Selected Publications

We used coarse-grained molecular dynamics to study the binding of transcription factors on nucleosomes. Our results revealed a new type of allostery via protein-binding regulated rotational sliding of the nucleosomal DNA.
Proc. Natl. Acad. Sci., 2020, 117 (34), 20586-20596.

We propose a new modeling method, PWMcos, that incorporates the PWM with complex structure data. The PWMcos is general and can be applied to both sequence-specific and nonspecific protein−DNA interactions.
J. Chem. Theory Comput., 2018, 14 (7), 3877-3889.

We investigated the dynamic coupling between protein binding and DNA bending for a bacterial protein HU and 14 other proteins. The sliding of positively-charged HU on negatively-charged DNA is highly coupled with local DNA distortion, which is reminiscent of polaron in physics.
J. Am. Chem. Soc., 2016, 138 (27), 8512–8522.

Recent Publications

More Publications

  • Nucleosome allostery in pioneer transcription factor binding
    Proc. Natl. Acad. Sci., 2020, 117 (34), 20586-20596.

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  • A singularity-free torsion angle potential for coarse-grained molecular dynamics simulations
    J. Chem. Phys., 2020, 153, 044110.

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  • Nucleosomes as allosteric scaffolds for genetic regulation
    Curr. Opin. Struct. Biol., 2020, 62, 93-101.

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  • Dynamic and Structural Modeling of the Specificity in Protein-DNA Interactions Guided by Binding Assay and Structure Data
    J. Chem. Theory Comput., 2018, 14 (7), 3877-3889.

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  • DNA sliding in nucleosomes via twist defect propagation revealed by molecular simulations
    Nucl. Acids Res., 2018, 46 (6), 2788-2801

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  • Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations
    PLoS Comp. Biol., 2017, 13 (12), e1005880

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  • Dynamic Coupling among Protein Binding, Sliding, and DNA Bending Revealed by Molecular Dynamics
    J. Am. Chem. Soc., 2016, 138 (27), 8512–8522.

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  • Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations
    Acc. Chem. Res., 2015, 48 (12), 3026–3035.

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  • Atomistic Picture for the Folding Pathway of a Hybrid-1 Type Human Telomeric DNA G-quadruplex
    PLoS Comput. Biol., 2014, 10 (4), e1003562.

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  • Localized Frustration and Binding-Induced Conformational Change in Recognition of 5S RNA by TFIIIA Zinc Finger
    J. Phys. Chem. B, 2013, 117 (50), 15917–15925.

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Recent & Upcoming Presentations

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Recent Posts

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I made a gif showing COVID19 infection distribution changes in Japan. Nothing new, just a showcase with python.

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I recently got this idea that we can show all the basic trigonometric functions and the derivatives in one figure. So I spent some time to plot it with LaTeX.

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This is the beginning of teaching my daughter Chinese characters.

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Another LaTeX template for this years documentation.

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Cheat Sheet for Maxima v5.42.2.

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Projects

py_sdvb

Yet another dictionary tool written in python. Allow regex.

esnippets

My snippets for Emacs yasnippet.

PyWMLogo

A simple tool to plot information content LOGO for PWM. Image format is svg.

pinang

This is a package consisting of several small handy tools for analyzing biomolecule structures (protein, RNA, DNA) and CafeMol MD trajectories.

respac_batch

Simple script to perform RESPAC calculations (including APBS) for coarse-grained protein charge distributions.

spacemacs_layers

My spacemacs configurations (init.el) and additional layer settings.

cafemol-mode

An Emacs major mode for editing CafeMol input file.

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