Wei Yang

Publications

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More Publications (Last OpenAlex import 11/5/24)

1. "Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment"
   2024 ▪ The Journal of Chemical Physics
   W. Yang; Jean-Philip Piquemal; Pengyu Ren; Michael J. Schnieders; Rose A Gogal; Aaron J Nessler; Andrew C Thiel; Hernan V Bernabe; Rae A Corrigan Grove; Leah M Cousineau; Jacob M Litman; Jacob M Miller; Guowei Qi; Matthew J Speranza; Mallory R Tollefson; Timothy D Fenn; Jacob J Michaelson; Okimasa Okada; Jay W Ponder; Jana Shen; Richard J H Smith;
   https://openalex.org/W4400294334
2. "Biomolecular Electrostatic Phenomena: An Evergreen Field"
   2023 ▪ The Journal of Physical Chemistry B
   W. Yang; Walter Rocchia;
   https://openalex.org/W4376133164
3. "Molecular Orientation of ?PO3H2 and ?COOH Functionalized Dyes on TiO2, Al2O3, ZrO2, and ITO: A Comparative Study"
   2023 ▪ The Journal of Physical Chemistry C
   Kenneth Hanson; Drake Beery; Dhruba Pattadar; Alex J. Robb; S. Scott Saavedra; W. Yang; Lianqing Zheng;
   https://openalex.org/W4318262978
4. "Molecular Dynamics and Free Energy Calculations of Dicyclohexano-18-crown-6 Diastereoisomers with Sm2+, Eu2+, Dy2+, Yb2+, Cf2+, and Three Halide Salts in Tetrahydrofuran and Acetonitrile Using the AMOEBA Force Field"
   2022 ▪ The Journal of Physical Chemistry B
   Thomas E. Albrecht?Schmitt; W. Yang; Pengyu Ren; Hesam Arabzadeh; Orlando Acevedo; Brandon Walker; Joseph M. Sperling;
   https://openalex.org/W4312115258
5. "Hydration of divalent lanthanides, Sm2+ and Eu2+: A molecular dynamics study with polarizable AMOEBA force field"
   2022 ▪ Journal of Computational Chemistry
   Thomas E. Albrecht?Schmitt; W. Yang; Pengyu Ren; Hesam Arabzadeh; Chengwen Liu; Orlando Acevedo;
   https://openalex.org/W4281713363
6. "Examining the Influence of Bilayer Structure on Energy Transfer and Molecular Photon Upconversion in Metal Ion Linked Multilayers"
   2020 ▪ The Journal of Physical Chemistry C
   Kenneth Hanson; Erica S. Knorr; Suliman Ayad; Ashley Arcidiacono; S. Scott Saavedra; W. Yang; Lianqing Zheng; Yan Zhou; Wendi Zhang; Jeffrey O. Ellison; Autumn N. Peters;
   https://openalex.org/W3092901940
7. "A fast and high-quality charge model for the next generation general AMBER force field"
   2020 ▪ The Journal of Chemical Physics
   W. Yang; Xibing He; Viet H. Man; Tai-Sung Lee; Junmei Wang;
   https://openalex.org/W3086801715
8. "Structural And Functional Versatility of Interferon?Inducible GTPases"
   2019 ▪ The FASEB Journal
   W. Yang; Qian Yin; Sayantan Roy; Bing Wang; Yuan Tian;
   https://openalex.org/W3176153189
9. "Ductile “Ice”: Frozen hydrogels with high ductility and compressive yielding strength"
   2019 ▪ Extreme Mechanics Letters
   W. Yang; Zi Liang Wu; Ping Rao; Tiefeng Li; Wei Hong; Xuxu Yang; Honghui Yu; Tuck-Whye Wong; Shaoxing Qu;
