| Year |
Citation |
Score |
| 2023 |
Popescu G, Abbott J, Wen H, Liu B, Gupta S, Iacobucci G, Zheng W. Allosteric Site Mediates Inhibition of Tonic NMDA Receptor Activity by Low Dose Ketamine. Research Square. PMID 37790558 DOI: 10.21203/rs.3.rs-3304783/v1 |
0.583 |
|
| 2022 |
Iacobucci GJ, Liu B, Wen H, Sincox B, Zheng W, Popescu GK. Complex functional phenotypes of NMDA receptor disease variants. Molecular Psychiatry. PMID 36117210 DOI: 10.1038/s41380-022-01774-6 |
0.602 |
|
| 2021 |
Iacobucci GJ, Wen H, Helou M, Liu B, Zheng W, Popescu GK. Cross-subunit interactions that stabilize open states mediate gating in NMDA receptors. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33384330 DOI: 10.1073/pnas.2007511118 |
0.619 |
|
| 2020 |
Zheng W, Wen H. Investigating dual Ca modulation of the ryanodine receptor 1 by molecular dynamics simulation. Proteins. PMID 32557910 DOI: 10.1002/Prot.25971 |
0.339 |
|
| 2019 |
Zheng W, Wen H. Molecular dynamics simulation of tropomyosin bound to actins/myosin in the closed and open states. Proteins. PMID 31090107 DOI: 10.1002/Prot.25707 |
0.379 |
|
| 2019 |
Moraczewska J, Robaszkiewicz K, Śliwinska M, Czajkowska M, Ly T, Kostyukova A, Wen H, Zheng W. Congenital myopathy-related mutations in tropomyosin disrupt regulatory function through altered actin affinity and tropomodulin binding. The Febs Journal. PMID 30768849 DOI: 10.1111/Febs.14787 |
0.329 |
|
| 2019 |
Tripathy S, Zheng W, Auerbach A. A single molecular distance predicts agonist binding energy in nicotinic receptors. The Journal of General Physiology. PMID 30635370 DOI: 10.1085/Jgp.201812212 |
0.365 |
|
| 2019 |
Iacobucci GJ, Wen H, Helou M, Zheng W, Popescu GK. Mapping Structural Elements to NMDA Receptor Activation Steps Biophysical Journal. 116: 106a. DOI: 10.1016/J.Bpj.2018.11.607 |
0.601 |
|
| 2019 |
Tripathy S, Muehlemann SM, Zheng W, Auerbach A. Structural Correlates of Agonist Binding to Neurotransmitter Binding Sites Biophysical Journal. 116: 529a. DOI: 10.1016/J.Bpj.2018.11.2851 |
0.319 |
|
| 2019 |
Tripathy S, Zheng W, Auerbach A. Structure Meets Function: Agonist Actions at Neurotransmitter Binding Sites Biophysical Journal. 116: 394a. DOI: 10.1016/J.Bpj.2018.11.2131 |
0.333 |
|
| 2018 |
Wen H, Zheng W. Decrypting the Heat Activation Mechanism of TRPV1 Channel by Molecular Dynamics Simulation. Biophysical Journal. 114: 40-52. PMID 29320695 DOI: 10.1016/J.Bpj.2017.10.034 |
0.34 |
|
| 2018 |
Tripathy S, Zheng W, Auerbach A. Simulations Suggest a Structural Basis for Nicotinic Receptor Activation by Agonists Biophysical Journal. 114: 48a. DOI: 10.1016/J.Bpj.2017.11.314 |
0.322 |
|
| 2017 |
Zheng W, Sachs F. Investigating the structural dynamics of the PIEZO1 channel activation and inactivation by coarse-grained modeling. Proteins. PMID 28905417 DOI: 10.1002/Prot.25384 |
0.394 |
|
| 2017 |
Zheng W, Wen H, Iacobucci GJ, Popescu GK. Probing the Structural Dynamics of the NMDA Receptor Activation by Coarse-Grained Modeling. Biophysical Journal. 112: 2589-2601. PMID 28636915 DOI: 10.1016/J.Bpj.2017.04.043 |
0.677 |
|
| 2017 |
Zheng W, Liu Z. Investigating the inter-subunit/subdomain interactions and motions relevant to disease mutations in the N-terminal domain of ryanodine receptors by molecular dynamics simulation. Proteins. PMID 28508509 DOI: 10.1002/Prot.25318 |
0.376 |
|
| 2017 |
Zheng W. Probing the Inter-Subunit/Subdomain Interactions Relevant to Disease Mutations in the N-Terminal Domain of Ryanodine Receptors by Molecular Dynamics Simulation Biophysical Journal. 112: 97a. DOI: 10.1016/J.Bpj.2016.11.563 |
