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Yilin Meng, Ph.D. - Publications

Affiliations: 
2010 University of Florida, Gainesville, Gainesville, FL, United States 
Area:
Physical Chemistry, Biochemistry, General Biophysics
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26 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Paul F, Meng Y, Roux B. Identification of druggable kinase target conformations using Markov model metastable states analysis of apo Abl. Journal of Chemical Theory and Computation. PMID 31999924 DOI: 10.1021/Acs.Jctc.9B01158  0.377
2018 Meng Y, Ahuja LG, Kornev AP, Taylor SS, Roux B. Corrigendum to "A Catalytically-Disabled Double Mutant of Src Tyrosine Kinase Can Be Stabilized into an Active-Like Conformation." J. Mol. Biol. 430(6) (Mar 16 2018), 881-889. Journal of Molecular Biology. PMID 30220583 DOI: 10.1016/J.Jmb.2018.09.001  0.332
2018 Meng Y, Gao C, Clawson DK, Atwell S, Russell M, Vieth M, Roux B. Predicting the Conformational Variability of Abl tyrosine kinase using Molecular Dynamics Simulations and Markov State Models. Journal of Chemical Theory and Computation. PMID 29474075 DOI: 10.1021/Acs.Jctc.7B01170  0.41
2018 Meng Y, Ahuja LG, Kornev AP, Taylor SS, Roux B. A Catalytically-Disabled Double Mutant of Src Tyrosine Kinase Can Be Stabilized into an Active-Like Conformation. Journal of Molecular Biology. PMID 29410316 DOI: 10.1016/J.Jmb.2018.01.019  0.383
2018 Ahuja LG, Meng Y, Kornev AP, Roux B, Taylor S. An Allosteric Region of Src Tyrosine Kinase Allows for Stabilization of Its Active-Like Conformation Biophysical Journal. 114: 398a. DOI: 10.1016/J.Bpj.2017.11.2201  0.338
2017 Meng Y, Pond MP, Roux B. Tyrosine Kinase Activation and Conformational Flexibility: Lessons from Src-Family Tyrosine Kinases. Accounts of Chemical Research. PMID 28426203 DOI: 10.1021/Acs.Accounts.7B00012  0.379
2016 Fajer M, Meng Y, Roux B. The Activation of c-Src Tyrosine Kinase: Conformational Transition Pathway and Free Energy Landscape. The Journal of Physical Chemistry. B. PMID 27715044 DOI: 10.1021/Acs.Jpcb.6B08409  0.375
2016 Meng Y, Shukla D, Pande VS, Roux B. Transition path theory analysis of c-Src kinase activation. Proceedings of the National Academy of Sciences of the United States of America. PMID 27482115 DOI: 10.1073/Pnas.1602790113  0.371
2016 Shen R, Li Q, Medovoy D, Meng Y, Roux B, Perozo E. Computational Characterization of Conformational Transitions in the Voltage-Sensing Domain of Ci-VSP Biophysical Journal. 110: 106a. DOI: 10.1016/J.Bpj.2015.11.629  0.366
2015 Meng Y, Roux B. Efficient Determination of Free Energy Landscapes in Multiple Dimensions from Biased Umbrella Sampling Simulations Using Linear Regression. Journal of Chemical Theory and Computation. 11: 3523-9. PMID 26574437 DOI: 10.1021/Ct501130R  0.308
2015 Meng Y, Roux B. Computational study of the W260A activating mutant of Src tyrosine kinase. Protein Science : a Publication of the Protein Society. PMID 26106037 DOI: 10.1002/Pro.2731  0.388
2015 Meng Y, Lin YL, Roux B. Computational study of the "DFG-flip" conformational transition in c-Abl and c-Src tyrosine kinases. The Journal of Physical Chemistry. B. 119: 1443-56. PMID 25548962 DOI: 10.1021/Jp511792A  0.371