   https://openalex.org/W2918366543
10. "The missing links within troponin"
    2018 ▪ Archives of Biochemistry and Biophysics
    Jose R. Pinto; Michelle S. Parvatiyar; Mayra A. Marques; Guilherme A.P. de Oliveira; W. Yang;
    https://openalex.org/W2906425296
11. "External Pressures and Organizational Learning from Serious Errors: Evidence from Major Oil Spills"
    2017 ▪ Academy of Management Proceedings
    W. Yang; Francisco Polidoro;
    https://openalex.org/W2766195740
12. "Staining of Lipid Droplets with Monodansylpentane"
    2017 ▪ Methods in molecular biology
    W. Yang; Bo-Hua Chen; Huei-Jiun Yang; He-Yen Chou; Guang-Chao Chen;
    https://openalex.org/W2585714766
13. "Advanced Sampling for Molecular Simulation is Coming of Age"
    2016 ▪ Journal of Computational Chemistry
    W. Yang;
    https://openalex.org/W2296244237
14. "Generalized Ensemble Sampling of Enzyme Reaction Free Energy Pathways"
    2016 ▪ Methods in enzymology on CD-ROM/Methods in enzymology
    W. Yang; Mikolai Fajer; Xiaolin Cheng; D. Wu; L. Cao;
    https://openalex.org/W2474000726
15. "Predictive Sampling of Rare Conformational Events in Aqueous Solution: Designing a Generalized Orthogonal Space Tempering Method"
    2015 ▪ Journal of Chemical Theory and Computation
    W. Yang; Lianqing Zheng; Dongsheng Wu; Chao Lu; Xubin Li;
    https://openalex.org/W2191051800
16. "Free energy landscape of a minimalist salt bridge model"
    2015 ▪ Protein Science
    W. Yang; Lianqing Zheng; Chao Lv; Dongsheng Wu; Xubin Li; Karen M. Corbett;
    https://openalex.org/W1896659694
17. "Comparative exploration of hydrogen sulfide and water transmembrane free energy surfaces via orthogonal space tempering free energy sampling"
    2015 ▪ Journal of Computational Chemistry
    W. Yang; Lianqing Zheng; Chao Lv; Erick W. Aitchison; Dongsheng Wu; Xiaolin Cheng;
    https://openalex.org/W2129280934
18. "Post-transcriptional modifications to tRNA—a response to the genetic code degeneracy"
    2015 ▪ RNA
    W. Yang; Ya-Ming Hou; Howard Gamper;
    https://openalex.org/W2052492339
19. "Full Atom Simulations of Spin Label Conformations"
    2015 ▪ Methods in enzymology on CD-ROM/Methods in enzymology
    W. Yang; Mikolai Fajer; Piotr G. Fajer; Michael Zawrotny;
    https://openalex.org/W2416915225
20. "Payoffs, Not Tradeoffs, in the Adaptation of a Virus to Ostensibly Conflicting Selective Pressures"
    2014 ▪ PLoS Genetics
    W. Yang; Lianqing Zheng; Lindsey W. McGee; Erick W. Aitchison; S. Brian Caudle; Anneliese J. Morrison; Darin R. Rokyta;
    https://openalex.org/W2019933774
21. "Hydration Free Energy from Orthogonal Space Random Walk and Polarizable Force Field"
    2014 ▪ Journal of Chemical Theory and Computation
    W. Yang; Pengyu Ren; Jayvee R. Abella; Sara Y. Cheng; Qiantao Wang;
    https://openalex.org/W2320322094
22. "Do Spin Labels Tell the Truth?"
