| Year |
Citation |
Score |
| 2020 |
Sullivan HJ, Chen B, Wu C. A molecular dynamics study on the binding of an anti-cancer DNA G-quadruplex stabilizer, CX-5461, to human telomeric, cKIT-1, and c-Myc G-quadruplexes and a DNA duplex. Journal of Chemical Information and Modeling. PMID 32820923 DOI: 10.1021/Acs.Jcim.0C00632 |
0.324 |
|
| 2020 |
Kumar V, Hoag H, Sader S, Scorese N, Liu H, Wu C. GDP Release from the Open Conformation of Gα Requires Allosteric Signaling from the Agonist-Bound Human β Adrenergic Receptor. Journal of Chemical Information and Modeling. PMID 32786510 DOI: 10.1021/Acs.Jcim.0C00432 |
0.353 |
|
| 2020 |
Sullivan HJ, Wang X, Nogle S, Liao S, Wu C. To Probe Full and Partial Activation of Human Peroxisome Proliferator-Activated Receptors by Pan-Agonist Chiglitazar Using Molecular Dynamics Simulations. Ppar Research. 2020: 5314187. PMID 32308671 DOI: 10.1155/2020/5314187 |
0.377 |
|
| 2020 |
Uba AI, Radicella C, Readmond C, Scorese N, Liao S, Liu H, Wu C. Binding of agonist WAY-267,464 and antagonist WAY-methylated to oxytocin receptor probed by all-atom molecular dynamics simulations. Life Sciences. 117643. PMID 32298738 DOI: 10.1016/J.Lfs.2020.117643 |
0.328 |
|
| 2020 |
Sullivan HJ, Tursi A, Moore K, Campbell A, Floyd C, Wu C. Binding interactions of ergotamine and dihydroergotamine to 5-hydroxytryptamine receptor 1B (5-HT1b) using Molecular Dynamics Simulations and Dynamic Network Analysis. Journal of Chemical Information and Modeling. PMID 32078320 DOI: 10.1021/Acs.Jcim.9B01082 |
0.367 |
|
| 2020 |
Liao S, Floyd C, Verratti N, Leung L, Wu C. Analysis of vismodegib resistance in D473G and W535L mutants of SMO receptor and design of novel drug derivatives using molecular dynamics simulations. Life Sciences. 117302. PMID 31953165 DOI: 10.1016/J.Lfs.2020.117302 |
0.3 |
|
| 2019 |
Mulholland K, Sullivan HJ, Garner J, Cai J, Chen B, Wu C. 3D Structure of RNA Monomeric G-Quadruplex Containing ALS and FTD Related G4C2 Repeat and It's Binding with TMPyP4 Probed by Homology Modelling based on Experimental Constraints and Molecular Dynamics Simulations. Acs Chemical Neuroscience. PMID 31800202 DOI: 10.1021/Acschemneuro.9B00572 |
0.323 |
|
| 2019 |
Keck TM, Free RB, Day MM, Brown SL, Maddaluna MS, Fountain G, Cooper C, Fallon B, Holmes M, Stang C, Burkhardt R, Bonifazi A, Ellenberger MP, Newman AH, Sibley DR, ... Wu C, et al. Dopamine D4 Receptor-Selective Compounds Reveal Structure-Activity Relationships that Engender Agonist Efficacy. Journal of Medicinal Chemistry. PMID 30883109 DOI: 10.1021/Acs.Jmedchem.9B00231 |
0.306 |
|
| 2019 |
Machireddy B, Sullivan HJ, Wu C. Binding of BRACO19 to a Telomeric G-Quadruplex DNA Probed by All-Atom Molecular Dynamics Simulations with Explicit Solvent. Molecules (Basel, Switzerland). 24. PMID 30871220 DOI: 10.3390/Molecules24061010 |
0.344 |
|
| 2018 |
Montgomery D, Campbell A, Sullivan HJ, Wu C. Molecular Dynamics Simulation of Biased Agonists at the Dopamine D2 Receptor Suggests the Mechanism of Receptor Functional Selectivity. Journal of Biomolecular Structure & Dynamics. 1-49. PMID 30124143 DOI: 10.1080/07391102.2018.1513378 |
0.346 |
|
| 2018 |
Ilitchev AI, Giammona MJ, Olivas C, Claud SL, Cantrell KL, Wu C, Buratto SK, Bowers MT. Hetero-oligomeric Amyloid Assembly and Mechanism: Prion Fragment PrP(106-126) Catalyzes the Islet Amyloid Polypeptide β-Hairpin. Journal of the American Chemical Society. PMID 29989407 DOI: 10.1021/Jacs.8B05925 |
0.33 |
|
| 2017 |