0.345 |
|
| 2016 |
Zheng W. Probing the energetics of dynactin filament assembly and the binding of cargo adaptor proteins using molecular dynamics simulation and electrostatics-based structural modeling. Biochemistry. PMID 27976861 DOI: 10.1021/Acs.Biochem.6B01002 |
0.388 |
|
| 2016 |
Zheng W. Probing the structural dynamics of the CRISPR-Cas9 RNA-guided DNA-cleavage system by coarse-grained modeling. Proteins. PMID 27936513 DOI: 10.1002/Prot.25229 |
0.375 |
|
| 2016 |
Zheng W, Wen H. A survey of coarse-grained methods for modeling protein conformational transitions. Current Opinion in Structural Biology. 42: 24-30. PMID 27810573 DOI: 10.1016/J.Sbi.2016.10.008 |
0.367 |
|
| 2016 |
Wen H, Qin F, Zheng W. Toward elucidating the heat activation mechanism of the TRPV1 channel gating by molecular dynamics simulation. Proteins. PMID 27699868 DOI: 10.1002/Prot.25177 |
0.372 |
|
| 2016 |
Zheng W, Hitchcock-DeGregori SE, Barua B. Investigating the effects of tropomyosin mutations on its flexibility and interactions with filamentous actin using molecular dynamics simulation. Journal of Muscle Research and Cell Motility. PMID 27376658 DOI: 10.1007/S10974-016-9447-3 |
0.329 |
|
| 2016 |
Bruetzel LK, Gerling T, Sedlak SM, Walker P, Zheng W, Dietz H, Lipfert J. Conformational Changes and Flexibility of DNA Devices Observed by Small-Angle X-Ray Scattering. Nano Letters. PMID 27356232 DOI: 10.1021/Acs.Nanolett.6B01338 |
0.52 |
|
| 2016 |
Nayak TK, Chakraborty S, Zheng W, Auerbach A. Structural correlates of affinity in fetal versus adult endplate nicotinic receptors. Nature Communications. 7: 11352. PMID 27101778 DOI: 10.1038/Ncomms11352 |
0.342 |
|
| 2016 |
Zheng W. Probing the structural dynamics of the SNARE recycling machine based on coarse-grained modeling. Proteins. PMID 27090373 DOI: 10.1002/Prot.25052 |
0.437 |
|
| 2016 |
Zheng W. A Combined Coarse-Grained and All-Atom Molecular Simulation of the TRPV1 Channel Biophysical Journal. 110. DOI: 10.1016/J.Bpj.2015.11.198 |
0.403 |
|
| 2015 |
Zheng W. Toward decrypting the allosteric mechanism of the ryanodine receptor based on coarse-grained structural and dynamic modeling. Proteins. PMID 26492335 DOI: 10.1002/Prot.24951 |
0.431 |
|
| 2015 |
Zheng W, Qin F. A combined coarse-grained and all-atom simulation of TRPV1 channel gating and heat activation. The Journal of General Physiology. 145: 443-56. PMID 25918362 DOI: 10.1085/Jgp.201411335 |
0.404 |
|
| 2015 |
Zheng W, Glenn P. Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation. The Journal of Chemical Physics. 142: 035101. PMID 25612731 DOI: 10.1063/1.4905606 |
0.377 |
|
| 2015 |
Chakraborty S, Zheng W. Decrypting the structural, dynamic, and energetic basis of a monomeric kinesin interacting with a tubulin dimer in three ATPase states by all-atom molecular dynamics simulation. Biochemistry. 54: 859-69. PMID 25537000 DOI: 10.1021/Bi501056H |
0.427 |
|
| 2015 |
Chakraborty S, Nayak TK, Bruhova I, Zheng W, Auerbach AL. Molecular Simulations of Muscle AChR Agonist Binding Sites Biophysical Journal. 108: 429a. DOI: 10.1016/J.Bpj.2014.11.2347 |
0.362 |
|
| 2014 |
Zheng W, Tekpinar M. High-resolution modeling of protein structures based on flexible fitting of low-resolution structural data. Advances in Protein Chemistry and Structural Biology. 96: 267-84. PMID 25443961 DOI: 10.1016/Bs.Apcsb.2014.06.004 |
0.386 |
|
| 2014 |
Nayak TK, Bruhova I, Chakraborty S, Gupta S, Zheng W, Auerbach A. Functional differences between neurotransmitter binding sites of muscle acetylcholine receptors. Proceedings of the National Academy of Sciences of the United States of America. 111: 17660-5. PMID 25422413 DOI: 10.1073/Pnas.1414378111 |
