期刊论文

2022

[31] Li W. Optimizing reaction coordinate by flux maximization in the transition path ensemble. The Journal of Chemical Physics, 2022, 156(5): 054117.

[30] Zhu L, Li W. Roles of Physicochemical and Structural Properties of RNA-Binding Proteins in Predicting the Activities of Trans-Acting Splicing Factors with Machine Learning. International Journal of Molecular Sciences, 2022, 23(8): 4426.

[29] Li W. Time-lagged Flux in the Transition Path Ensemble: Flux Maximization and Relation to Transition Path Theory. The Journal of Physical Chemistry A, 2022, 126(23): 3797-3810.

[28] Li W. Energy Decomposition along Reaction Coordinate: Theory and Applications to Nonequilibrium Ensembles of Trajectories. The Journal of Physical Chemistry A, 2022, 126(42): 7763-7773.

[27] Li W. Potential Energy Weighted Reactive Flux and Total Rate of Change of Potential Energy: Theory and Illustrative Applications. The Journal of Physical Chemistry A, 2022, 126(42): 7774-7786.

2021

[26] Wang X, Li W. Comparative Study of Interactions between Human cGAS and Inhibitors: Insights from Molecular Dynamics and MM/PBSA Studies. International Journal of Molecular Sciences, 2021, 22(3): 1164.

[25] Fu Q, Fu C, Teng L, Li W, Sheng Y, Handschuh-Wang, S. Rapid synthesis and growth process deconvolution of Au nanoflowers with ultrahigh catalytic activity based on microfluidics. Journal of Materials Science, 2021, 56: 6315-6326.

[24] Zhu L, Davari M D, Li W. Recent advances in the prediction of protein structural classes: Feature descriptors and machine learning algorithms. Crystals, 2021, 11(4): 324.

[23] Lin L, Zou H, Li W, Xu L Y, Li E M, Dong G. Redox Potentials of Disulfide Bonds in LOXL2 Studied by Nonequilibrium Alchemical Simulation. Frontiers in Chemistry, 2021, 9: 797036.

[22] Singh N, Mao S Q, Li W. Identification of Novel Inhibitors of Type-I Mycobacterium Tuberculosis Fatty Acid Synthase Using Docking-Based Virtual Screening and Molecular Dynamics Simulation. Applied Sciences, 2021, 11(15): 6977.

2020

[21] Wang X, Li W. Development and testing of force field parameters for phenylalanine and tyrosine derivatives. Frontiers in Molecular Biosciences, 2020, 7: 608931.

[20] Wang X, Zhang H, Li W. DNA-binding mechanisms of human and mouse cGAS: A comparative MD and MM/GBSA study. Physical Chemistry Chemical Physics, 2020, 22(45): 26390-26401.

[19] Singh N, Li W. Absolute Binding Free Energy Calculations for Highly Flexible Protein MDM2 and its inhibitors.  International journal of molecular sciences, 2020, 21(13): 4765.

[18] Cai M, Liu Y, Yin X, Zhou Z, Friedrich MW, Richter-Heitmann T, Nimzyk R, Kulkarni A, Wang X, Li W, Pan J. Diverse Asgard archaea including the novel phylum Gerdarchaeota participate in organic matter degradation. Science China Life Sciences. 2020 Mar 16:1-2.

[17] Gutierrez Moreno J J, Pan K, Wang Y, Li W. Computational Study of APTES Surface Functionalization of Diatom-like Amorphous SiO2 Surfaces for Heavy Metal Adsorption. Langmuir, 2020, 36(20): 5680-5689.

[16] Li W. Residue-Residue Mutual Work Analysis of Retinal-Opsin Interaction in Rhodopsin: Implications for Protein-Ligand Binding, Journal of Chemical Theory and Computation, 2020, 16(3): 1834-1842.

2019

[15] Gutierrez Moreno J J, Fronzi M, Lovera P, O'Riordan A, Ford M, Li W, M Nolan. Structure, stability and water adsorption on ultra-thin TiO2 supported on TiN. Physical Chemistry Chemical Physics, 2019, 21(45): 25344-25361.

[14] Singh N, Li W. Recent Advances in Coarse-Grained Models for Biomolecules and Their Applications. International journal of molecular sciences, 2019, 20(15): 3774.

2018

[13] Li W. Equipartition terms in transition path ensemble: Insights from molecular dynamics simulations of alanine dipeptide. The Journal of chemical physics, 2018, 148(8): 084105.

成为课题组长前

[12] Li W, Ma A. A benchmark for reaction coordinates in the transition path ensemble. The Journal of chemical physics, 2016, 144(13): 134104.

[11] Li W, Ma A. Reaction mechanism and reaction coordinates from the viewpoint of energy flow. The Journal of chemical physics, 2016, 144(11): 114103.

[10] Li W, Ma A. Some studies on generalized coordinate sets for polyatomic molecules. The Journal of chemical physics, 2015, 143(22): 224103.

[9] Li W, Ma A. Reducing the cost of evaluating the committor by a fitting procedure. The Journal of chemical physics, 2015, 143(17): 174103.

[8] Li W, Baldus I B, Gräter F. Redox potentials of protein disulfide bonds from free-energy calculations. The Journal of Physical Chemistry B, 2015, 119(17): 5386-5391.

[7] Li W, Ma A. Recent developments in methods for identifying reaction coordinates. Molecular simulation, 2014, 40(10-11): 784-793.

[6] Zhou B, Baldus I B, Li W, Edwards SA, Graeter F. Identification of allosteric disulfides from prestress analysis. Biophysical journal, 2014, 107(3): 672-681.

[5] Li W, Edwards SA, Lu L, Kubar T, Patil SP, Grubmueller H, Groenhof G, and Graeter F. Force Distribution Analysis of Mechanochemically Reactive Dimethylcyclobutene. ChemPhysChem, 2013, 14(12): 2687-2697.

[4] Li W, Rudack T, Gerwert K, Graeter F, and Schlitter J. Exploring the Multi-Dimensional Free Energy Surface of Phosphoester Hydrolysis with Constrained QM/MM Dynamics. Journal of chemical theory and computation, 2012, 8(10): 3596-3604.

[3] Li W, Gräter F. Atomistic evidence of how force dynamically regulates thiol/disulfide exchange. Journal of the American Chemical Society, 2010, 132(47): 16790-16795.

[2] Chen L, Lu L, Feng K, Li W, Song J, Zheng L, ... and Cai Y. Multiple classifier integration for the prediction of protein structural classes. Journal of Computational Chemistry, 2009, 30(14): 2248-2254.

[1] Li W, Lin K, Feng K, et al. Prediction of protein structural classes using hybrid properties. Molecular diversity, 2008, 12(3-4): 171-179.

专著章节：

[4] Li W. Mechanophores in Polymer Mechanochemistry: Insights from Single-Molecule Experiments and Computer Simulations.In Functional Tactile Sensors, Elsevier, 2021: 113-139.

[3] Wang X, Singh N, Li W. Molecular Dynamics Simulation of Biomolecular Interactions. In Systems Medicine: Integrative, Qualitative and Computational Approaches, Elsevier, 2019: 182–189.

[2] Gräter F, Li W. Studying Functional Disulphide Bonds by Computer Simulations. In Functional Disulphide Bonds. Humana, New York, NY, 2019: 87-113.

[1] Gräter F, Li W. Transition path sampling with quantum/classical mechanics for reaction rates. In Molecular Modeling of Proteins. Humana Press, New York, NY, 2015: 27-45.