Sader S, Anant K, Wu C. To probe interaction of morphine and IBNtxA with 7TM and 6TM variants of the human μ-opioid receptor using all-atom molecular dynamics simulations with an explicit membrane. Physical Chemistry Chemical Physics : Pccp. PMID 29265141 DOI: 10.1039/C7Cp06745C |
0.303 |
|
| 2017 |
Machireddy B, Kalra G, Jonnalagadda SC, Ramanujachary KV, Wu C. Probing the binding pathway of BRACO19 to a parallel-stranded human telomeric G-quadruplex using molecular dynamics binding simulation with AMBER DNA OL15 and ligand GAFF2 force fields. Journal of Chemical Information and Modeling. PMID 29028340 DOI: 10.1021/Acs.Jcim.7B00287 |
0.354 |
|
| 2017 |
Shen Z, Mulholland KA, Zheng Y, Wu C. Binding of anticancer drug daunomycin to a TGGGGT G-quadruplex DNA probed by all-atom molecular dynamics simulations: additional pure groove binding mode and implications on designing more selective G-quadruplex ligands. Journal of Molecular Modeling. 23: 256. PMID 28785893 DOI: 10.1007/S00894-017-3417-6 |
0.32 |
|
| 2017 |
Mulholland K, Siddiquei F, Wu C. Binding modes and pathway of RHPS4 to human telomeric G-quadruplex and duplex DNA probed by all-atom molecular dynamics simulations with explicit solvent. Physical Chemistry Chemical Physics : Pccp. PMID 28696445 DOI: 10.1039/C7Cp03313C |
0.326 |
|
| 2017 |
Sader S, Wu C. Computational analysis of Amsacrine resistance in human topoisomerase II alpha mutants (R487K and E571K) using homology modeling, docking and all-atom molecular dynamics simulation in explicit solvent. Journal of Molecular Graphics & Modelling. 72: 209-219. PMID 28110185 DOI: 10.1016/J.Jmgm.2016.11.019 |
0.351 |
|
| 2016 |
Mulholland KA, Wu C. Binding of Telomestatin to a Telomeric G-Quadruplex DNA Probed by All-Atom Molecular Dynamics Simulations with Explicit Solvent. Journal of Chemical Information and Modeling. PMID 27632666 DOI: 10.1021/Acs.Jcim.6B00473 |
0.347 |
|
| 2016 |
Levine ZA, Rapp MV, Wei W, Mullen RG, Wu C, Zerze GH, Mittal J, Waite JH, Israelachvili JN, Shea JE. Surface force measurements and simulations of mussel-derived peptide adhesives on wet organic surfaces. Proceedings of the National Academy of Sciences of the United States of America. PMID 27036002 DOI: 10.1073/Pnas.1603065113 |
0.312 |
|
| 2015 |
Wong AG, Wu C, Hannaberry E, Watson MD, Shea JE, Raleigh DP. Analysis of the Amyloidogenic Potential of Pufferfish (Takifugu rubripes) Islet Amyloid Polypeptide Highlights the Limitations of Thioflavin-T Assays and the Difficulties in Defining Amyloidogenicity. Biochemistry. PMID 26694855 DOI: 10.1021/Acs.Biochem.5B01107 |
0.318 |
|
| 2015 |
Zheng X, Wu C, Liu D, Li H, Bitan G, Shea JE, Bowers MT. Mechanism of C-Terminal Fragments of Amyloid β-Protein as Aβ Inhibitors: Do C-Terminal Interactions Play a Key Role in Their Inhibitory Activity? The Journal of Physical Chemistry. B. PMID 26439281 DOI: 10.1021/Acs.Jpcb.5B08177 |
0.317 |
|
| 2013 |
Bleiholder C, Do TD, Wu C, Economou NJ, Bernstein SS, Buratto SK, Shea JE, Bowers MT. Ion mobility spectrometry reveals the mechanism of amyloid formation of Aβ(25-35) and its modulation by inhibitors at the molecular level: epigallocatechin gallate and scyllo-inositol. Journal of the American Chemical Society. 135: 16926-37. PMID 24131107 DOI: 10.1021/Ja406197F |
0.322 |
|
| 2013 |
Wu C, Shea JE. Structural similarities and differences between amyloidogenic and non-amyloidogenic islet amyloid polypeptide (IAPP) sequences and implications for the dual physiological and pathological activities of these peptides. Plos Computational Biology. 9: e1003211. PMID 24009497 DOI: 10.1371/Journal.Pcbi.1003211 |
0.35 |
|
| 2012 |