    2014 ▪ Biophysical Journal
    W. Yang; Michael Zawrotny; Peter Fajer; Fajer Mikolai;
    https://openalex.org/W2061263563
23. "Erratum: On?the?path random walk sampling for efficient optimization of minimum free energy path"
    2013 ▪ Journal of Computational Chemistry
    W. Yang; M. E. Chen;
    https://openalex.org/W4250544326
24. "Computer-Aided Drug Design: Using Numbers to Your Advantage"
    2013 ▪ ACS Medicinal Chemistry Letters
    W. Yang; John C. Faver; Kenneth M. Merz; Melek N. Ucisik;
    https://openalex.org/W2037927540
25. "Hidden Conformation Events in DNA Base Extrusions: A Generalized-Ensemble Path Optimization and Equilibrium Simulation Study"
    2013 ▪ Journal of Chemical Theory and Computation
    W. Yang; Chao Lv; Liaoran Cao;
    https://openalex.org/W2023537139
26. "Exploring shear yielding and strain localization at the die entry during extrusion of entangled melts"
    2012 ▪ Journal of Rheology
    W. Yang; Xiangyang Zhu; Shi-Qing Wang;
    https://openalex.org/W2022845617
27. "The Structure, Thermodynamics, and Solubility of Organic Crystals from Simulation with a Polarizable Force Field"
    2012 ▪ Journal of Chemical Theory and Computation
    W. Yang; Lianqing Zheng; Pengyu Ren; Michael J. Schnieders; Jonas Baltrusaitis; Yue Shi; Gaurav Chattree;
    https://openalex.org/W2091454857
28. "The Effects of Computational Modeling Errors on the Estimation of Statistical Mechanical Variables"
    2012 ▪ Journal of Chemical Theory and Computation
    W. Yang; John C. Faver; Kenneth M. Merz;
    https://openalex.org/W2036250557
29. "Modeling Structural Coordination and Ligand Binding in Zinc Proteins with a Polarizable Potential"
    2012 ▪ Journal of Chemical Theory and Computation
    W. Yang; Jiajing Zhang; Jean-Philip Piquemal; Pengyu Ren;
    https://openalex.org/W2069124995
30. "Practically Efficient and Robust Free Energy Calculations: Double-Integration Orthogonal Space Tempering"
    2012 ▪ Journal of Chemical Theory and Computation
    W. Yang; Lianqing Zheng;
    https://openalex.org/W2332177667
31. "Generalized essential energy space random walks to more effectively accelerate solute sampling in aqueous environment"
    2012 ▪ The Journal of Chemical Physics
    W. Yang; Lianqing Zheng; Chao Lv;
    https://openalex.org/W2095007841
32. "Evaluation of biological control agents of Ralstonia wilt on ginger. Biol Control"
    2012 ▪
    W. Yang; Quan Xu; Hong-Xia Liu; Yun-Peng Wang; Yong-Ming Wang; He-Tong Yang; Jian-Hua Guo;
    https://openalex.org/W2912763555
33. "Pharmaceutical Applications of the Polarizable Amoeba Potential, Including Protein-Ligand Binding Affinity and Drug Solubility, using the Force Field X Software"
    2012 ▪ Biophysical Journal
    W. Yang; Pengyu Ren; Michael J. Schnieders; Jonas Baltrusaitis; Yue Shi; Johnny Wu;
    https://openalex.org/W2079628089
34. "Allosteric Activation via Kinetic Control: Potassium Accelerates a Conformational Change in IMP Dehydrogenase"
    2011 ▪ Biochemistry
    W. Yang; Lianqing Zheng; Donghong Min; Helen R Josephine; Lizbeth Hedstrom; Thomas V. Riera;
    https://openalex.org/W2045626725
35. "Thermal Elimination of Precursors to Poly(phenylenevinylene) with a Macrocounterion versus a Small Counterion: A Coordinated Experimental and Simulation Study"
    2011 ▪ Macromolecules
    Joseph B. Schlenoff; W. Yang; Lianqing Zheng; Lara A. Al-Hariri;
    https://openalex.org/W1996997244
36. "Developing hybrid approaches to predict pKa values of ionizable groups"
    2011 ▪ Proteins Structure Function and Bioinformatics
    W. Yang; Shawn Witham; Kemper Talley; Lin Wang; Zhe Zhang; Subhra Sarkar; Daquan Gao; Emil Alexov;
    https://openalex.org/W2089579036
