Deng Y - Search Results

1

Sigmoid Accelerated Molecular Dynamics: An Efficient Enhanced Sampling Method for Biosystems.

Zhao Y, Zhang J, Zhang H, Gu S, Deng Y, Tu Y, Hou T, Kang Y. Zhao Y, et al. Among authors: deng y. J Phys Chem Lett. 2023 Feb 2;14(4):1103-1112. doi: 10.1021/acs.jpclett.2c03688. Epub 2023 Jan 26. J Phys Chem Lett. 2023. PMID: 36700836

2

Boosting Protein-Ligand Binding Pose Prediction and Virtual Screening Based on Residue-Atom Distance Likelihood Potential and Graph Transformer.

Shen C, Zhang X, Deng Y, Gao J, Wang D, Xu L, Pan P, Hou T, Kang Y. Shen C, et al. Among authors: deng y. J Med Chem. 2022 Aug 11;65(15):10691-10706. doi: 10.1021/acs.jmedchem.2c00991. Epub 2022 Aug 2. J Med Chem. 2022. PMID: 35917397

3

PROTAC-DB 2.0: an updated database of PROTACs.

Weng G, Cai X, Cao D, Du H, Shen C, Deng Y, He Q, Yang B, Li D, Hou T. Weng G, et al. Among authors: deng y. Nucleic Acids Res. 2023 Jan 6;51(D1):D1367-D1372. doi: 10.1093/nar/gkac946. Nucleic Acids Res. 2023. PMID: 36300631 Free PMC article.

4

ALipSol: An Attention-Driven Mixture-of-Experts Model for Lipophilicity and Solubility Prediction.

Wu J, Wang J, Wu Z, Zhang S, Deng Y, Kang Y, Cao D, Hsieh CY, Hou T. Wu J, et al. Among authors: deng y. J Chem Inf Model. 2022 Dec 12;62(23):5975-5987. doi: 10.1021/acs.jcim.2c01290. Epub 2022 Nov 23. J Chem Inf Model. 2022. PMID: 36417544

5

ReMODE: a deep learning-based web server for target-specific drug design.

Wang M, Wang J, Weng G, Kang Y, Pan P, Li D, Deng Y, Li H, Hsieh CY, Hou T. Wang M, et al. Among authors: deng y. J Cheminform. 2022 Dec 12;14(1):84. doi: 10.1186/s13321-022-00665-w. J Cheminform. 2022. PMID: 36510307 Free PMC article.

6

Reducing false positive rate of docking-based virtual screening by active learning.

Wang L, Shi SH, Li H, Zeng XX, Liu SY, Liu ZQ, Deng YF, Lu AP, Hou TJ, Cao DS. Wang L, et al. Brief Bioinform. 2023 Jan 19;24(1):bbac626. doi: 10.1093/bib/bbac626. Brief Bioinform. 2023. PMID: 36642412

7

Comprehensive assessment of nine target prediction web services: which should we choose for target fishing?

Ji KY, Liu C, Liu ZQ, Deng YF, Hou TJ, Cao DS. Ji KY, et al. Brief Bioinform. 2023 Mar 19;24(2):bbad014. doi: 10.1093/bib/bbad014. Brief Bioinform. 2023. PMID: 36681902

8

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

Zhang H, Li S, Zhang J, Wang Z, Wang J, Jiang D, Bian Z, Zhang Y, Deng Y, Song J, Kang Y, Hou T. Zhang H, et al. Among authors: deng y. Chem Sci. 2023 Jan 12;14(6):1557-1568. doi: 10.1039/d2sc04429c. eCollection 2023 Feb 8. Chem Sci. 2023. PMID: 36794194 Free PMC article.

9

Improved GNNs for Log D_7.4 Prediction by Transferring Knowledge from Low-Fidelity Data.

Duan YJ, Fu L, Zhang XC, Long TZ, He YH, Liu ZQ, Lu AP, Deng YF, Hsieh CY, Hou TJ, Cao DS. Duan YJ, et al. J Chem Inf Model. 2023 Apr 24;63(8):2345-2359. doi: 10.1021/acs.jcim.2c01564. Epub 2023 Mar 31. J Chem Inf Model. 2023. PMID: 37000044

10

Chemistry-intuitive explanation of graph neural networks for molecular property prediction with substructure masking.

Wu Z, Wang J, Du H, Jiang D, Kang Y, Li D, Pan P, Deng Y, Cao D, Hsieh CY, Hou T. Wu Z, et al. Among authors: deng y. Nat Commun. 2023 May 4;14(1):2585. doi: 10.1038/s41467-023-38192-3. Nat Commun. 2023. PMID: 37142585 Free PMC article.

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