Lei H, Wang X, Wu C. Early stage intercalation of doxorubicin to DNA fragments observed in molecular dynamics binding simulations. Journal of Molecular Graphics & Modelling. 38: 279-89. PMID 23079648 DOI: 10.1016/J.Jmgm.2012.05.006 |
0.339 |
|
| 2012 |
Wu C, Scott J, Shea JE. Binding of Congo red to amyloid protofibrils of the Alzheimer Aβ(9-40) peptide probed by molecular dynamics simulations. Biophysical Journal. 103: 550-7. PMID 22947871 DOI: 10.1016/J.Bpj.2012.07.008 |
0.347 |
|
| 2012 |
Gessel MM, Wu C, Li H, Bitan G, Shea JE, Bowers MT. Aβ(39-42) modulates Aβ oligomerization but not fibril formation. Biochemistry. 51: 108-17. PMID 22129303 DOI: 10.1021/Bi201520B |
0.344 |
|
| 2011 |
Dupuis NF, Wu C, Shea JE, Bowers MT. The amyloid formation mechanism in human IAPP: dimers have β-strand monomer-monomer interfaces. Journal of the American Chemical Society. 133: 7240-3. PMID 21517093 DOI: 10.1021/Ja1081537 |
0.335 |
|
| 2011 |
Wu C, Shea JE. Coarse-grained models for protein aggregation. Current Opinion in Structural Biology. 21: 209-20. PMID 21371882 DOI: 10.1016/J.Sbi.2011.02.002 |
0.302 |
|
| 2011 |
Wu C, Bowers MT, Shea JE. On the origin of the stronger binding of PIB over thioflavin T to protofibrils of the Alzheimer amyloid-β peptide: a molecular dynamics study. Biophysical Journal. 100: 1316-24. PMID 21354405 DOI: 10.1016/J.Bpj.2011.01.058 |
0.374 |
|
| 2010 |
Wu C, Shea JE. On the origins of the weak folding cooperativity of a designed ββα ultrafast protein FSD-1. Plos Computational Biology. 6: e1000998. PMID 21124953 DOI: 10.1371/Journal.Pcbi.1000998 |
0.302 |
|
| 2010 |
Wu C, Bowers MT, Shea JE. Molecular structures of quiescently grown and brain-derived polymorphic fibrils of the Alzheimer amyloid abeta9-40 peptide: a comparison to agitated fibrils. Plos Computational Biology. 6: e1000693. PMID 20221247 DOI: 10.1371/Journal.Pcbi.1000693 |
0.326 |
|
| 2010 |
Grabenauer M, Wu C, Soto P, Shea JE, Bowers MT. Oligomers of the prion protein fragment 106-126 are likely assembled from beta-hairpins in solution, and methionine oxidation inhibits assembly without altering the peptide's monomeric conformation. Journal of the American Chemical Society. 132: 532-9. PMID 20020713 DOI: 10.1021/Ja905595K |
0.326 |
|
| 2010 |
Jiang J, Wu Y, Wang Z, Wu C. Assessing the Performance of Popular Quantum Mechanics and Molecular Mechanics Methods and Revealing the Sequence-Dependent Energetic Features Using 100 Tetrapeptide Models Journal of Chemical Theory and Computation. 6: 1199-1209. DOI: 10.1021/Ct100008Q |
0.302 |
|
| 2009 |
Dupuis NF, Wu C, Shea JE, Bowers MT. Human islet amyloid polypeptide monomers form ordered beta-hairpins: a possible direct amyloidogenic precursor. Journal of the American Chemical Society. 131: 18283-92. PMID 19950949 DOI: 10.1021/Ja903814Q |
0.338 |
|
| 2009 |
Lei H, Wang ZX, Wu C, Duan Y. Dual folding pathways of an alpha/beta protein from all-atom ab initio folding simulations. The Journal of Chemical Physics. 131: 165105. PMID 19894980 DOI: 10.1063/1.3238567 |
0.326 |
|
| 2009 |
Wu C, Biancalana M, Koide S, Shea JE. Binding modes of thioflavin-T to the single-layer beta-sheet of the peptide self-assembly mimics. Journal of Molecular Biology. 394: 627-33. PMID 19799914 DOI: 10.1016/J.Jmb.2009.09.056 |
0.367 |
|
| 2009 |
Wu C, Murray MM, Bernstein SL, Condron MM, Bitan G, Shea JE, Bowers MT. The structure of Abeta42 C-terminal fragments probed by a combined experimental and theoretical study. Journal of Molecular Biology. 387: 492-501. PMID 19356595 DOI: 10.1016/J.Jmb.2009.01.029 |
0.335 |
|
| 2008 |