37. "Strain-Induced Molecular Reorientation and Birefringence Reversion of a Robust, Anisotropic Double-Network Hydrogel"
    2011 ▪ Macromolecules
    W. Yang; Hidemitsu Furukawa; Jian Ping Gong; Zi Liang Wu; Daisuke Sawada; Takayuki Kurokawa; Akira Kakugo;
    https://openalex.org/W2087703949
38. "Enhancing QM/MM Molecular Dynamics Sampling in Explicit Environments via an Orthogonal-Space-Random-Walk-Based Strategy"
    2011 ▪ The Journal of Physical Chemistry B
    Qing-Xiang Sang; M Schwartz; W. Yang; Lianqing Zheng; Mengen Chen; Donghong Min; Yonghao Jin;
    https://openalex.org/W2319864391
39. "Practically Efficient QM/MM Alchemical Free Energy Simulations: The Orthogonal Space Random Walk Strategy"
    2010 ▪ Journal of Chemical Theory and Computation
    W. Yang; Lianqing Zheng; Mengen Chen; Donghong Min; William Harris; Chao Lv;
    https://openalex.org/W2066425873
40. "Glycosidic Bond Conformation Preference Plays a Pivotal Role in Catalysis of RNA Pseudouridylation: A Combined Simulation and Structural Study"
    2010 ▪ Journal of Molecular Biology
    W. Yang; Mengen Chen; Hong Li; Jing Zhou; Chao Lv; Bo Liang;
    https://openalex.org/W2010511445
41. "Sampling Long Time Scale Protein Motions: OSRW Simulation of Active Site Loop Conformational Free Energies in Formyl-CoA:Oxalate CoA Transferase"
    2010 ▪ Journal of the American Chemical Society
    W. Yang; Mengen Chen; Sangbae Lee; Nigel G. J. Richards;
    https://openalex.org/W2085428477
42. "QM/MM Alchemical Free Energy Simulations: Challenges and Recent Developments"
    2010 ▪ Annual reports in computational chemistry
    Q. Cui; W. Yang; Hongzhi Li; Donghong Min;
    https://openalex.org/W48056008
43. "Structural Change of N-terminus in Smooth Muscle Myosin Regularly Light Chain using Accelerated Molecular Dynamics"
    2010 ▪ Biophysical Journal
    W. Yang; Lianqing Zheng; Zhuan Qin; Kenneth A. Taylor;
    https://openalex.org/W1974450135
44. "Structural basis of activation-dependent binding of ligand-mimetic antibody AL-57 to integrin LFA-1"
    2009 ▪ Proceedings of the National Academy of Sciences
    W. Yang; Timothy A. Springer; Motomu Shimaoka; Hongmin Zhang; Jin-huan Liu; Jia-huai Wang;
    https://openalex.org/W1975649958
45. "Molecular mechanisms of functional rescue mediated by P53 tumor suppressor mutations"
    2009 ▪ Biophysical Chemistry
    W. Yang; Ray Luo; Yu-Hong Tan; Y. Morris Chen; Xiang Ye; Qiang Lu; Vira Tretyachenko-Ladokhina; Donald F. Senear;
    https://openalex.org/W1966217539
46. "Mesoscopic Network Structure of a Semi?Rigid Polyion Complex Nested in a Polycationic Hydrogel"
    2009 ▪ Advanced Materials
    W. Yang; Hidemitsu Furukawa; Jian Ping Gong; Zi Liang Wu;
    https://openalex.org/W2158242908
47. "Roles of Boundary Conditions in DNA Simulations: Analysis of Ion Distributions with the Finite-Difference Poisson-Boltzmann Method"
    2009 ▪ Biophysical Journal
    W. Yang; Xiang Ye; Qin Cai; Ray Luo;
    https://openalex.org/W2029788853
48. "Simultaneous escaping of explicit and hidden free energy barriers: Application of the orthogonal space random walk strategy in generalized ensemble based conformational sampling"
    2009 ▪ The Journal of Chemical Physics
    W. Yang; Lianqing Zheng; Mengen Chen;
    https://openalex.org/W1992066600
49. "1D subsurface electromagnetic fields excited by energized steel casing"
    2009 ▪ Geophysics
    W. Yang; Carlos Torres-Verdín; Junsheng Hou; Zhiyi (Ian) Zhang;
    https://openalex.org/W2097017543
50. "On?the?path random walk sampling for efficient optimization of minimum free?energy path"
    2009 ▪ Journal of Computational Chemistry
    W. Yang; Mengen Chen;
