Li Z - Search Results

1

Research and Evaluation of the Allosteric Protein-Specific Force Field Based on a Pre-Training Deep Learning Model.

Ji X, Cui X, Li Z, Choi T, Wang Y, Xiao W, Zhao Y, Zha J, Zhang J, Chen HF, Yu Z. Ji X, et al. Among authors: li z. J Chem Inf Model. 2023 Apr 24;63(8):2456-2468. doi: 10.1021/acs.jcim.2c01369. Epub 2023 Apr 14. J Chem Inf Model. 2023. PMID: 37057817

2

RNA-Specific Force Field Optimization with CMAP and Reweighting.

Chen J, Liu H, Cui X, Li Z, Chen HF. Chen J, et al. Among authors: li z. J Chem Inf Model. 2022 Jan 24;62(2):372-385. doi: 10.1021/acs.jcim.1c01148. Epub 2022 Jan 12. J Chem Inf Model. 2022. PMID: 35021622

3

Base-specific RNA force field improving the dynamics conformation of nucleotide.

Li Z, Mu J, Chen J, Chen HF. Li Z, et al. Int J Biol Macromol. 2022 Dec 1;222(Pt A):680-690. doi: 10.1016/j.ijbiomac.2022.09.183. Epub 2022 Sep 24. Int J Biol Macromol. 2022. PMID: 36167105

4

Sequence-based machine learning method for predicting the effects of phosphorylation on protein-protein interactions.

Hong X, Lv J, Li Z, Xiong Y, Zhang J, Chen HF. Hong X, et al. Among authors: li z. Int J Biol Macromol. 2023 Jul 15;243:125233. doi: 10.1016/j.ijbiomac.2023.125233. Epub 2023 Jun 6. Int J Biol Macromol. 2023. PMID: 37290543

5

Synthesis and degradation of the cyclic dinucleotide messenger c-di-AMP in the hyperthermophilic archaeon Pyrococcus yayanosii.

Jin Z, Song D, Wang WW, Feng L, Li ZX, Chen HF, Xiao X, Liu XP. Jin Z, et al. Among authors: li zx. Protein Sci. 2023 Dec;32(12):e4829. doi: 10.1002/pro.4829. Protein Sci. 2023. PMID: 37921047

6

Phanto-IDP: compact model for precise intrinsically disordered protein backbone generation and enhanced sampling.

Zhu J, Li Z, Tong H, Lu Z, Zhang N, Wei T, Chen HF. Zhu J, et al. Among authors: li z. Brief Bioinform. 2023 Nov 22;25(1):bbad429. doi: 10.1093/bib/bbad429. Brief Bioinform. 2023. PMID: 38018910 Free PMC article.

7

Comprehensive Comparison and Critical Assessment of RNA-Specific Force Fields.

Choi T, Li Z, Song G, Chen HF. Choi T, et al. Among authors: li z. J Chem Theory Comput. 2024 Mar 26;20(6):2676-2688. doi: 10.1021/acs.jctc.4c00066. Epub 2024 Mar 6. J Chem Theory Comput. 2024. PMID: 38447040

8

Graphormer supervised de novo protein design method and function validation.

Mu J, Li Z, Zhang B, Zhang Q, Iqbal J, Wadood A, Wei T, Feng Y, Chen HF. Mu J, et al. Among authors: li z. Brief Bioinform. 2024 Mar 27;25(3):bbae135. doi: 10.1093/bib/bbae135. Brief Bioinform. 2024. PMID: 38557677 Free PMC article.

9

Map conformational landscapes of intrinsically disordered proteins with polymer physics quantities.

Shadman H, Ziebarth JD, Gallops CE, Luo R, Li Z, Chen HF, Wang Y. Shadman H, et al. Among authors: li z. Biophys J. 2024 May 21;123(10):1253-1263. doi: 10.1016/j.bpj.2024.04.010. Epub 2024 Apr 12. Biophys J. 2024. PMID: 38615193

10

Excited-Ground-State Transition of the RNA Strand Slippage Mechanism Captured by the Base-Specific Force Field.

Li Z, Song G, Zhu J, Mu J, Sun Y, Hong X, Choi T, Cui X, Chen HF. Li Z, et al. J Chem Theory Comput. 2024 Jul 23;20(14):6082-6097. doi: 10.1021/acs.jctc.4c00497. Epub 2024 Jul 9. J Chem Theory Comput. 2024. PMID: 38980289

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