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<div id="publications">
<h1 align=center> Publications </h1><br>
<h3 align=center><a href="http://scholar.google.com/citations?user=wmjVxgYAAAAJ"><u>Google Scholar Profile</u></a></h3>
<br>
<h3 align=center> <p><a href="https://www.ncbi.nlm.nih.gov/myncbi/12EM6BbKktwkq/bibliography/public/"><u>PubMed Bibliography</u></a></p></h3>
<p><h3 align=center><a href="https://orcid.org/0000-0002-2488-0239" target="orcid.widget" rel="noopener noreferrer" style="vertical-align:top;"><img src="https://orcid.org/sites/default/files/images/orcid_16x16.png" style="width:1em;margin-right:.5em;" alt="ORCID iD icon"><u>Orcid.org/0000-0002-2488-0239</u></a></h3></p>
<br>
<h3 align=left>The PDF copies provided on this page are for preview only. Downloading is not permitted.</h3>
<br><br>
<ul>
<h2 align=left> Publications Affiliated with SMU: </h2>
<p><a href="doc/publication/63.pdf">63.</a> Song, Z.; Trozzi, F.; Tian, H.; Chao, Y.; Tao, P.* Mechanistic Insights into Enzyme Catalysis from Explaining Machine-Learned Quantum Mechanical and Molecular Mechanical Minimum Energy Pathways. 2022, ACS Phys. Chem Au, 2, 316−330 <a href="https://doi.org/10.1021/acsphyschemau.2c00005">DOI: 10.1021/acsphyschemau.2c00005</a></p>
</p>
</p> <img border="0" src="doc/publication/63.jpg" alt="XAI" width="298" height="397" align=center>
</p>
</p>
<p><a href="doc/publication/62.pdf">62.</a> Song, Z.; Tao, P.* Graph-learning guided mechanistic insights into imipenem hydrolysis in GES carbapenemases. 2022, Electron. Struct. 4, 034001 <a href="https://doi.org/10.1088/2516-1075/ac7993">DOI: 10.1088/2516-1075/ac7993</a></p>
</p>
</p> <img border="0" src="doc/publication/62.jpg" alt="GES" width="271" height="200" align=center>
</p>
</p>
<p><a href="doc/publication/61.pdf">61.</a> Trozzi, F.; Karki, N.; Song, Z.; Verma, N.; Kraka, E.; Zoltowski, B. D.; Tao, P.* Allosteric control of ACE2 peptidase domain dynamics. 2022, Org. Biomol. Chem. 20, 3605 <a href="https://doi.org/10.1039/D2OB00606E">DOI: 10.1039/d2ob00606e</a></p>
</p>
</p> <img border="0" src="doc/publication/61.jpg" alt="ACE2" width="318" height="200" align=center>
</p>
</p>
<p><a href="doc/publication/60.pdf">60.</a> Ibrahim, M. T.; Lee, J.; Tao, P* Homology modeling of Forkhead box protein C2: identification of potential inhibitors using ligand and structure‐based virtual screening. 2022, Molecular Diversity. <a href="https://doi.org/10.1007/s11030-022-10519-0">DOI: 10.1007/s11030-022-10519-0</a></p>
</p>
</p> <img border="0" src="doc/publication/60.jpg" alt="FOXC2" width="362" height="200" align=center>
</p>
</p>
<p><a href="doc/publication/59.pdf">59.</a> Ibrahim, M. T.; Tao, P* Computational investigation of peptidomimetics as potential inhibitors of SARS-CoV-2 spike protein. 2022, Journal of Biomolecular Structure and Dynamics. <a href="https://doi.org/10.1080/07391102.2022.2116601">DOI: 10.1080/07391102.2022.2116601</a></p>