    https://openalex.org/W2153466219
51. "CHARMM: The biomolecular simulation program"
    2009 ▪ Journal of Computational Chemistry
    B. R. Brooks; C. L. Brooks; A. D. Mackerell; L. Nilsson; R. J. Petrella; B. Roux; Y. Won; G. Archontis; C. Bartels; S. Boresch; A. Caflisch; L. Caves; Q. Cui; A. R. Dinner; M. Feig; S. Fischer; J. Gao; M. Hodoscek; W. Im; K. Kuczera; T. Lazaridis; J. Ma; V. Ovchinnikov; E. Paci; R. W. Pastor; C. B. Post; J. Z. Pu; M. Schaefer; B. Tidor; R. M. Venable; H. L. Woodcock; X. Wu; W. Yang; D. M. York; M. Karplus;
    https://openalex.org/W2132262459
52. "Molecular Dynamics Simulation Reveals The Role Of Cross-linkers In Semi-flexible Filament Assembly"
    2009 ▪ Biophysical Journal
    Linda S. Hirst; W. Yang; Lam T. Nguyen;
    https://openalex.org/W2073027391
53. "Molecular dynamics simulation of F-actin reveals the role of cross-linkers in semi-flexible filament assembly"
    2009 ▪ Soft Matter
    Linda S. Hirst; W. Yang; Lam T. Nguyen; Qi Wang;
    https://openalex.org/W2092288865
54. "Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems"
    2008 ▪ Proceedings of the National Academy of Sciences
    W. Yang; Lianqing Zheng; Mengen Chen;
    https://openalex.org/W1984604072
55. "Highly Extensible Double?Network Gels with Self?Assembling Anisotropic Structure"
    2008 ▪ Advanced Materials
    W. Yang; Hidemitsu Furukawa; Jian Ping Gong;
    https://openalex.org/W2021927779
56. "On the simulated scaling based free energy simulations: Adaptive optimization of the scaling parameter intervals"
    2008 ▪ The Journal of Chemical Physics
    W. Yang; Lianqing Zheng;
    https://openalex.org/W1997177076
57. "An Enzymatic Atavist Revealed in Dual Pathways for Water Activation"
    2008 ▪ PLoS Biology
    W. Yang; Donghong Min; Helen R Josephine; Hongzhi Li; Clemens Lakner; Iain S MacPherson; Gavin J. P Naylor; David Swofford; Lizbeth Hedstrom;
    https://openalex.org/W2078482632
58. "A hybrid recursion method to robustly ensure convergence efficiencies in the simulated scaling based free energy simulations"
    2008 ▪ The Journal of Chemical Physics
    W. Yang; Lianqing Zheng; Bernd A. Berg; Irina Carbone; Alexey Lugovskoy;
    https://openalex.org/W2045367444
59. "Essential energy space random walks to accelerate molecular dynamics simulations: Convergence improvements via an adaptive-length self-healing strategy"
    2008 ▪ The Journal of Chemical Physics
    W. Yang; Lianqing Zheng;
    https://openalex.org/W2031035403
60. "Energy difference space random walk to achieve fast free energy calculations"
    2008 ▪ The Journal of Chemical Physics
    W. Yang; Donghong Min;
    https://openalex.org/W1992569857
61. "A divide-and-conquer strategy to improve diffusion sampling in generalized ensemble simulations"
    2008 ▪ The Journal of Chemical Physics
    W. Yang; Donghong Min;
    https://openalex.org/W1995354251
62. "Efficient sampling of ion motions in molecular dynamics simulations on DNA: Variant Hamiltonian replica exchange method"
    2008 ▪ Chemical Physics Letters
    W. Yang; Hongzhi Li; Guohui Li; Bernd A. Berg; Donghong Min; Marcia O. Fenley;
    https://openalex.org/W2031166494
63. "Self-Assembling Structure in Solution of a Semirigid Polyelectrolyte"
    2008 ▪ Macromolecules
    W. Yang; Hidemitsu Furukawa; Jian Ping Gong; Yukari Shigekura; Kazuhiro Shikinaka; Yoshihito Osada;
    https://openalex.org/W2001788342
64. "Numerical calculation of the combinatorial entropy of partially ordered ice"
    2007 ▪ The Journal of Chemical Physics
    W. Yang; Bernd A. Berg;
    https://openalex.org/W3098163864
65. "Quantifying Intrinsic Specificity: A Potential Complement to Affinity in Drug Screening"
