Publications
Refereed Journal Articles
Yang, W., Cao, L. R., Lv, C., & Chen, M. E. (submitted). On reaction coordinates describing DNA base extrusions: A combined on-the-path random walk path optimization and generalized ensemble simulation study. J. Chem. Theor. Comput. Manuscript submitted for publication.
Yang, W., & Lv, C. (submitted). Determinants of small molecule localization and orientation in lipid bilayers: Orthogonal space tempering potential of mean force calculations. J. Amer. Chem. Soc. Manuscript submitted for publication.
Yang, W., Faver, J. C., & Merz, K. M. (2012). The effects of computational modeling errors on the estimation of statistical mechanical variables. J. Chem. Theor. Comput, ASAP.
Lv, C., Zheng, L. Q., & Yang, W. (2012). Generalized essential energy space random walks to more effectively accelerate solute sampling in aqueous environment. J. Chem. Phys, 136, 044103. Link
Yang, W., Schnieders, M. J., Baltrusaitis, J., Shi, Y., Chattree, G., Zheng, L. Q., & Ren, P. Y. (2012). The structure, thermodynamics, and solubility of organic crystals from simulation with a polarizable force field. J. Chem. Theor. Comput, ASAP.
Yang, W., Zheng, J. J., Piquemal, J. P., & Ren, P. Y. (2012). Modeling structural coordination and ligand binding in Zinc proteins with a polarizable potential. J. Chem. Theor. Comput, 8, 1314-1324. Link
Yang, W., & Zheng, L. Q. (2012). Practically efficient and robust free energy calculations: Double-integration orthogonal space tempering. J. Chem. Theor. Comput, 8, 810–823.
Yang, W., Al-Hariri, L. A., Zheng, L. Q., & Schlenoff, J. B. (2011). Thermal elimination of precursors to poly(phenylenevinylene) with a macrocounterion versus a small counterion: A coordinated experimental and simulation study. Macromolecules, 44, 6663–6668.
Yang, W., Min, D. H., Chen, M. E., Zheng, L. Q., Jin, Y. H., Schwartz, M. A., & Sang, Q. X. A. (2011). Enhancing QM/MM molecular dynamics sampling in explicit environments via an orthogonal space random walk based strategy. J. Phys. Chem. B, 115, 3924-3935
Yang, W., Riera, T. V., Zheng, L. Q., Josephine, H. R., Min, D., & Hedstrom, L. (2011). Allosteric activation via kinetic control: Potassium accelerates a conformational change in IMP Dehydrogenase. Biochemistry, 50, 8508–8518.
Yang, W., Witham, S., Talley, K., Wang, L., Zhang, Z., Sarkar, S., Gao, D., & Alexov, E. (2011). Developing hybrid approaches to predict pKa values of ionizable groups. Proteins: Struct. Funct. Bioinf, 79, 3389–3399.
Lee, S., Chen, M., Yang, W., & Richards, N. G. J. (2010). Sampling long timescale protein motions: OSRW simulation of active site loop conformational free energies in formyl-CoA:oxalate CoA transferase. Journal of the American Chemical Society, 132, 7252–7253.
This paper reports orthogonal space random walk algorithm based simulation studies of active site loop conformational free energies in formyl-CoA:oxalate CoA transferase. This is one of the first reports on quantitative analysis of long timescale protein loop motions in large protein complexes. The computational predictions were verified by the experimental measurements that were carried out by the lab of the co-corresponding author, Dr. Richards. This paper demonstrates a significant advantage of the orthogonal space random walk algorithm in realizing long timescale sampling.
Min, D., Zheng, L., Harris, W., Chen, M., Lv, C., & Yang, W. (2010). Practically efficient QM/MM alchemical free energy simulations: The orthogonal space random walk strategy. Journal of Chemical Theory and Computation, 6, 2253–2266.
This paper reports a practically efficient combined quantum mechanical/molecular mechanical (QM/MM) potential based free energy simulation algorithm, which was enabled based on our orthogonal space random walk sampling strategy. It is noted that achieving practically efficient quantum mechanical potential based simulation methods has been a long-sought target in computational chemistry. D. Min, M. Chen, and L. Zheng were postdoctoral fellows and W. Harris and C. Lv were graduate students in the Yang group.
Yang, W., Cui, Q., Min, D., & Li, H. Z. (2010). QM/MM alchemical free energy simulations: Challenges and recent developments. Ann. Rep. Comput. Chem, 6, 51-62.
Zhou, J., Lv, C., Liang, B., Chen, M., Yang, W., & Li, H. (2010). Glycosidic bond conformation preference plays a pivotal role in catalysis of RNA pseudouridylation: A combined simulation and structural study. Journal of Molecular Biology, 401, 690-695.