</p>
</p> <img border="0" src="doc/publication/59.jpg" alt="SARS-COV-2" width="500" height="200" align=center>
</p>
</p>
<p><a href="doc/publication/58.pdf">58.</a> Xiao S.; Tian H.; Tao, P* PASSer2.0: Accurate Prediction of Protein Allosteric Sites Through Automated Machine Learning. 2022, Frontiers in Molecular Biosciences. 9:879251. <a href="https://doi.org/10.3389/fmolb.2022.879251">DOI: 10.3389/fmolb.2022.879251</a></p>
</p>
</p> <img border="0" src="doc/publication/58.jpg" alt="PASS2.0" width="324" height="200" align=center>
</p>
</p>
<p><a href="doc/publication/57.pdf">57.</a> Bai, F.; Puk, K. M.; Liu, J.; Zhou, H.; Tao, P.; Zhou, W.; Wang, S.* Sparse group selection and analysis of function-related residue for protein-state recognition. 2022, J Comput Chem. 43: 1342–1354. <a href="https://doi.org/10.1002/jcc.26937">DOI: 10.1002/jcc.26937</a></p>
</p>
</p> <img border="0" src="doc/publication/57.jpg" alt="Features" width="236" height="400" align=center>
</p>
</p>
<p><a href="doc/publication/56.pdf">56.</a> Ibrahim, M. T.; Trozzi, F.; Tao, P* Dynamics of hydrogen bonds in the secondary structures of allosteric protein Avena Sativa phototropin 1. 2021, Computational and Structural Biotechnology Journal. 20, 50-64. <a href="https://doi.org/10.1016/j.csbj.2021.11.038">DOI: 10.1016/j.csbj.2021.11.038</a></p>
</p>
</p> <img border="0" src="doc/publication/56.jpg" alt="AsLOV2" width="426" height="200" align=center>
</p>
</p>
<p>
<a href="doc/publication/55.pdf">55.</a>
Tian H.; Jiang X.; Trozzi F.; Xiao S.; Larson E.; Tao P.* Explore protein conformational space with variational autoencoder. Front. Mol. Biosci. 8:781635.
<a href="https://doi.org/10.3389/fmolb.2021.781635">DOI: 10.3389/fmolb.2021.781635</a>
</p>
</p> <img border="0" src="doc/publication/55.jpg" alt="ZTL" width="399" height="200" align=center>
</p>
</p>
<p><a href="doc/publication/54.pdf">54.</a> Song, Z.; Trozzi, F.; Palzkill, T.; Tao, P.* QM/MM modeling of class A β-lactamases reveals distinct acylation pathways for ampicillin and cefalexin, 2021, Org. Biomol. Chem., 19, 9182-9189. <a href="https://doi.org/10.1039/D1OB01593A">DOI: 10.1039/d1ob01593a</a></p>
</p>
</p> <img border="0" src="doc/publication/54.jpg" alt="ZTL" width="323" height="189" align=center>
</p>
</p>
<p><a href="doc/publication/53.pdf">53.</a> Trozzi, F.; Wang, X; Tao, P.* UMAP as a Dimensionality Reduction Tool for Molecular Dynamics Simulations of Biomacromolecules: A Comparison Study. 2021, J. Phys. Chem. B 125, 5022−5034. <a href="https://doi.org/10.1021/acs.jpcb.1c02081">DOI: 10.1021/acs.jpcb.1c02081</a></p>
</p>
</p> <img border="0" src="doc/publication/53.jpg" alt="UMAP" width="353" height="200" align=center>
</p>
</p>
<p>
<a href="doc/publication/52.pdf">52.</a>
Trozzi F.; Wang F.; Verkhivker G.; Zoltowski BD.; Tao P.* Dimeric allostery mechanism of the plant circadian clock photoreceptor ZEITLUPE. PLoS computational biology. 2021 Jul 26;17(7):e1009168.