    2007 ▪ Physical Review Letters
    W. Yang; Jin Wang; Xiliang Zheng; Yongliang Yang; Dale Drueckhammer; Gennardy Verkhivker; Erkang Wang;
    https://openalex.org/W2062792348
66. "Mapping Electron Paramagnetic Resonance Spin Label Conformations by the Simulated Scaling Method"
    2007 ▪ Journal of the American Chemical Society
    W. Yang; Hongzhi Li; Mikolai Fajer; Piotr G. Fajer;
    https://openalex.org/W2094886980
67. "Essential energy space random walk via energy space metadynamics method to accelerate molecular dynamics simulations"
    2007 ▪ The Journal of Chemical Physics
    W. Yang; Donghong Min; Hongzhi Li; Yusong Liu;
    https://openalex.org/W2084728700
68. "Quantitative computer simulations of biomolecules: A snapshot"
    2007 ▪ Journal of Computational Chemistry
    Huan-Xiang Zhou; W. Yang; Bernd A. Berg; Hugh Nymeyer; Rafael Brüschweiler;
    https://openalex.org/W2113346257
69. "Alternative Conformations of the Archaeal Nop56/58-Fibrillarin Complex Imply Flexibility in Box C/D RNPs"
    2007 ▪ Journal of Molecular Biology
    W. Yang; Hongzhi Li; Sri Oruganti; Yanming Zhang; Howard Robinson; Michael P. Terns; Rebecca M. Terns; Hong Li;
    https://openalex.org/W2067456654
70. "'In-line attack' conformational effect plays a modest role in an enzyme-catalyzed RNA cleavage: a free energy simulation study"
    2007 ▪ Nucleic Acids Research
    W. Yang; Donghong Min; Hong Li; S. Xue;
    https://openalex.org/W2130328997
71. "On the convergence improvement in the metadynamics simulations: A Wang-Landau recursion approach"
    2007 ▪ The Journal of Chemical Physics
    W. Yang; Donghong Min; Yusong Liu; Irina Carbone;
    https://openalex.org/W2094695023
72. "Synergistic approach to improve “alchemical” free energy calculation in rugged energy surface"
    2007 ▪ The Journal of Chemical Physics
    W. Yang; Ryan Bitetti-Putzer; Hongzhi Li; Guohui Li; Donghong Min;
    https://openalex.org/W1594503666
73. "Nature of “Hydrogen Bond” in the Diborane?Benzene Complex: Covalent, Electrostatic, or Dispersive?"
    2007 ▪ Inorganic Chemistry
    W. Yang; Hongzhi Li; Donghong Min; Sheldon G. Shore; William N. Lipscomb;
    https://openalex.org/W1993467583
74. "Forging the missing link in free energy estimations: ?-WHAM in thermodynamic integration, overlap histogramming, and free energy perturbation"
    2007 ▪ Chemical Physics Letters
    W. Yang; Hongzhi Li;
    https://openalex.org/W2063631800
75. "Sampling enhancement for the quantum mechanical potential based molecular dynamics simulations: A general algorithm and its extension for free energy calculation on rugged energy surface"
    2007 ▪ The Journal of Chemical Physics
    W. Yang; Hongzhi Li;
    https://openalex.org/W1979883283
76. "Anisotropic Gelation Seeded by a Rod-Like Polyelectrolyte"
    2007 ▪ Macromolecules
    W. Yang; Hidemitsu Furukawa; Jian Ping Gong; Yukari Shigekura; Yoshihito Osada; Yong Mei Chen; Tatsuo Kaneko;
    https://openalex.org/W1989705795
77. "Simulated scaling method for localized enhanced sampling and simultaneous “alchemical” free energy simulations: A general method for molecular mechanical, quantum mechanical, and quantum mechanical/molecular mechanical simulations"
    2007 ▪ The Journal of Chemical Physics
    W. Yang; Hongzhi Li; Mikolai Fajer;
    https://openalex.org/W2052471564
78. "Finite reservoir replica exchange to enhance canonical sampling in rugged energy surfaces"
    2006 ▪ The Journal of Chemical Physics
    W. Yang; Hongzhi Li; Guohui Li; Bernd A. Berg;
    https://openalex.org/W2010386565
79. "A Small Molecule Agonist of an Integrin, ?L?2"
    2006 ▪ Journal of Biological Chemistry
