Tao, Peng - Southern Methodist University -

个人简介

Peng joined the Department of Chemistry in the fall of 2013 as an Assistant Professor. He received his B.S. in Chemistry (1998) and M.S. in Physical Chemistry (2001) from the Peking University in China. He obtained his Ph.D. in Computational Chemistry from the Ohio State University in 2007. Peng’s research interest focuses on developing highly efficient and accurate computational methods to calculate free energy for chemical and biological processes, and their application to solve real world chemistry and biological problems.

研究领域

Computational methodologies are becoming indispensable techniques to determine chemical and biological reaction mechanisms and to provide structural and functional insight that is critical for further biomedical and pharmaceutical development. Our research emphasizes both methodology development and their applications to solve real world chemistry and biology problems.

近期论文

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Zhou, H.; Dong, Z.; Verkhivker, G.; Zoltowski, B. D.; Tao, P.*; Allosteric mechanism of the circadian protein Vivid resolved through Markov state model and machine learning analysis. PLoS Comput Biol. 2019, 15(2): e1006801 DOI: 10.1371/journal.pcbi.1006801 Zhou, H.; Tao, P.*; REDAN: relative entropy-based dynamical allosteric network model. Mol. Phys. 2018 DOI: 10.1080/00268976.2018.1543904 Zhou, H.; Wang, F.; Tao, P.*; t-Distributed Stochastic Neighbor Embedding (t-SNE) Method with the Least Information Loss for Macromolecular Simulations. J. Chem. Theory Comput. 2018, 14, 5499-5510. DOI: 10.1021/acs.jctc.8b00652 Mehmood, A.; Jones, S. I.; Tao, P.; Janesko, B. G.*, An Orbital-Overlap Complement to Ligand and Binding Site Electrostatic Potential Maps. J. Chem. Inf. Model. 2018, 58, 1836-1846. DOI: 10.1021/acs.jcim.8b00370 Zahler, C. T.; Zhou, H.; Abdolvdahabi, A.; Holden, R. L.; Rasouli, S.; Tao, P.; Shaw, B. F. Direct Measurement of Charge Regulation in Metalloprotein ElectronTransfer, Angew. Chem. Int. Ed. 2018, 57, 5364-5368 DOI: 10.1002/anie.201712306 This paper was selected as Very Important Paper (VIP) by the journal editor and featured on the journal cover. Zhou, H.; Dong, Z.; Tao, P.*; Novel Application of Machine Learning Approaches on the Recognition of Protein States and Identification of Function-Related Residues. J. Comput. Chem., 2018, 39, 1481-1490 DOI: 10.1002/jcc.25218 Wang, F.; Zhou, H.; Olademehin, O. P.; Kim, S. J.; Tao, P. Insights into Key Interactions between Vancomycin and Bacterial Wall Structures. ACS Omega 2018, 3, 37−45 DOI: 10.1021/acsomega.7b01483 Check out a short online liveslides presentation featuring this work. link Zhou, H.; Tao, P. Dynamics Sampling in Transition Pathway Space. J. Chem. Theory Comput. 2018, 14, 14−29 DOI: 10.1021/acs.jctc.7b00606 Check out a short online liveslides presentation featuring this work. link Dong, Z.; Zhou, H.; Tao, P. Combining protein sequence, structure, and dynamics: A novel approach for functional evolution analysis of PAS domain superfamily. Protein Science 2017, 27, 421-430 DOI: 10.1002/pro.3329 Zhou, H.; Zoltowski, B. D.; Tao, P. Revealing Hidden Conformational Space of LOV Protein VIVID Through Rigid Residue Scan Simulations. Scientific Reports 2017, 7, 46626 DOI: 10.1038/srep46626 Tao, P.; Hackett, J. C.; Kim, J. Y.; Saffen, D.; Hayes, C. J.; Hadad, C. “Molecular Determinants of TRPC6 Channel Recognition by FKBP12” in Computational Chemistry Methodology in Structural Biology and Materials Sciences, ISBN 978-1-77188-568-3, Apple Academic Press, Inc., 2017. Chang, J.; Zhou, H.; Preobrazhenskaya, M.; Tao, P.;Kim, S. J. The Carboxyl Terminus of Eremomycin Facilitates Binding to the Non-d-Ala-d-Ala Segment of the Peptidoglycan Pentapeptide Stem. Biochemistry 2016, 55, 3383–3391. DOI: 10.1021/acs.biochem.6b00188 Kalescky, R.; Zhou, H.; Liu, J.; Tao, P. (2016) Rigid Residue Scan Simulations Systematically Reveal Residue Entropic Roles in Protein Allostery. PLoS Comput Biol 12(4): e1004893. DOI: 10.1371/ journal.pcbi.1004893 Cao, J.; Lopez, R.; Thacker J. M.; Moon, J. Y.; Jiang, C.; Morris, S. N. S.; Bauer, J. H.; Tao, P.; Mason, R. P.; Lippert, A. R.* "Chemiluminescent Probes for Imaging H2S in Living Animals." Chem. Sci. 2015, 6, 1979-1985. DOI: 10.1039/C4SC03516J Kalesky, R.; Liu, J.; Tao, P.; “Identifying Key Residues for Protein Allostery through Rigid Residue Scan”. J. Phys. Chem. A 2015, 119, 1689-1700. DOI: 10.1021/jp5083455 Sodt, A. J.; Mei, Y.; König, G.; Tao, P.; Steele, R.; Brooks, B. R.; Shao, Y. “Multiple Environment Single System Quantum Mechanical/Molecular Mechanical (MESS-QM/MM) Calculations. 1. Estimation of Polarization Energies”. J. Phys. Chem. A 2015, 119, 1511-1523. DOI: 10.1021/jp5072296 Tao, P.; Alexander J. Sodt, Yihan Shao, Gerhard König, Bernard R. Brooks; “Computing the Free Energy along a Reaction Coordinate Using Rigid Body Dynamics”. J. Chem. Theory Comput. 2014, 10, 4198-4207. DOI: 10.1021/ct500342h Tao, P.; Larkin, J. D.; Brooks, B. R. “Reaction Path Optimization and Sampling Methods and Their Applications for Rare Events” in Some Applications of Quantum Mechanics, ISBN 979-953-51-0059-1, InTech, 2012.DOI: 10.5772/35351 Tao, P.; Hodošček, M.; Larkin, J. D; Shao, Y.; Brooks, B. R; “Comparison of Three Chain-of-States Methods: Nudged Elastic Band, Replica Path with Restraints or Constraints”. J. Chem. Theory Comput. 2012, 8, 5035-5051. DOI: 10.1021/ct3006248 Tao, P.; Wu, X.; Brooks, B. R; “Maintain Rigid Structures in Verlet Based Cartesian Molecular Dynamics Simulations”. J. Chem. Phys. 2012, 137, 134110. DOI:10.1063/1.4756796