0.351 |
|
| 2014 |
Tekpinar M, Zheng W. Unzipping of neuronal snare protein with steered molecular dynamics occurs in three steps. Journal of Molecular Modeling. 20: 2381. PMID 25079079 DOI: 10.1007/S00894-014-2381-7 |
0.304 |
|
| 2014 |
Zheng W. All-atom and coarse-grained simulations of the forced unfolding pathways of the SNARE complex. Proteins. 82: 1376-86. PMID 24403006 DOI: 10.1002/Prot.24505 |
0.332 |
|
| 2014 |
Zheng W, Tekpinar M. Analysis of protein conformational transitions using elastic network model. Methods in Molecular Biology (Clifton, N.J.). 1084: 159-72. PMID 24061921 DOI: 10.1007/978-1-62703-658-0_9 |
0.389 |
|
| 2014 |
Chakraborty S, Zheng W. A Comparative Study of the Major Biochemical States of Kinesin-MT Complex using Computational Techniques and All-Atom Structural Models Biophysical Journal. 106: 443a. DOI: 10.1016/J.Bpj.2013.11.2496 |
0.394 |
|
| 2013 |
Li M, Zheng W. All-atom molecular dynamics simulations of actin-myosin interactions: a comparative study of cardiac α myosin, β myosin, and fast skeletal muscle myosin. Biochemistry. 52: 8393-405. PMID 24224850 DOI: 10.1021/Bi4006896 |
0.365 |
|
| 2013 |
Zheng W, Barua B, Hitchcock-DeGregori SE. Probing the flexibility of tropomyosin and its binding to filamentous actin using molecular dynamics simulations. Biophysical Journal. 105: 1882-92. PMID 24138864 DOI: 10.1016/J.Bpj.2013.09.003 |
0.335 |
|
| 2013 |
Tekpinar M, Zheng W. Coarse-grained and all-atom modeling of structural states and transitions in hemoglobin. Proteins. 81: 240-52. PMID 22987685 DOI: 10.1002/Prot.24180 |
0.372 |
|
| 2013 |
Zheng W, Li M. All-Atom Simulations of Actin-Myosin Interactions --- A Comparative Study of Cardiac Alpha Myosin, Beta Myosin and Skeletal Muscle Myosin Biophysical Journal. 104. DOI: 10.1016/J.Bpj.2012.11.1711 |
0.313 |
|
| 2012 |
Zheng W, Tekpinar M. Structure-based simulations of the translocation mechanism of the hepatitis C virus NS3 helicase along single-stranded nucleic acid. Biophysical Journal. 103: 1343-53. PMID 22995507 DOI: 10.1016/J.Bpj.2012.08.026 |
0.348 |
|
| 2012 |
Li M, Zheng W. All-atom structural investigation of kinesin-microtubule complex constrained by high-quality cryo-electron-microscopy maps. Biochemistry. 51: 5022-32. PMID 22650362 DOI: 10.1021/Bi300362A |
0.391 |
|
| 2012 |
Zheng W. Coarse-grained modeling of the structural states and transition underlying the powerstroke of dynein motor domain. The Journal of Chemical Physics. 136: 155103. PMID 22519354 DOI: 10.1063/1.4704661 |
0.395 |
|
| 2011 |
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. Biophysical Journal. 101: 2981-91. PMID 22208197 DOI: 10.1016/J.Bpj.2011.11.003 |
0.374 |
|
| 2011 |
Grant BJ, Gheorghe DM, Zheng W, Alonso M, Huber G, Dlugosz M, McCammon JA, Cross RA. Electrostatically biased binding of kinesin to microtubules. Plos Biology. 9: e1001207. PMID 22140358 DOI: 10.1371/Journal.Pbio.1001207 |
0.346 |
|
| 2011 |
Hafner J, Zheng W. All-atom modeling of anisotropic atomic fluctuations in protein crystal structures. The Journal of Chemical Physics. 135: 144114. PMID 22010705 DOI: 10.1063/1.3646312 |
0.336 |
|
| 2011 |
Li M, Zheng W. Probing the structural and energetic basis of kinesin-microtubule binding using computational alanine-scanning mutagenesis. Biochemistry. 50: 8645-55. PMID 21910419 DOI: 10.1021/Bi2008257 |
0.377 |
|
| 2011 |