    W. Yang; Minsoo Kim; Christopher V. Carman; Azucena Salas; Timothy A. Springer; Motomu Shimaoka;
    https://openalex.org/W2143510208
80. "AL-57, a ligand-mimetic antibody to integrin LFA-1, reveals chemokine-induced affinity up-regulation in lymphocytes"
    2006 ▪ Proceedings of the National Academy of Sciences
    W. Yang; Minsoo Kim; Azucena Salas; Timothy A. Springer; Motomu Shimaoka; Edward H. Cohen; Nathan Astrof; Dan Peer; Audrey Ferrand;
    https://openalex.org/W2112043257
81. "Regulation of outside-in signaling and affinity by the ?2I domain of integrin ?L?2"
    2006 ▪ Proceedings of the National Academy of Sciences
    W. Yang; Minsoo Kim; Christopher V. Carman; Timothy A. Springer; JianFeng Chen;
    https://openalex.org/W1501066791
82. "Conformational sampling via a self-regulating effective energy surface"
    2006 ▪ The Journal of Chemical Physics
    A. R. Dinner; W. Yang; M. Karplus; Ryan Bitetti-Putzer;
    https://openalex.org/W2024900053
83. "Living Cells as Test Tubes"
    2006 ▪ Science
    W. Yang; X. Sunney Xie; Ji Yu;
    https://openalex.org/W2138857126
84. "Binary and Ternary Aggregation within Tethered Protein Constructs"
    2006 ▪ Biophysical Journal
    W. Yang; Martin Gruebele;
    https://openalex.org/W2023562343
85. "Thermodynamics and kinetic analysis of F0F1-ATPase"
    2006 ▪ Elsevier eBooks
    W. Yang; M. Karplus; Yi Qin Gao;
    https://openalex.org/W2479012819
86. "A Structure-Based Model for the Synthesis and Hydrolysis of ATP by F1-ATPase"
    2005 ▪ Cell
    W. Yang; M. Karplus; Yi Qin Gao;
    https://openalex.org/W2031045201
87. "Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA"
    2005 ▪ Nature
    W. Yang; M. Karplus; Anirban Banerjee; Gregory L. Verdine;
    https://openalex.org/W2077615862
88. "Kinetic equivalence of the heat and cold structural transitions of ? 6–85"
    2005 ▪ Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences
    W. Yang; Martin Gruebele;
    https://openalex.org/W1995460539
89. "Numerical simulation of dual?laterolog measurements in the presence of dipping, anisotropic, and invaded rock formations"
    2005 ▪
    W. Yang; Carlos Torres-Verdín;
    https://openalex.org/W1964216001
90. "The primacy of affinity over clustering in regulation of adhesiveness of the integrin ?L?2"
    2004 ▪ The Journal of Cell Biology
    W. Yang; Minsoo Kim; Christopher V. Carman; Azucena Salas; Timothy A. Springer;
    https://openalex.org/W2006657990
91. "Protein structural transitions and their functional role"
    2004 ▪ Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences
    Arjan van der Vaart; J. Ma; W. Yang; M. Karplus; Yi Qin Gao;
    https://openalex.org/W1996191001
92. "Rate?Temperature Relationships in ?-Repressor Fragment ?6-85 Folding"
    2004 ▪ Biochemistry
    W. Yang; Martin Gruebele;
    https://openalex.org/W2066952483
93. "A similarity measure for partially folded proteins: application to unfolded and native-like conformational fluctuations"
    2004 ▪ Chemical Physics
    W. Yang; Martin Gruebele; Edgar Larios; K. Schulten;
    https://openalex.org/W2070439872
94. "CARS microscopy lights up lipids in living cells"
    2004 ▪
    W. Yang; X. Sunney Xie; Xiaolin Nan;
    https://openalex.org/W2596514872
95. "Folding ?-Repressor at Its Speed Limit"
    2004 ▪ Biophysical Journal
    W. Yang; Martin Gruebele;
    https://openalex.org/W2062759724
96. "Detection-Dependent Kinetics as a Probe of Folding Landscape Microstructure"
    2004 ▪ Journal of the American Chemical Society
    W. Yang; Martin Gruebele;
    https://openalex.org/W2019079366
97. "Chaperoned alchemical free energy simulations: A general method for QM, MM, and QM/MM potentials"
