227 Fronczak Hall
Computational biophysics and structural biology, Molecular
simulation and modeling
My long-term goal is to investigate biomolecular functions
through the multi-scale modeling of biomolecular dynamics at a wide
range of length scales from whole molecules down to individual
atoms. I will employ various structural models of biomolecules from
coarse-grained to atomistic models. These complementary models will
be welded coherently to achieve both efficiency and accuracy. I am
interested in integrating computer modeling with experiments via
collaborations so that my models are correctly parameterized by
fitting experimental data, and then make informative predictions to
guide future experiments. My ultimate goal is to computationally
elucidate the molecular functions of various biomolecular
"nanomachines" such as motor proteins (myosins, kinesins,
polymerases and helicases).
- Zheng W and Wen H. A survey of coarse-grained methods for
modeling protein conformationaltransitions. Current Opinion in
Structural Biology 42, 24-30 (2017).
- Wen H, Qin F, and Zheng W. Toward elucidating the heat
activation mechanism of the TRPV1 channelgating by molecular
dynamics simulation. Proteins 84, 1938-49 (2016).
- Zheng W. Toward decrypting the allosteric mechanism of the
ryanodine receptor based on coarse-grained structural and dynamic
modeling. Proteins 83, 2307-18 (2015).
- Zheng W & Qin F. A combined coarse-grained and all-atom
simulation of TRPV1 channel gating andheat activation . J.
Gen. Physiology 145, 443-456 (2015)
- Chakraborty S & Zheng W. Decrypting the structural,
dynamic, and energetic basis of a monomericKinesin interacting with
a tubulin dimer in three ATPase States by all-atom molecular
dynamicssimulation. Biochemistry 54, 859-69 (2015).
- Zheng W, Barua B, and Hitchcock-DeGregori SE. Probing the
flexibility of tropomyosin and its bindingto filamentous actin
using molecular dynamics simulations. Biophys. J. 105,
- Zheng W & Tekpinar M. Structure-Based Simulations of the
Translocation Mechanism of the HepatitisC Virus NS3 Helicase along
Single-Stranded Nucleic Acid. Biophys. J. 103, 1343-53
- Zheng W & Tekpinar M. Accurate flexible fitting of
high-resolution protein structures to small-angle x-ray scattering
data using a coarse-grained model with implicit hydration
shell. Biophys. J. 101, 2981-91 (2011).
- Zheng W. Accurate Flexible Fitting of High-Resolution Protein
Structures into Cryo-Electron MicroscopyMaps Using Coarse-Grained
Pseudo-Energy Minimization. Biophys. J. 100, 478-88
- Zheng W & Auerbach A. Decrypting the Sequence of Structural
Events during the Gating Transition ofPentameric Ligand-Gated Ion
Channels Based on an Interpolated Elastic Network
Model. PLoSComputational Biology 7, e1001046 (2011).
- Tekpinar M & Zheng W. Predicting order of conformational
changes during protein conformationaltransitions using an
interpolated elastic network model. Proteins 78, 2469-81
- Zheng W. Multiscale modeling of structural dynamics underlying
force generation and product releasein actomyosin
complex.Proteins 78, 638-60 (2010).
- Zheng W & Tekpinar M. Large-scale evaluation of dynamically
important residues in proteins predictedby the perturbation
analysis of a coarse-grained elastic model. BMC Struct.
Biol. 9, 45 (2009).
For a complete list of publications and citations, please see Google Scholar and http://www.acsu.buffalo.edu/~wjzheng/refs.html