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, 1882-92 (2013).
- 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 (2012).
- 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 (2011).
- 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 (2010).
- 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