Zheng W. Coarse-grained modeling of conformational transitions underlying the processive stepping of myosin V dimer along filamentous actin. Proteins. 79: 2291-305. PMID 21590746 DOI: 10.1002/Prot.23055 |
0.352 |
|
| 2011 |
He Y, Chen JY, Knab JR, Zheng W, Markelz AG. Evidence of protein collective motions on the picosecond timescale. Biophysical Journal. 100: 1058-65. PMID 21320451 DOI: 10.1016/J.Bpj.2010.12.3731 |
0.324 |
|
| 2011 |
Zheng W, Auerbach A. Decrypting the sequence of structural events during the gating transition of pentameric ligand-gated ion channels based on an interpolated elastic network model. Plos Computational Biology. 7: e1001046. PMID 21253563 DOI: 10.1371/Journal.Pcbi.1001046 |
0.375 |
|
| 2011 |
Zheng W. Accurate flexible fitting of high-resolution protein structures into cryo-electron microscopy maps using coarse-grained pseudo-energy minimization. Biophysical Journal. 100: 478-88. PMID 21244844 DOI: 10.1016/J.Bpj.2010.12.3680 |
0.377 |
|
| 2011 |
Hafner JP, Zheng W. Coarse-Grained and Atomistic Modeling of Anisotropic Atomic Fluctuations in Protein Crystal Structures Biophysical Journal. 100: 1-1. DOI: 10.1016/J.Bpj.2010.12.1158 |
0.332 |
|
| 2010 |
Tekpinar M, Zheng W. Predicting order of conformational changes during protein conformational transitions using an interpolated elastic network model. Proteins. 78: 2469-81. PMID 20602461 DOI: 10.1002/Prot.22755 |
0.415 |
|
| 2010 |
Zheng W. Anharmonic normal mode analysis of elastic network model improves the modeling of atomic fluctuations in protein crystal structures. Biophysical Journal. 98: 3025-34. PMID 20550915 DOI: 10.1016/J.Bpj.2010.03.027 |
0.363 |
|
| 2010 |
Zheng W. Computer modeling of helicases using elastic network model. Methods in Molecular Biology (Clifton, N.J.). 587: 235-43. PMID 20225154 DOI: 10.1007/978-1-60327-355-8_17 |
0.402 |
|
| 2010 |
Hafner J, Zheng W. Optimal modeling of atomic fluctuations in protein crystal structures for weak crystal contact interactions. The Journal of Chemical Physics. 132: 014111. PMID 20078153 DOI: 10.1063/1.3288503 |
0.353 |
|
| 2010 |
Zheng W. Multiscale modeling of structural dynamics underlying force generation and product release in actomyosin complex. Proteins. 78: 638-60. PMID 19790263 DOI: 10.1002/Prot.22594 |
0.383 |
|
| 2010 |
Zheng W. Multiscale Modeling of Structural Dynamics in Actomyosin Complex Biophysical Journal. 98: 2-8. DOI: 10.1016/J.Bpj.2009.12.1291 |
0.387 |
|
| 2009 |
Zheng W, Tekpinar M. Large-scale evaluation of dynamically important residues in proteins predicted by the perturbation analysis of a coarse-grained elastic model. Bmc Structural Biology. 9: 45. PMID 19591676 DOI: 10.1186/1472-6807-9-45 |
0.405 |
|
| 2009 |
Hafner J, Zheng W. Approximate normal mode analysis based on vibrational subsystem analysis with high accuracy and efficiency. The Journal of Chemical Physics. 130: 194111. PMID 19466825 DOI: 10.1063/1.3141022 |
0.333 |
|
| 2009 |
Zheng W, Brooks BR, Thirumalai D. Allosteric transitions in biological nanomachines are described by robust normal modes of elastic networks. Current Protein & Peptide Science. 10: 128-32. PMID 19355980 DOI: 10.2174/138920309787847608 |
0.347 |
|
| 2009 |
Zheng W, Thirumalai D. Coupling between normal modes drives protein conformational dynamics: illustrations using allosteric transitions in myosin II. Biophysical Journal. 96: 2128-37. PMID 19289039 DOI: 10.1016/J.Bpj.2008.12.3897 |
0.367 |
|
| 2009 |
Zheng W. Normal-mode-based modeling of allosteric couplings that underlie cyclic conformational transition in F(1) ATPase. Proteins. 76: 747-62. PMID 19280602 DOI: 10.1002/Prot.22386 |