<a href="https://doi.org/10.1371/journal.pcbi.1009168">DOI: 10.1371/journal.pcbi.1009168</a>
</p>
</p> <img border="0" src="doc/publication/52.png" alt="ZTL" width="712" height="200" align=center>
</p>
<p>
<a href="doc/publication/51.pdf">51.</a>
Tian, H.; Jiang, X.; Tao, P.* PASSer: Prediction of Allosteric Sites Server. 2021, Machine Learning: Science and Technology.
<a href="https://doi.org/10.1088/2632-2153/abe6d6">DOI: 10.1088/2632-2153.abe6d6</a>
<a href="https://passer.smu.edu/">PASSer websever</a>
</p>
<p>
<img border="0" src="doc/publication/51.png" alt="PASSer" width="418" height="200" align=center>
</p>
<p>
<a href="doc/publication/50.pdf">50.</a>
Stojanoski, V.; Hu, L.; Sankaran, B.; Wang, F.; Tao, P.; Prasad, B. V. V.; and Palzkill, T.* Mechanistic Basis of OXA-48-like β‐Lactamases’ Hydrolysis of Carbapenems. 2021, ACS Infect. Dis. 7, 445-460
<a href="https://dx.doi.org/10.1021/acsinfecdis.0c00798">DOI: 10.1021/acsinfecdis.0c00798</a>
</p>
<p>
<img border="0" src="doc/publication/50.gif" alt="OXA48" width="613" height="200" align=center>
</p>
<p>
<a href="doc/publication/49.pdf">49.</a>
Karki, N.; Verma, N.; Trozzi, F.; Tao, P.; Kraka, E.; and Zoltowski, B. Predicting Potential SARS-COV-2 Drugs—In Depth Drug Database Screening Using Deep Neural Network Framework SSnet, Classical Virtual Screening and Docking. 2021, Int. J. Mol. Sci. 22, 1573
<a href="https://doi.org/10.3390/ijms22041573">DOI: 10.3390/ijms22041573</a>
</p>
<p>
<a href="doc/publication/48.pdf">48.</a>
Verkhivker, G. M.*; Agajanian, S.; Hu, G.; and Tao, P. Allosteric Regulation at the Crossroads of New Technologies: Multiscale Modeling, Networks, and Machine Learning. 2020, Front. Mol. Biosci., 7, 136
<a href="https://doi.org/10.3389/fmolb.2020.00136">DOI: 10.3389/fmolb.2020.00136</a>
</p>
<p>
<a href="doc/publication/47.pdf">47.</a>
Song, Z.; Zhou, H.; Tian, H.; Wang, X.; Tao, P.* Unraveling the energetic significance of chemical events in enzyme catalysis via machine-learning based regression approach. 2020, Communications Chemistry 3, 134
<a href=" https://doi.org/10.1038/s42004-020-00379-w">DOI: 10.1038/s42004-020-00379-w</a>
</p>
<p>
<img border="0" src="doc/publication/47.jpg" alt="TEM1" width="171" height="200" align=center>
</p>
<p>
<a href="doc/publication/46.pdf">46.</a>
Tian, H.; Trozzi, F.; Zoltowski, B. D.; Tao, P.* Deciphering the Allosteric Process of the Phaeodactylum tricornutum Aureochrome 1a LOV Domain. 2020, J. Phys. Chem. B, 124, 41, 8960–8972
<a href="https://dx.doi.org/10.1021/acs.jpcb.0c05842">DOI: 10.1021/acs.jpcb.0c05842</a>
</p>
<p>
<img border="0" src="doc/publication/46.jpg" alt="PtAu1a" width="398" height="200" align=center>
</p>
<p>
<a href="doc/publication/45.pdf">45.</a>
Tian, H.; Tao, P.* ivis Dimensionality Reduction Framework for Biomacromolecular Simulations. 2020, J. Chem. Inf. Model.
