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Yan Lu

luyan AT xidian.edu.cn

Research Overview

 

Use theoretical and molecular modeling approaches to understand:
1. Dynamic processes and biophysical basis of protein folding and aggregation.
2. Mechanisms of protein-DNA recognition.
3. Structure-based drug design.
4. Allosteric communication in protein-DNA complex.

 

Publications

 (Web of Science)

12. Yan Lu, Xiao-Feng Shi, Freddie R. Salsbury Jr., and Philippe Derreumaux.

Small static electric field strength promotes aggregation-prone structures in amyloid-β(29-42).

The Journal of Chemical Physics, 146, 145101 (2017).

 

11. Yan Lu and Freddie R. Salsbury Jr.

Recapturing the Correlated Motions of Protein Using Coarse-Grained Models.

Protein & Peptide Letters 2015, 22(7): 654-659.

 

10. Yan Lu and Freddie R. Salsbury Jr.

Autoinhibitory mechanisms of ERG studied by molecular dynamics simulations.

AIP Advances 2015, 5, 017130.

 

9. Xiaojun Zhang, Ana Carolina Dantas Machado, Yuan Ding, Yongheng Chen, Yan Lu, Yankun Duan, Kenneth Tham, Lin Chen, Remo Rohs, and Peter Qin.

Conformations of p53 Response Elements in Solution Deduced Using Site-Directed Spin Labeling and Monte Carlo Sampling.

Nucleic acids research 2014, 42 (4), 2789-2797.

 

8. Karin Drotschmann Scarpinato, ElShimaa AbdelHafez, Andrew Diamanduros, Lacramioara Negureanu, Yan Lu, Jessica Hayley Bean, Katherine Zielke, Brittany Crowe, Aksana Vasilyeva, Jill Clodfelter, Omar Aly, Gamal Abuo-Rahma, Freddie R Salsbury, and Stephen Bruce King.

Computational and synthetic studies towards improving rescinnamine as an inducer of MSH2-dependent apoptosis in cancer treatment.

Molecular Cancer Biology 2013, 1(1).

 

7. Tianyin Zhou, Lin Yang, Yan Lu, Iris Dror, Ana Carolina Dantas Machado, Tahereh Ghane, Rosa Di Felice, and Remo Rohs.

DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale.

Nucleic acids research 2013, 41 (W1),W56-W62.

 

6. RECOMB/ISCB Top-10 Paper in Regulatory and Systems Genomics in 2012/13

Allan Lazarovici, Tianyin Zhou, Anthony Shafer, Ana Carolina Dantas Machado, Richard Sandstrom, Peter J. Sabo, Yan Lu, Remo Rohs, John A. Stamatoyannopoulos, and Harmen J. Bussemaker.

Probing DNA shape and methylation state on a genomic scale with DNase I.

Proceedings of the National Academy of Sciences of the United States of America 2013, 110 (16), 6376-6381.

 

5. Yan Lu, Wenhui Xi, and Guanghong Wei.

Structural insight into the polymorphism of NNQNTF protofibril: importance of interfacial water, polar and aromatic residues.
Journal of Theoretical and Computational Chemistry 2013, 12(08, 1341012).

 

4. Yan Lu, Guanghong Wei, and Phillippe Derreumaux.

Structural, thermodynamic, and dynamic properties of oligomers formed by the amyloid NNQQ peptide: insights from coarse-grained simulations.

J. Chem. Phys. 2012, 137, 025101.

 

3. Yan Lu, Guanghong Wei, and Phillippe Derreumaux.

Effects of G33A and G33I mutations on the structures of monomer and dimer of the amyloid β fragment 29-42 by replica exchange molecular dynamics simulations.

J. Phys. Chem. B 2011, 115(5), 1282–1288.

 

2. Yuxiang Mo, Yan Lu, Guanghong Wei, and Phillippe Derreumaux.

Structural diversity of the soluble trimers of the human amylin(20-29) peptide revealed by molecular dynamics simulations.

J. Chem. Phys. 2009, 130, 125101.

 

1. Yan Lu, Philippe Derreumaux, Zhi Guo, Normand Mousseau, and Guanghong Wei.
Thermodynamics and dynamics of amyloid peptide oligomerisation are sequence dependent.
Proteins 2009, 75, 954-963.

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