深圳市计算化学与药物设计重点实验室
Lab of Computational Chemistry and Drug Design

Dr. Fan Jiang

时间:2013-04-08

 

JF_大

蒋帆 Dr. Fan Jiang

Research Assoc. Prof.(2014~)

Ph. D Peking University

Date of Birth: March 8, 1982

 

Research Interests

Computational Molecular Sciences: Especially focusing on develop more accurate methods for modeling and simulating biomolecular systems at all-atom level by combining physics-based and informatics-based approaches, and their applications.

1.Residue-Specific Force Fields (RSFFs): PDB statistical analysis, coil library quantum mechanics calculation, force field parameterization, water model and implicit solvation.

2.Folding and Structure Prediction of Peptides and Proteins: Ab initio folding, enhanced sampling, structure refinement, model quality assessment, cyclic peptides, NMR.

 

Education and Work Experience

1999-2003: B. Sc. in Chemistry, Peking University

2003-2008: PhD in Physical Chemistry, Peking University (Advisor: Prof. Yun-Dong Wu)

2008-2010: Postdoctoral Researcher, the Hong Kong University of Science and Technology

2010-2014: Senior Research Assoc., Peking University Shenzhen Graduate School

2014-present: Research Assoc. Prof, Peking University Shenzhen Graduate School

 

Awards and Grants

1999: Outstanding Freshman Award, Peking University

2005-2006: Dong-Gang Scholarship, Peking University

2008: China Thomson-Reuters Research Fronts Award

2013-2015: NSFC, Young Scientist Fund, No. 21203004, “Protein Force Field Development Towards Structure Prediction”

2016-2019: NSFC, General Program, No. 21573009, “Ab Initio Prediction of Protein Structures Based on Residue-Specific Force Fields”

2017: Special Supporting Program for Outstanding Young Scholars of Guangdong Province

 

Invited Talks

1.4th Chinese-French Workshop in Theoretical Chemistry, June 2013, Nanjing

2.International Symposium on Nanotechnology in Health and Environment, Nov. 2013, Shenzhen

3.249th ACS National Meeting, March 2015, Denver

4.2015 Conference on Bioinformatics and Computational Biology, Nov. 2015, Beijing

5.30th Chinese Chemical Society National Conference, July 2016, Dalian

6.4th International Conference on Molecular Simulation, Oct 2016, Shanghai

7.2016 Symposium on Computational Statistical Mechanics of Complex Systems, Nov. 2016, Shenzhen

8.Symposium on Theoretical & Computational Studies of Biological Systems, Oct. 2017, Beijing

 

Publications:

1. Tang, Z.; Jiang, F.; Yu, L. T.; Cui, X.; Gong, L. Z.; Mi, A. Q.; Jiang, Y. Z.; Wu, Y.-D. Novel small organic molecules for a highly enantioselective direct Aldol reaction. J. Am. Chem. Soc. 2003, 125, 5262-5263.

2. Tang, Z.;† Jiang, F.;† Cui, X.; Gong, L. Z.; Mi, A. Q.; Jiang, Y. Z.; Wu, Y.-D. Enantioselective direct aldol reactions catalyzed by L-prolinamide derivatives. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 5755-5760. (†co-first author)

3. Zhang, H. L.; Jiang, F.; Zhang, X. M.; Cui, X.; Gong, L. Z.; Mi, A. Q.; Jiang, Y. Z.; Wu, Y.-D. Modification of (1R,2S)-1,2-diphenyl-2-aminoethanol for the highly enantioselective, asymmetric alkylation of N-diphenylphosphinoyl arylimines with dialkylzinc. Chem. Eur. J. 2004, 10, 1481-1492.

4. Cheng, C. L.; Sun, J.; Wang, C.; Zhang, Y.; Wei, S. Y.; Jiang, F.; Wu, Y.-D. Protonated N’-benzyl-N’- prolyl proline hydrazide as highly enantioselective catalyst for direct asymmetric aldol reaction. Chem. Commun. 2006, 215-217.

5. Jiang, F.; Wu, Y.-D. Theoretical studies on shortest a-helix. Chem. J. Chin. Univ. 2008, 29, 2371-2376.

6. Jiang, F.; Han, W.; Wu, Y.-D. Influence of side chain conformations on local conformational features of amino acids and implication for force field development. J. Phys. Chem. B. 2010, 114, 5840-5850.

7. Han, W.; Wan, C.; Jiang, F.; Wu, Y.-D. PACE force field for protein simulations. 1. Full parameterization of version 1 and verification. J. Chem. Theory Comput. 2010, 6, 3373-3389.

8. Wu, X.-H.; Wang, Y.; Zhuo, Z.; Jiang, F.; Wu, Y.-D. Identifying the hotspots on the top faces of WD40-repeat proteins from their primary sequences by b-bulges and DHSW tetrads. Plos One 2012, 7, e43005.