<a href="https://dx.doi.org/10.1021/acs.jcim.0c00485">DOI: 10.1021/acs.jcim.0c00485</a>
</p>
<p>
<img border="0" src="doc/publication/45.jpg" alt="ivis" width="509" height="200" align=center>
</p>
<p>
<a href="doc/publication/44.pdf">44.</a>
Tian, H.; Tao, P.* Deciphering the protein motion of S1 subunit in SARS-CoV-2 spike glycoprotein through integrated computational methods. 2020, Journal of Biomolecular Structure and Dynamics
<a href="https://doi.org/10.1080/07391102.2020.1802338">DOI: 10.1080/07391102.2020.1802338</a>
</p>
<p>
<img border="0" src="doc/publication/44.png" alt="Spike" width="455" height="200" align=center>
</p>
<p>
<a href="doc/publication/43.pdf">43.</a>
Wang, F.; Tao, P.* Exploring free energy profile of petroleum thermal cracking mechanisms. 2020, J. Mol. Mod., 26:15 <a href="https://doi.org/10.1007/s00894-019-4273-3">DOI: 10.1007/s00894-019-4273-3</a>
</p>
<p>
<img border="0" src="doc/publication/43.jpg" alt="Petroleum" width="319" height="200" align=center>
</p>
<p>
<a href="doc/publication/42.pdf">42.</a>
Wang, F.; Zhou, H.; Wang, X.; Tao, P.* Dynamical Behavior of β-Lactamases and Penicillin-Binding Proteins in Different Functional States and Its Potential Role in Evolution. 2019, Entropy, 21(11), 1130
<a href="https://doi.org/10.3390/e21111130">DOI: 10.3390/e21111130</a>
</p>
<p>
<img border="0" src="doc/publication/42.jpg" alt="LactamasesPBP" width="814" height="200" align=center>
</p>
<p>
<a href="doc/publication/41.pdf">41.</a>
Zhou, H.*; Wang, F.; Bennett, D. I. G.; Tao, P.* Directed kinetic transition network model. 2019, J. Chem. Phys. 151, 144112
<a href="https://doi.org/10.1063/1.5110896">DOI: 10.1063/1.5110896</a>
</p>
<p>
<iframe width="560" height="315" src="https://www.youtube.com/embed/p60Dh8lV-v0" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
</p>
<p>
<a href="doc/publication/40.pdf">40.
</a> Hayatshahi, H. S.; Ahuactzin, E.; Tao, P.; Wang, S.; Liu, J.* Probing Protein Allostery as a Residue-Specific Concept via Residue Response Maps. 2019, J. Chem. Inf. Model. 59, 4691-4705
<a href="https://doi.org/10.1021/acs.jcim.9b00447">DOI: 10.1021/acs.jcim.9b00447</a>
</p>
<p>
<img border="0" src="doc/publication/40.jpg" alt="Maps" width="417" height="200" align=center>
</p>
<p>
<a href="doc/publication/39.pdf">39.</a>
Wang, F.; Shen, L.; Zhou, H.; Wang, S.; Wang, X.; Tao, P.* Machine Learning Classification Model for Functional Binding Modes of TEM-1 β-Lactamase. 2019, Front. Mol. Biosci. 6:47
<a href="https://doi.org/10.3389/fmolb.2019.00047">DOI: 10.3389/fmolb.2019.00047</a>
</p>
<p>
<img border="0" src="doc/publication/39.jpg" alt="TEM1" width="238" height="200" align=center>
</p>
<p>
<a href="doc/publication/38.pdf">38.</a>
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
<a href="https://doi.org/10.1371/journal.pcbi.1006801">DOI: 10.1371/journal.pcbi.1006801</a>
</p>
<p>
<img border="0" src="doc/publication/38.jpg" alt="VVD" width="262" height="200" align=center>
</p>
<p>
<a href="doc/publication/37.pdf">37.</a>
Zhou, H.; Tao, P.*; REDAN: relative entropy-based dynamical allosteric network model. Mol. Phys. 2018
<a href="https://doi.org/10.1080/00268976.2018.1543904">DOI: 10.1080/00268976.2018.1543904</a>
</p>
<p>
<img border="0" src="doc/publication/37.jpg" alt="REDAN" width="525" height="200" align=center>
</p>
<p>
<a href="doc/publication/36.pdf">36.</a>
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.