0.366 |
|
| 2009 |
Zheng W, Tekpinar M. Evaluation Of Three Transition Pathway Modeling Techniques In Capturing Structural Intermediates In F1 Atpase, Myosin, Kinesin, And Chaperonin Groel Biophysical Journal. 96. DOI: 10.1016/J.Bpj.2008.12.2193 |
0.37 |
|
| 2008 |
Miller BT, Zheng W, Venable RM, Pastor RW, Brooks BR. Langevin network model of myosin. The Journal of Physical Chemistry. B. 112: 6274-81. PMID 18311963 DOI: 10.1021/Jp077042V |
0.315 |
|
| 2008 |
Zheng W. A unification of the elastic network model and the Gaussian network model for optimal description of protein conformational motions and fluctuations. Biophysical Journal. 94: 3853-7. PMID 18234807 DOI: 10.1529/Biophysj.107.125831 |
0.34 |
|
| 2007 |
Zheng W, Brooks BR, Hummer G. Protein conformational transitions explored by mixed elastic network models. Proteins. 69: 43-57. PMID 17596847 DOI: 10.1002/Prot.21465 |
0.387 |
|
| 2007 |
Zheng W, Brooks BR, Thirumalai D. Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations. Biophysical Journal. 93: 2289-99. PMID 17557788 DOI: 10.1529/Biophysj.107.105270 |
0.377 |
|
| 2007 |
Zheng W, Liao JC, Brooks BR, Doniach S. Toward the mechanism of dynamical couplings and translocation in hepatitis C virus NS3 helicase using elastic network model. Proteins. 67: 886-96. PMID 17373706 DOI: 10.1002/Prot.21326 |
0.59 |
|
| 2006 |
Zheng W, Brooks BR, Thirumalai D. Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations. Proceedings of the National Academy of Sciences of the United States of America. 103: 7664-9. PMID 16682636 DOI: 10.1073/Pnas.0510426103 |
0.372 |
|
| 2006 |
Zheng W, Brooks BR. Modeling protein conformational changes by iterative fitting of distance constraints using reoriented normal modes. Biophysical Journal. 90: 4327-36. PMID 16565046 DOI: 10.1529/Biophysj.105.076836 |
0.394 |
|
| 2005 |
Zheng W, Brooks BR. Probing the local dynamics of nucleotide-binding pocket coupled to the global dynamics: myosin versus kinesin. Biophysical Journal. 89: 167-78. PMID 15879477 DOI: 10.1529/Biophysj.105.063305 |
0.4 |
|
| 2005 |
Zheng W, Doniach S. Fold recognition aided by constraints from small angle X-ray scattering data. Protein Engineering, Design & Selection : Peds. 18: 209-19. PMID 15845555 DOI: 10.1093/Protein/Gzi026 |
0.537 |
|
| 2005 |
Zheng W, Brooks BR, Doniach S, Thirumalai D. Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved. Structure (London, England : 1993). 13: 565-77. PMID 15837195 DOI: 10.1016/J.Str.2005.01.017 |
0.558 |
|
| 2005 |
Zheng W, Brooks BR. Normal-modes-based prediction of protein conformational changes guided by distance constraints. Biophysical Journal. 88: 3109-17. PMID 15722427 DOI: 10.1529/Biophysj.104.058453 |
0.368 |
|
| 2005 |
Zheng W, Brooks B. Identification of dynamical correlations within the myosin motor domain by the normal mode analysis of an elastic network model. Journal of Molecular Biology. 346: 745-59. PMID 15713460 DOI: 10.1016/J.Jmb.2004.12.020 |
0.394 |
|
| 2003 |
Zheng W, Doniach S. A comparative study of motor-protein motions by using a simple elastic-network model. Proceedings of the National Academy of Sciences of the United States of America. 100: 13253-8. PMID 14585932 DOI: 10.1073/Pnas.2235686100 |
0.586 |
|
| 2002 |
Zheng W, Doniach S. Protein structure prediction constrained by solution X-ray scattering data and structural homology identification. Journal of Molecular Biology. 316: 173-87. PMID 11829511 DOI: 10.1006/Jmbi.2001.5324 |
0.557 |
|
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