Wu C, Wang Z, Lei H, Duan Y, Bowers MT, Shea JE. The binding of thioflavin T and its neutral analog BTA-1 to protofibrils of the Alzheimer's disease Abeta(16-22) peptide probed by molecular dynamics simulations. Journal of Molecular Biology. 384: 718-29. PMID 18851978 DOI: 10.1016/J.Jmb.2008.09.062 |
0.377 |
|
| 2008 |
Lei H, Wu C, Wang ZX, Zhou Y, Duan Y. Folding processes of the B domain of protein A to the native state observed in all-atom ab initio folding simulations. The Journal of Chemical Physics. 128: 235105. PMID 18570534 DOI: 10.1063/1.2937135 |
0.351 |
|
| 2007 |
Wang ZX, Wu C, Lei H, Duan Y. Accurate ab Initio Study on the Hydrogen-Bond Pairs in Protein Secondary Structures. Journal of Chemical Theory and Computation. 3: 1527-1537. PMID 26221082 DOI: 10.1021/Ct700021F |
0.316 |
|
| 2007 |
Lei H, Wu C, Liu H, Duan Y. Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations. Proceedings of the National Academy of Sciences of the United States of America. 104: 4925-30. PMID 17360390 DOI: 10.1073/Pnas.0608432104 |
0.322 |
|
| 2007 |
Wu C, Wang Z, Lei H, Zhang W, Duan Y. Dual binding modes of Congo red to amyloid protofibril surface observed in molecular dynamics simulations. Journal of the American Chemical Society. 129: 1225-32. PMID 17263405 DOI: 10.1021/Ja0662772 |
0.359 |
|
| 2006 |
Wu C, Lei H, Wang Z, Zhang W, Duan Y. Phenol red interacts with the protofibril-like oligomers of an amyloidogenic hexapeptide NFGAIL through both hydrophobic and aromatic contacts. Biophysical Journal. 91: 3664-72. PMID 16935948 DOI: 10.1529/Biophysj.106.081877 |
0.369 |
|
| 2006 |
Wang ZX, Zhang W, Wu C, Lei H, Cieplak P, Duan Y. Strike a balance: optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides. Journal of Computational Chemistry. 27: 781-90. PMID 16526038 DOI: 10.1002/Jcc.20386 |
0.313 |
|
| 2006 |
Lei H, Wu C, Wang Z, Duan Y. Molecular dynamics simulations and free energy analyses on the dimer formation of an amyloidogenic heptapeptide from human beta2-microglobulin: implication for the protofibril structure. Journal of Molecular Biology. 356: 1049-63. PMID 16403526 DOI: 10.1016/J.Jmb.2005.11.087 |
0.36 |
|
| 2005 |
Zhang W, Wu C, Duan Y. Convergence of replica exchange molecular dynamics. The Journal of Chemical Physics. 123: 154105. PMID 16252940 DOI: 10.1063/1.2056540 |
0.325 |
|
| 2005 |
Wu C, Lei H, Duan Y. Elongation of ordered peptide aggregate of an amyloidogenic hexapeptide NFGAIL observed in molecular dynamics simulations with explicit solvent. Journal of the American Chemical Society. 127: 13530-7. PMID 16190716 DOI: 10.1021/Ja050767X |
0.346 |
|
| 2005 |
Wu C, Lei H, Duan Y. The role of Phe in the formation of well-ordered oligomers of amyloidogenic hexapeptide (NFGAIL) observed in molecular dynamics simulations with explicit solvent. Biophysical Journal. 88: 2897-906. PMID 15653723 DOI: 10.1529/Biophysj.104.055574 |
0.346 |
|
| 2004 |
Wu C, Lei H, Duan Y. Formation of partially ordered oligomers of amyloidogenic hexapeptide (NFGAIL) in aqueous solution observed in molecular dynamics simulations. Biophysical Journal. 87: 3000-9. PMID 15326028 DOI: 10.1529/Biophysj.104.047076 |
0.348 |
|
| 2003 |
Duan Y, Wu C, Chowdhury S, Lee MC, Xiong G, Zhang W, Yang R, Cieplak P, Luo R, Lee T, Caldwell J, Wang J, Kollman P. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. Journal of Computational Chemistry. 24: 1999-2012. PMID 14531054 DOI: 10.1002/Jcc.10349 |
0.31 |
|
| 2003 |
Chowdhury S, Zhang W, Wu C, Xiong G, Duan Y. Breaking non-native hydrophobic clusters is the rate-limiting step in the folding of an alanine-based peptide. Biopolymers. 68: 63-75. PMID 12579580 DOI: 10.1002/Bip.10216 |
0.32 |
|
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