<a href="https://pubs.acs.org/doi/10.1021/acs.jctc.8b00652">DOI: 10.1021/acs.jctc.8b00652</a>
</p>
<p>
<img border="0" src="doc/publication/36.jpg" alt="t-SNE" width="277" height="200" align=center>
</p>
<p>
<a href="doc/publication/35.pdf">35.</a>
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.
<a href="https://pubs.acs.org/doi/10.1021/acs.jcim.8b00370">DOI: 10.1021/acs.jcim.8b00370</a>
</p>
<p>
<img border="0" src="doc/publication/35.jpg" alt="Orbital Overlap" width="586" height="200" align=center>
</p>
<p>
<a href="doc/publication/34.pdf">34.</a>
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
<a href="https://doi.org/10.1002/anie.201712306">DOI: 10.1002/anie.201712306</a>
</p>
<p>
This paper was selected as Very Important Paper (VIP) by the journal editor and featured on the journal cover.
</p>
<p>
<img border="0" src="doc/publication/34.jpg" alt="pKa" width="284" height="400" align=center>
</p>
<p>
<a href="doc/publication/33.pdf">33.</a>
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
<a href="https://doi.org/10.1002/jcc.25218">DOI: 10.1002/jcc.25218</a>
</p>
<p>
<img border="0" src="doc/publication/33.jpg" alt="JCC" width="245" height="200" align=center>
</p>
<p>
<a href="doc/publication/32.pdf">32.</a>
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
<a href="http://pubs.acs.org/doi/full/10.1021/acsomega.7b01483">DOI: 10.1021/acsomega.7b01483</a>
</p>
<p>
Check out a short online liveslides presentation featuring this work. <a href="https://pubs.acs.org/doi/suppl/10.1021/acsomega.7b01483">link </a>
</p>
<p>
<img border="0" src="doc/publication/32.jpg" alt="LCTA" width="682" height="200" align=center>
</p>
<p>
<a href="doc/publication/31.pdf">31.</a>
Zhou, H.; Tao, P. Dynamics Sampling in Transition Pathway Space. J. Chem. Theory Comput. 2018, 14, 14−29
<a href="http://pubs.acs.org/doi/abs/10.1021/acs.jctc.7b00606">DOI: 10.1021/acs.jctc.7b00606</a>
</p>
<p>
Check out a short online liveslides presentation featuring this work.
<a href="http://pubs.acs.org/doi/suppl/10.1021/acs.jctc.7b00606/suppl_file/ct7b00606_liveslides.mp4">link </a>
</p>
<p>
<img border="0" src="doc/publication/31.jpg" alt="LCTA" width="200" height="200" align=center>
</p>
<p>
<a href="doc/publication/30.pdf">30.</a>
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
<a href="http://onlinelibrary.wiley.com/doi/10.1002/pro.3329/abstract">DOI: 10.1002/pro.3329</a>
</p>
<p>
<img border="0" src="doc/publication/30.jpg" alt="LCTA" width="198" height="200" align=center>
</p>
<p>
<a href="doc/publication/29.pdf">29.</a>
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
<a href="https://www.nature.com/articles/srep46626">DOI: 10.1038/srep46626</a>
</p>
<p>
<img border="0" src="doc/publication/29.jpg" alt="LCTA" width="278" height="200" align=center>
</p>
<p>
<a href="doc/publication/28.pdf">28.</a>
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.
</p>
<p>
<a href="doc/publication/27.pdf">27.</a>
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.
<a href="http://pubs.acs.org/doi/abs/10.1021/acs.biochem.6b00188">DOI: 10.1021/acs.biochem.6b00188</a>
</p>
<p>
<img border="0" src="doc/publication/27.gif" alt="LCTA" width="342" height="200" align=center>
</p>
<p>
<a href="doc/publication/26.pdf">26.</a>
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.
