe wang
grade
Preferred source (of 2)‎

Binding affinity and dissociation pathway predictions for a series of USP7 inhibitors with pyrimidinone scaffold by multiple computational methods.

Physical chemistry chemical physics : PCCP
2020-02-26 | Journal article
Contributors: Wang Z; Wang X; Yu Kang; Zhong H; Shen C; Yao X; Dongsheng Cao; Tingjun Hou
Source: Self-asserted source
zhe wang

Combined strategies in structure-based virtual screening.

Physical chemistry chemical physics : PCCP
2020-01-29 | Journal article
Contributors: Wang Z; Huiyong Sun; Shen C; Hu X; Gao J; Dan Li; Dongsheng Cao; Tingjun Hou
Source: Self-asserted source
zhe wang

Comprehensive assessment of nine docking programs on type II kinase inhibitors: prediction accuracy of sampling power, scoring power and screening power.

Briefings in bioinformatics
2020-01-01 | Journal article
Contributors: Shen C; Wang Z; Yao X; Li Y; Tailong Lei; Wang E; Xu L; Feng ZHU; Li D; Hou T
Source: Self-asserted source
zhe wang

Importance of a crystalline water network in docking-based virtual screening: a case study of BRD4.

Physical chemistry chemical physics : PCCP
2019-11-08 | Journal article
Contributors: Zhong H; Wang Z; Wang X; Liu H; Dan Li; Huanxiang Liu; Yao X; Tingjun Hou
Source: Self-asserted source
zhe wang
grade
Preferred source (of 2)‎

ADMET Evaluation in Drug Discovery. 19. Reliable Prediction of Human Cytochrome P450 Inhibition Using Artificial Intelligence Approaches.

Journal of chemical information and modeling
2019-11-05 | Journal article
Contributors: Wu Z; Tailong Lei; Shen C; Wang Z; Dongsheng Cao; Tingjun Hou
Source: Self-asserted source
zhe wang
grade
Preferred source (of 2)‎

DNA methyltransferases: emerging targets for the discovery of inhibitors as potent anticancer drugs.

Drug discovery today
2019-09-05 | Journal article
Contributors: Jie Yu; Xie T; Wang Z; Wang X; Zeng S; Yu Kang; Hou T
Source: Self-asserted source
zhe wang

Assessing the performance of the MM/PBSA and MM/GBSA methods. 10. Impacts of enhanced sampling and variable dielectric model on protein-protein Interactions.

Physical chemistry chemical physics : PCCP
2019-08-27 | Journal article
Contributors: Wang E; Weng G; Huiyong Sun; Du H; Feng ZHU; Chen F; Wang Z; Tingjun Hou
Source: Self-asserted source
zhe wang

HawkDock: a web server to predict and analyze the protein-protein complex based on computational docking and MM/GBSA.

Nucleic acids research
2019-07-01 | Journal article
Contributors: Weng G; Wang E; Wang Z; Liu H; Feng ZHU; Li D; Hou T
Source: Self-asserted source
zhe wang
grade
Preferred source (of 2)‎

End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design.

Chemical reviews
2019-06-24 | Journal article
Contributors: Wang E; Huiyong Sun; Junmei Wang; Wang Z; Hui Liu; John Zhang; Tingjun Hou
Source: Self-asserted source
zhe wang
grade
Preferred source (of 2)‎

Insight into the selective binding mechanism of DNMT1 and DNMT3A inhibitors: a molecular simulation study.

Physical chemistry chemical physics : PCCP
2019-06-05 | Journal article
Contributors: Xie T ; Yu J ; Fu W ; Wang Z ; Xu L ; Shan Chang; Wang E ; Feng ZHU; Zeng S ; Yu Kang et al.
Source: Self-asserted source
zhe wang
grade
Preferred source (of 2)‎

Assessing the performance of MM/PBSA and MM/GBSA methods. 9. Prediction reliability of binding affinities and binding poses for protein-peptide complexes.

Physical chemistry chemical physics : PCCP
2019-05-01 | Journal article
Contributors: Weng G ; Wang E ; Chen F ; Huiyong Sun; Wang Z ; Tingjun Hou
Source: Self-asserted source
zhe wang
grade
Preferred source (of 2)‎

farPPI: a webserver for accurate prediction of protein-ligand binding structures for small-molecule PPI inhibitors by MM/PB(GB)SA methods.

Bioinformatics (Oxford, England)
2019-05-01 | Journal article
Contributors: Wang Z; Wang X; Li Y; Tailong Lei; Wang E; Li D; Yu Kang; Feng ZHU; Hou T
Source: Self-asserted source
zhe wang

Reliability of Docking-Based Virtual Screening for GPCR Ligands with Homology Modeled Structures: A Case Study of the Angiotensin II Type I Receptor.

ACS chemical neuroscience
2018-10-17 | Journal article
Contributors: Chen H; Weitao Fu; Wang Z; Wang X; Tailong Lei; Feng ZHU; Li D; Chang S; Xu L; Tingjun Hou
Source: Self-asserted source
zhe wang

Assessing the performance of MM/PBSA and MM/GBSA methods. 8. Predicting binding free energies and poses of protein-RNA complexes.

RNA (New York, N.Y.)
2018-06-21 | Journal article
Contributors: Chen F; Huiyong Sun; Wang J; Feng ZHU; Liu H; Wang Z; Tailong Lei; Li Y; Hou T
Source: Self-asserted source
zhe wang
grade
Preferred source (of 2)‎

Assessing the performance of MM/PBSA and MM/GBSA methods. 7. Entropy effects on the performance of end-point binding free energy calculation approaches.

Physical chemistry chemical physics : PCCP
2018-05-01 | Journal article
Contributors: Huiyong Sun; Duan L; Chen F; Liu H; Wang Z; Pan P; Feng ZHU; Zhang JZH; Tingjun Hou
Source: Self-asserted source
zhe wang

Benchmark Study Based on 2P2IDB to Gain Insights into the Discovery of Small-Molecule PPI Inhibitors.

The journal of physical chemistry. B
2018-02-22 | Journal article
Contributors: Wang Z; Yu Kang; Li D; Huiyong Sun; Dong X; Xiaojun Yao; Xu L; Shan Chang; Youyong Li; Tingjun Hou
Source: Self-asserted source
zhe wang
grade
Preferred source (of 2)‎

ADMET Evaluation in Drug Discovery. 18. Reliable Prediction of Chemical-Induced Urinary Tract Toxicity by Boosting Machine Learning Approaches.

Molecular pharmaceutics
2017-10-27 | Journal article
Contributors: Tailong Lei; Huiyong Sun; Yu Kang; Feng ZHU; Liu H; Zhou W; Wang Z; Li D; Youyong Li; Tingjun Hou
Source: Self-asserted source
zhe wang

Comprehensive evaluation of ten docking programs on a diverse set of protein-ligand complexes: the prediction accuracy of sampling power and scoring power.

Physical chemistry chemical physics : PCCP
2016-04-25 | Journal article
Contributors: Wang Z; Sun H; Yao X; Li D; Xu L; Li Y; Tian S; Hou T
Source: Self-asserted source
zhe wang