2014 Lin YL, Meng Y, Huang L, Roux B. Computational study of Gleevec and G6G reveals molecular determinants of kinase inhibitor selectivity. Journal of the American Chemical Society. 136: 14753-62. PMID 25243930 DOI: 10.1021/Ja504146X  0.353
2014 Jiang W, Phillips JC, Huang L, Fajer M, Meng Y, Gumbart JC, Luo Y, Schulten K, Roux B. Generalized Scalable Multiple Copy Algorithms for Molecular Dynamics Simulations in NAMD. Computer Physics Communications. 185: 908-916. PMID 24944348 DOI: 10.1016/J.Cpc.2013.12.014  0.38
2014 Shukla D, Meng Y, Roux B, Pande VS. Activation pathway of Src kinase reveals intermediate states as targets for drug design. Nature Communications. 5: 3397. PMID 24584478 DOI: 10.1038/Ncomms4397  0.39
2014 Meng Y, Roux B. Locking the active conformation of c-Src kinase through the phosphorylation of the activation loop Journal of Molecular Biology. 426: 423-435. PMID 24103328 DOI: 10.1016/J.Jmb.2013.10.001  0.388
2014 Fajer M, Meng Y, Roux B. Simulation of the Conformational Transition Pathway for the Activation of Full-Length C-Src Kinase using the String Method Biophysical Journal. 106: 639a-640a. DOI: 10.1016/J.Bpj.2013.11.3541  0.395
2014 Jiang W, Phillips J, Huang L, Fajer M, Meng Y, Gumbart JC, luo y, Schulten K, roux b. Generalized Scalable Multiple Copy Algorithms for Biological Molecular Dynamics Simulations in NAMD Biophysical Journal. 106: 412a. DOI: 10.1016/J.Bpj.2013.11.2316  0.384
2013 Wojtas-Niziurski W, Meng Y, Roux B, Bernèche S. Self-Learning Adaptive Umbrella Sampling Method for the Determination of Free Energy Landscapes in Multiple Dimensions. Journal of Chemical Theory and Computation. 9: 1885-1895. PMID 23814508 DOI: 10.1021/Ct300978B  0.336
2013 Lin YL, Meng Y, Jiang W, Roux B. Explaining why Gleevec is a specific and potent inhibitor of Abl kinase Proceedings of the National Academy of Sciences of the United States of America. 110: 1664-1669. PMID 23319661 DOI: 10.1073/Pnas.1214330110  0.351
2012 Sabri Dashti D, Meng Y, Roitberg AE. pH-replica exchange molecular dynamics in proteins using a discrete protonation method. The Journal of Physical Chemistry. B. 116: 8805-11. PMID 22694266 DOI: 10.1021/Jp303385X  0.598
2011 Meng Y, Dashti DS, Roitberg AE. Computing Alchemical Free Energy Differences with Hamiltonian Replica Exchange Molecular Dynamics (H-REMD) Simulations. Journal of Chemical Theory and Computation. 7: 2721-2727. PMID 22125475 DOI: 10.1021/Ct200153U  0.552
2010 Meng Y, Roitberg AE. Constant pH replica exchange molecular dynamics in biomolecules using a discrete protonation model. Journal of Chemical Theory and Computation. 6: 1401-1412. PMID 20514364 DOI: 10.1021/Ct900676B  0.601
2009 Swails JM, Meng Y, Walker FA, Marti MA, Estrin DA, Roitberg AE. pH-dependent mechanism of nitric oxide release in nitrophorins 2 and 4. The Journal of Physical Chemistry. B. 113: 1192-201. PMID 19159340 DOI: 10.1021/Jp806906X  0.624
2009 Long JR, Mehta AK, Meng Y, Roitberg A, Antharam V, Ganesh O, Farver S. The Structural Plasticity Of Lung Surfactant Peptide KL4 In Lipid Membranes Biophysical Journal. 96: 159a. DOI: 10.1016/J.Bpj.2008.12.725  0.508
2008 Sindhikara D, Meng Y, Roitberg AE. Exchange frequency in replica exchange molecular dynamics. The Journal of Chemical Physics. 128: 024103. PMID 18205439 DOI: 10.1063/1.2816560  0.618
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