<a href="http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004893">DOI: 10.1371/ journal.pcbi.1004893</a>
</p>
<p>
<img border="0" src="doc/publication/26.png" alt="RRS" width="492" height="200" align=center>
</p>
<p>
<a href="doc/publication/25.pdf">25.</a>
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.
<a href="http://pubs.rsc.org/en/content/articlelanding/2015/sc/c4sc03516j">DOI: 10.1039/C4SC03516J</a>
</p>
<p>
<img border="0" src="doc/publication/25.jpeg" alt="RRS" width="370" height="189" align=center>
</p>
<p>
<a href="doc/publication/24.pdf">24.</a>
Kalesky, R.; Liu, J.; Tao, P.; “Identifying Key Residues for Protein Allostery through Rigid Residue Scan”. J. Phys. Chem. A 2015, 119, 1689-1700.
<a href="http://pubs.acs.org/doi/abs/10.1021/jp5083455">DOI: 10.1021/jp5083455</a>
</p>
<p>
<img border="0" src="doc/publication/24.jpg" alt="RRS" width="353" height="200" align=center>
</p>
<p>
<a href="doc/publication/23.pdf">23.</a>
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.
<a href="http://pubs.acs.org/doi/abs/10.1021/jp5072296">DOI: 10.1021/jp5072296</a>
</p>
<p>
<img border="0" src="doc/publication/23.gif" alt="MESS" width="500" height="213" align=center>
</p>
<p>
<a href="doc/publication/22.pdf">22.</a>
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.
<a href="http://pubs.acs.org/doi/abs/10.1021/ct500342h">DOI: 10.1021/ct500342h</a>
</p>
<p>
<img border="0" src="doc/publication/22.gif" alt="FEGRBD" width="319" height="200" align=center>
</p>
<h2 align=left>Publications Unaffiliated with SMU:</h2>
<p>
<a href="doc/publication/21.pdf">21.</a>
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.
<a href="http://www.intechopen.com/books/some-applications-of-quantum-mechanics/reaction-path-optimization-and-sampling-methods-and-their-applications-for-rare-events">DOI: 10.5772/35351</a>
</p>
<p>
<a href="doc/publication/20.pdf">20.</a>
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. <a href="http://pubs.acs.org/doi/abs/10.1021/ct3006248">DOI: 10.1021/ct3006248</a>
</p>
<p>
<a href="doc/publication/19.pdf">19.</a>
Tao, P.; Wu, X.; Brooks, B. R; “Maintain Rigid Structures in Verlet Based Cartesian Molecular Dynamics Simulations”. J. Chem. Phys. 2012, 137, 134110.
<a href="http://scitation.aip.org/content/aip/journal/jcp/137/13/10.1063/1.4756796">DOI:10.1063/1.4756796</a>
</p>
<p>
<a href="doc/publication/18.pdf">18.</a>
Tao, P.; Parquette, J. R; Hadad, C. M; “Right- and Left-Handed Helices, What is in between? Interconversion of Helical Structures of Alternating Pyridinedicarboxamide/m-(phenylazo)azobenzene Oligomers”. J. Chem. Theory Comput. 2012, 8, 5137-5149.
<a href="http://pubs.acs.org/doi/abs/10.1021/ct2009335">DOI:10.1021/ct2009335 </a>
</p>
<p>
<a href="doc/publication/17.pdf">17.</a>
Bao, X.; Tao, P.; Villamena, F. A.; Hadad, C. M; “Spin Trapping of Hydroperoxyl Radical by a Cyclic Nitrone Conjugated to β-Cyclodextrin: A Computational Study”. Theor. Chem. Acc. 2012, 131, 1248-1257.