    2004 ▪ The Journal of Chemical Physics
    W. Yang; M. Karplus; Ryan Bitetti-Putzer;
    https://openalex.org/W2052553173
98. "Intersubunit signal transmission in integrins by a receptor-like interaction with a pull spring"
    2004 ▪ Proceedings of the National Academy of Sciences
    W. Yang; Azucena Salas; Timothy A. Springer; Motomu Shimaoka; Junichi Takagi;
    https://openalex.org/W2015826818
99. "Activation of integrin ?-subunit I-like domains by one-turn C-terminal ?-helix deletions"
    2004 ▪ Proceedings of the National Academy of Sciences
    W. Yang; Timothy A. Springer; Motomu Shimaoka; JianFeng Chen;
    https://openalex.org/W2013379647
100. "Free energy simulations: Use of reverse cumulative averaging to determine the equilibrated region and the time required for convergence"
     2004 ▪ The Journal of Chemical Physics
     W. Yang; M. Karplus; Ryan Bitetti-Putzer;
     https://openalex.org/W2064060593
101. "Heterogeneous Folding of the trpzip Hairpin: Full Atom Simulation and Experiment"
     2003 ▪ Journal of Molecular Biology
     W. Yang; Martin Gruebele; Jed W. Pitera; William C. Swope;
     https://openalex.org/W2063742152
102. "On the Extended ?-Conformation Propensity of Polypeptides at High Temperature"
     2003 ▪ Journal of the American Chemical Society
     W. Yang; Martin Gruebele; Edgar Larios;
     https://openalex.org/W1970829620
103. "Structural Biology of the Cell Adhesion Protein CD2: From Molecular Recognition to Protein Folding and Design"
     2003 ▪ Current Protein and Peptide Science
     W. Yang; A. Wilkins; J. Yang;
     https://openalex.org/W2008797861
104. "A model for the cooperative free energy transduction and kinetics of ATP hydrolysis by F 1 -ATPase"
     2003 ▪ Proceedings of the National Academy of Sciences
     W. Yang; M. Karplus; Yi Qin Gao; Rudolph A. Marcus;
     https://openalex.org/W2031187997
105. "Small Molecule Integrin Antagonists that Bind to the ?2 Subunit I-like Domain and Activate Signals in One Direction and Block Them in the Other"
     2003 ▪ Immunity
     W. Yang; Azucena Salas; Timothy A. Springer; Motomu Shimaoka; Gabriele Weitz-Schmidt;
     https://openalex.org/W2085979652
106. "Generalized ensembles serve to improve the convergence of free energy simulations"
     2003 ▪ Chemical Physics Letters
     W. Yang; M. Karplus; Ryan Bitetti-Putzer;
     https://openalex.org/W2113640492
107. "Folding at the speed limit"
     2003 ▪ Nature
     W. Yang; Martin Gruebele;
     https://openalex.org/W1972675000
108. "Product-assisted catalysis in base-excision DNA repair"
     2003 ▪ Nature Structural & Molecular Biology
     W. Yang; M. Karplus; Gregory L. Verdine; J. Christopher Fromme; Steven D. Bruner;
     https://openalex.org/W2077486912
109. "The missing link between thermodynamics and structure in F 1 -ATPase"
     2003 ▪ Proceedings of the National Academy of Sciences
     Q. Cui; J. Ma; W. Yang; M. Karplus; Yi Qin Gao;
     https://openalex.org/W2064927549
110. "Folding Thermodynamic and Kinetic Characterization of Small Model Proteins: Lambda Repressor, U1A, Trpzip2 and PAO -12"
     2003 ▪
     W. Yang;
     https://openalex.org/W2594633502
111. "Fermentation of starch for enhanced alkaline protease production by constructing an alkalophilic Bacillus pumilus strain"
     2001 ▪ Applied Microbiology and Biotechnology
     W. Yang; Feng Y.; Ong S.; Hu J.; Ng W.;
     https://openalex.org/W2026314765
112. "Transition from Exponential to Nonexponential Kinetics during Formation of a Nonbiological Helix"
     2000 ▪ Journal of the American Chemical Society
     W. Yang; Martin Gruebele; Ryan B. Prince; Jobiah Sabelko; Jeffrey S. Moore;
     https://openalex.org/W2021123356