9. Wang, Y.; Jiang, F.; Zhuo, Z.; Wu, X.; Wu, Y.-D. A method for WD40 repeat detection and secondary structure prediction. Plos One 2013, 8, e65705.

10. Jiang, F.; Han, W.; Wu, Y.-D. The intrinsic conformational features of amino acids from a protein coil library and their applications in force field development. Phys. Chem. Chem. Phys. 2013, 15, 3413-3428. (invited perspective article)

11. Jiang, F.;* Zhou, C.-Y.; Wu, Y.-D.* Residue-specific force field based on the protein coil library. RSFF1: modification of OPLS-AA/L. J. Phys. Chem. B. 2014, 118, 6983-6998. (*co-corresponding author, invited feature article with cover art)

12. Jiang, F.;* Wu, Y.-D.* Folding of fourteen small proteins with a residue-specific force field and replica-exchange molecular dynamics. J. Am. Chem. Soc. 2014, 136, 9536–9539. (*co-corresponding author)

13. Zhou, C.-Y.; Jiang, F.;* Wu, Y.-D.* Residue-specific force field based on protein coil library. RSFF2: modification of Amber ff99SB. J. Phys. Chem. B 2015, 119, 1035–1047. (*co-corresponding author)

14. Xun, S.; Jiang, F.;* Wu, Y.-D.* Significant refinement of protein structure models using a residue-specific force field. J. Chem. Theory Comput. 2015, 11, 1949–1956. (*co-corresponding author)

15. Zhou, C.; Jiang, F.;* Wu, Y.-D.* Folding Thermodynamics and Mechanism of Five Trp-Cage Variants from Replica-Exchange MD Simulations with RSFF2 Force Field. J. Chem. Theory Comput. 2015, 11, 5473-5480.

16. Zeng, J.; Jiang, F.;* Wu, Y.-D.* Folding simulations of an α‑helical hairpin motif αtα with residue-specific force fields. J. Phys. Chem. B 2016, 120, 33–41.

17. Geng, H.; Jiang, F.;* Wu, Y.-D.* Accurate Structure Prediction and Conformational Analysis of Cyclic Peptides with Residue-Specific Force Fields. J. Phys. Chem. Lett. 2016, 7, 1805–1810.

18. Hu, K.; Geng, H.; Zhang, Q.; Liu, Q.; Xie, M.; Sun, C.; Li, W.; Lin, H.; Jiang, F.; Wang, T.;* Wu, Y.-D.;* Li, Z.* An in-tether chiral center modulates the helicity, cell permeability, and target binding affinity of a peptide. Angew. Chem. Int. Ed. 2016, 55, 8013–8017.

19. Zhao, H.; Liu, Q.; Geng, H.; Tian, Y.; Cheng, M.; Jiang, Y.; Xie, M.; Niu, X.; Jiang, F.; Zhang, Y.; Lao, Y.; Wu, Y.-D.;* Xu, N.;* Li, Z.* Crosslinked aspartic acids as helix-nucleating templates. Angew. Chem. Int. Ed. 2016, 55, 12088-12093.

20. Xun, S.; Jiang, F.;* Wu, Y.-D.* Intrinsically disordered regions stabilize the helical form of the C-terminal domain of RfaH: A molecular dynamics study. Bioorg. Med. Chem. 2016, 24, 4970-4977.

21. Zhang, Q.; Jiang, F.; Zhao, B.; Lin, H.; Tian, Y.; Xie, M.; Bai, G.; Gilbert, A. M.; Goetz, G. H.; Liras, S.; Mathiowetz, A. A.; Price, D. A.; Song, K.; Tu, M.; Wu, Y.; Wang, T.;* Flanagan, M. E.;* Wu, Y.-D.;* Li, Z.* Chiral sulfoxide-induced single turn peptide α-helicity. Sci. Rep. 2016, 6, 38573.

22. Zeng, J.; Jiang, F.;* Wu, Y.-D.* The mechanism of phosphorylation-induced folding of 4E-PB2 revealed by molecular dynamics simulations. J. Chem. Theory Comput. 2017, 13, 320-328.

23. Wu, H.; Jiang, F.;* Wu, Y.-D. Significantly improved protein folding thermodynamics using a dispersion-corrected water model and a new residue-specific force field. J. Phys. Chem. Lett. 2017, 8, 3199-3205.

24. Yuan, Y.; Zhao, Y.; Chen, L.; Wu, J.; Chen, G.; Li, S.; Zou, J.; Chen, R.; Wang, J.;* Jiang, F.;* Tang, Z.* Selective tumor cell death induced by irradiated riboflavin through recognizing DNA G–T mismatch. Nucleic Acids Res. 2017, 45, 8676–8683.