<a href="http://link.springer.com/article/10.1007%2Fs00214-012-1248-1">DOI: 10.1007/s00214-012-1248-1</a>
</p>
<p>
<a href="doc/publication/16.pdf">16.</a>
Zhang, S.; Qu, Z.; Tao, P.; Brooks, B. R; Shao, Y.; Chen, X.; Liu, C.; "Quantum Chemical Study of the Ground and Excited State Electronic Structures of Carbazole Oligomers with and without Triarylborane Substitutes", J. Phys. Chem. C, 2012, 116, 12434-12442.
<a href="http://pubs.acs.org/doi/abs/10.1021/jp3027447">DOI: 10.1021/jp3027447</a>
</p>
<p>
<a href="doc/publication/15.pdf">15.</a>
Zhou, J.; Tao, P.; Fisher, J. F.; Shi, Q.; Mobashery, S.; Schlegel, H. B. “QM/MM Studies of the Matrix Metalloproteinase 2 (MMP2) Inhibition Mechanism of (S) SB-3CT and its Oxirane Analogue”, J. Chem. Theory Comput. 2010, 6, 3580-3587. (Selected as cover article)
<a href="http://pubs.acs.org/doi/abs/10.1021/ct100382k">DOI: 10.1021/ct100382k</a>
</p>
<p>
<a href="doc/publication/14.pdf">14.</a>
Tao, P.; Gatti, D. L.; Schlegel, H. B. “Common Basis for the Mechanism of Metallo and Non-metallo KDO8P Synthases”, J. Inorg. Biochem. 2010, 104, 1267-1275.
<a href="http://www.sciencedirect.com/science/article/pii/S0162013410001923">DOI: 10.1016/j.jinorgbio.2010.08.008</a>
</p>
<p>
<a href="doc/publication/13.pdf">13.</a>
Psciuk, T. B.; Tao, P.; Schlegel, H. B. “Ab Initio Classical Trajectory Study of the Fragmentation of C3H4 Dications on the Singlet and Triplet Surfaces”, J. Phys. Chem. A 2010, 114, 7653-7660.
<a href="http://pubs.acs.org/doi/abs/10.1021/jp102238g">DOI: 10.1021/jp102238g</a>
</p>
<p>
<a href="doc/publication/12.pdf">12.</a>
Tao, P.; Schlegel, H. B. “A Toolkit to Assist ONIOM Calculations”, J. Comput. Chem. 2010, 31, 2363-2369.
<a href="http://onlinelibrary.wiley.com/doi/10.1002/jcc.21524/abstract">DOI: 10.1002/jcc.21524</a>
</p>
<p>
<a href="doc/publication/11.pdf">11.</a>
Sanan, T. T.; Muthukrishnan, S.; Beck, J. M.; Tao, P.; Hayes, C. J.; Otto, T. C.; Cerasoli, D. M.; Lenz, D. E.; Hadad, C. M. “Computational modeling of human paraoxonase 1: preparation of protein models, binding studies, and mechanistic insights”, J. Phys. Org. Chem., 2010, 23, 357-369.
<a href="http://onlinelibrary.wiley.com/doi/10.1002/poc.1678/abstract">DOI: 10.1002/poc.1678</a>
</p>
<p>
<a href="doc/publication/10.pdf">10.</a>
Tao, P.; Fisher, J. F.; Shi, Q.; Mobashery, S.; Schlegel, H. B. “Matrix Metalloproteinase 2 (MMP2) Inhibition: DFT and QM/MM Studies of the Deprotonation-Initialized Ring-Opening Reaction of Sulfoxide Analog of SB-3CT”, J. Phys. Chem. B, 2010, 114, 1030-1037.
