| CHARMM: the biomolecular simulation program BR Brooks, CL Brooks, AD MacKerell, L Nilsson, RJ Petrella, B Roux, ... Journal of Computational Chemistry 30 (10), 1545-1614, 2009 | 8550 | 2009 |
| Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA A Banerjee, W Yang, M Karplus, GL Verdine Nature 434 (7033), 612-618, 2005 | 422 | 2005 |
| Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems L Zheng, M Chen, W Yang Proceedings of the National Academy of Sciences 105 (51), 20227-20232, 2008 | 332 | 2008 |
| Computer‐guided design in molecular recognition: Design and synthesis of a glucopyranose receptor W Yang, H He, DG Drueckhammer Angewandte Chemie International Edition 40 (9), 1714-1718, 2001 | 292 | 2001 |
| A fast and high-quality charge model for the next generation general AMBER force field X He, VH Man, W Yang, TS Lee, J Wang The Journal of Chemical Physics 153 (11), 114502, 2020 | 230 | 2020 |
| Product-assisted catalysis in base-excision DNA repair JC Fromme, SD Bruner, W Yang, M Karplus, GL Verdine Nature Structural Biology 10 (3), 204-211, 2003 | 203 | 2003 |
| A structure-based model for the synthesis and hydrolysis of ATP by F1-ATPase YQ Gao, W Yang, M Karplus Cell 123 (2), 195-205, 2005 | 177 | 2005 |
| Understanding the relative acyl-transfer reactivity of oxoesters and thioesters: Computational analysis of transition state delocalization effects W Yang, DG Drueckhammer Journal of the American Chemical Society 123 (44), 11004-11009, 2001 | 155 | 2001 |
| The missing link between thermodynamics and structure in F1-ATPase W Yang, YQ Gao, Q Cui, J Ma, M Karplus Proceedings of the National Academy of Sciences 100 (3), 874-879, 2003 | 131 | 2003 |
| Modeling structural coordination and ligand binding in zinc proteins with a polarizable potential J Zhang, W Yang, JP Piquemal, P Ren Journal of Chemical Theory and Computation 8 (4), 1314-1324, 2012 | 126 | 2012 |
| Free energy simulations: Use of reverse cumulative averaging to determine the equilibrated region and the time required for convergence W Yang, R Bitetti-Putzer, M Karplus The Journal of Chemical Physics 120, 2618, 2004 | 118 | 2004 |
| Simultaneous escaping of explicit and hidden free energy barriers: Application of the orthogonal space random walk strategy in generalized ensemble based conformational sampling L Zheng, M Chen, W Yang The Journal of Chemical Physics 130, 234105, 2009 | 105 | 2009 |
| Practically efficient and robust free energy calculations: Double-integration orthogonal space tempering L Zheng, W Yang Journal of Chemical Theory and Computation 8 (3), 810-823, 2012 | 103 | 2012 |
| Simulated scaling method for localized enhanced sampling and simultaneous “alchemical” free energy simulations: A general method for molecular mechanical, quantum mechanical … H Li, M Fajer, W Yang The Journal of Chemical Physics 126, 024106, 2007 | 102 | 2007 |
| Computational studies of the aminolysis of oxoesters and thioesters in aqueous solution W Yang, DG Drueckhammer Organic Letters 2 (26), 4133-4136, 2000 | 101 | 2000 |
| The structure, thermodynamics, and solubility of organic crystals from simulation with a polarizable force field MJ Schnieders, J Baltrusaitis, Y Shi, G Chattree, L Zheng, W Yang, P Ren Journal of Chemical Theory and Computation 8 (5), 1721-1736, 2012 | 93 | 2012 |
| Generalized ensembles serve to improve the convergence of free energy simulations R Bitetti-Putzer, W Yang, M Karplus Chemical Physics Letters 377 (5), 633-641, 2003 | 68 | 2003 |
| A model for the cooperative free energy transduction and kinetics of ATP hydrolysis by F1-ATPase YQ Gao, W Yang, RA Marcus, M Karplus Proceedings of the National Academy of Sciences 100 (20), 11339-11344, 2003 | 66 | 2003 |
| Protein structural transitions and their functional role M Karplus, YQ Gao, J Ma, A van der Vaart, W Yang Philosophical Transactions of the Royal Society A: Mathematical, Physical …, 2005 | 65 | 2005 |
| Finite reservoir replica exchange to enhance canonical sampling in rugged energy surfaces H Li, G Li, BA Berg, W Yang The Journal of Chemical Physics 125 (14), 144902, 2006 | 60 | 2006 |
Lianqing ZhengInstitute of Molecular Biophysics, Florida State UniversityVerified email at fsu.edu