<a href="http://pubs.acs.org/doi/abs/10.1021/jp909327y">DOI: 10.1021/jp909327y</a>
</p>
<p>
<a href="doc/publication/9.pdf">9.</a>
Tao, P.; Gatti, D. L.; Schlegel, H. B. “The energy landscape of 3-Deoxy- D-manno-octulosonate 8-Phosphate Synthase”, Biochemistry, 2009, 48, 11706-11714
<a href="http://pubs.acs.org/doi/abs/10.1021/bi901341h">DOI: 10.1021/bi901341h</a>
</p>
<p>
<a href="doc/publication/8.pdf">8.</a>
Tao, P.; Fisher, J. F.; Shi, Q.; Vreven, T.; Mobashery, S.; Schlegel, H. B. “Matrix Metalloproteinase 2 (MMP2) Inhibition: Combined Quantum Mechanics and Molecular Mechanics Studies of the Inhibition Mechanism of (4-Phenoxyphenylsulfonyl) methylthiirane and Its Oxirane Analogue”, Biochemistry, 2009, 48, 9839-9847
<a href="http://pubs.acs.org/doi/abs/10.1021/bi901118r">DOI: 10.1021/bi901118r</a>
</p>
<p>
<a href="doc/publication/7.pdf">7.</a>
Tao, P.; Fisher, J. F.; Mobashery, S.; Schlegel, H. B. “DFT Studies of the Ring-Opening Mechanism of SB-3CT, a Potent Inhibitor of Matrix Metalloproteinase 2”, Org. Lett., 2009, 11, 2559-2562
<a href="http://pubs.acs.org/doi/abs/10.1021/ol9008393">DOI: 10.1021/ol9008393</a>
</p>
<p>
<a href="doc/publication/6.pdf">6.</a>
Kona, F.; Tao, P.; Martin, P.; Xu, X.; Gatti, D. L.. “Electronic Structure of the Metal Center in the Cd2+, Zn2+, and Cu2+ Substituted Forms of KDO8P Synthase: Implications for Catalysis”, Biochemistry, 2009, 48, 3610-3630 (Kona, K. and Tao, P. contributed equally to this work)
<a href="http://pubs.acs.org/doi/abs/10.1021/bi801955h">DOI: 10.1021/bi801955h</a>
</p>
<p>
<a href="doc/publication/5.pdf">5.</a>
King, E. D.; Tao, P.; Sanan, T. T.; Hadad, C. M.; Parquette, J. R. “Photomodulated chiral induction in helical azobenzene oligomers”. Org. Lett. 2008, 10, 1671-1674
<a href="http://pubs.acs.org/doi/abs/10.1021/ol8004722">DOI: 10.1021/ol8004722</a>
</p>
<p>
<a href="doc/publication/4.pdf">4.</a>
Mendlik, M. T.; Tao, P.; Hadad, C. M.; Coleman, R. S.; Lowary, T. L. “Synthesis of L-Daunosamine and L-Ristosamine Glycosides via Photoinduced Aziridination. Conversion to Thioglycosides for Use in Glycosylation Reactions.” J. Org. Chem. 2006, 71, 8059-8070
<a href="http://pubs.acs.org/doi/abs/10.1021/jo061167z">DOI: 10.1021/jo061167z</a>
</p>
<p>
<a href="doc/publication/3.pdf">3.</a>
Tao, P.; Lai, L. “Protein Ligand Docking Based on Empirical Method for Binding Affinity Estimation” J. Comput.-Aided Mol. Des. 2001, 15, 429-446.
<a href="http://link.springer.com/article/10.1023%2FA%3A1011188704521">DOI: 10.1023/A:1011188704521</a>
</p>
<p>
<a href="doc/publication/2.pdf">2.</a>
Tao, P.; Wang, R.; Lai, L. “Calculating Partition Coefficients of Peptides by the Addition Method” J. Mol. Mod. 1999, 5, 189-195. <a href="http://link.springer.com/article/10.1007%2Fs008940050118">DOI: 10.1007/s008940050118</a>
</p>
<p>
<a href="doc/publication/1.pdf">1.</a>
Tao, P.; Wang, R.; Lai, L. “Calculation of Peptide’s Partition Coefficients by Amino Acid Addition Method” Wuli Huaxue Xuebao 1999, 15, 449-453.
</p>
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</tr>
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