This paper reports a combined computational and experimental study of glycosidic bond conformation preferences in the pre-reactive states of uridine and its derivatives. The strong correlation between glycosidic bond conformation preferences and RNA pseudouridylation reactivities suggests a C6 nucleophilic attack pre-reactive state conformation and favors a C6-based catalytic mechanism. Notably, the enzymatic mechanism of RNA pseudouridylation has been a long-sought problem; until the present work, there has been little suggestive evidence on possible reaction paths. The Yang group provided computational analysis based on the recently orthogonal space random walk free energy simulation algorithm; particularly, the computational method was customized as a “pseudo-alchemical” strategy to more reliably realize effective glycosidic bond rotations. The co-corresponding author, H. Li, a colleague of W. Yang, is co-responsible for the overall research and her lab carried out the experiments.
Chen, M., & Yang, W. (2009). On-the-path random walk to efficiently optimize minimum free energy path. Journal of Computational Chemistry, 30, 1649-1653.
This paper reports the first generalized ensemble based minimum free energy path optimization algorithm; with this development, minimum free energy path optimization can be more efficiently achieved on the complex systems. M. Chen was a postdoctoral fellow in the Yang group.
Nguyen, L. T., Yang, W., Wang, Q., & Hirst, L. S. (2009). Molecular dynamics simulation of F-actin: Studying the mechanisms for semi-flexible filament assembly reveals the role of cross-linkers. Soft Matter, 5, 2033-2036
This paper reports a coarse-grained molecular dynamics study of the mechanisms of semi-flexible filament assembly. W. Yang designed the numerical scheme and supervised the graduate student of L. T. Nguyen on the specific simulation designs. The senior author, L. S. Hirst, a former colleague of W. Yang designed the overall research. Another former colleague of W. Yang, Q. Wang, contributed to this research by providing useful suggestions.
Tan, Y. H., Chen, Y. M., Ye, X., Lu, Q., Tretyachenko-Ladokhina, V., Yang, W., Senear, D. F., & Luo, R. (2009). Molecular mechanisms of functional rescue mediated by p53 tumor. Biophysical Chemistry, 145, 37-44.
This paper reports a molecular dynamics simulation study of the functional rescue mechanism mediated by p53 tumor. W. Yang contributed to this work by designing the sampling scheme (essential energy space random walk based scheme) for the simulation studies. R. Luo, a W. Yang’ collaborator from UC at Irvine, designed the overall research and his group members performed the research.
Yang, W., Brooks, B. R., Brooks, C. L. I., MacKerell, A. D., Jr., Nilsson, L., Petrella, R. J., Roux, B., Won, Y., Archontis, G., & et. al. (2009). CHARMM: The Biomolecular Simulation Program. J. Comput. Chem, 30, 1545-1614.
Ye, X., Yang, W., & Luo, R. (2009). Roles of boundary conditions in DNA simulations: Analysis of ion distributions with the finite-difference Poisson-Boltzmann method. Biophysical Journal, 97, 554-562
This paper reports the effects of various boundary conditions in the DNA simulations. W. Yang contributed to this research by designing the sampling scheme (variant Hamiltonian replica exchange scheme) for the simulation studies. R. Luo, a W. Yang’ collaborator from UC at Irvine, designed the overall research and his group member, X. Ye, performed the research.
Zheng, L., Chen, M., & Yang, W. (2009). Simultaneous escaping of explicit and hidden free energy barriers: Application of the orthogonal space random walk strategy in generalized ensemble conformational sampling. Journal of Chemical Physics, 130, 234105 (10 pages)
This paper reports a highly efficient conformational sampling algorithm based on the orthogonal space random walk strategy, which was earlier developed in the context of free energy simulation. L. Zheng and M. Chen were postdoctoral fellows in the Yang group. It was selected by JCP: BioChemical Physics and Virtual Journal of Biological Physics Research.
Min, D., Josephine, H., Li, H., Lakner, C., Swofford, D., Naylor, G. P., Hedstrom, L., & Yang, W. (2008). An enzymatic atavist revealed in dual pathways for water activation. PLoS Biology, 6, 1802-1810.
This paper reports a study of the water activation process in an enzyme, IMP dehydrogenase, based on the combined efforts of biomolecular simulation, enzyme kinetics studies and computational evolutionary analysis; based on the computational prediction, biochemical studies were performed and showed a unique enzymatic evolution mechanism. D. Min and Li H. were postdoctoral fellows in the Yang group. The co-corresponding author, L. Hedstrom, an experimental collaborator from Brandeis university co-designed the overall research with W. Yang; her group members, H. Josephine, performed the experiments. D. Swofford and G. P. Naylor, W. Yang’s Florida State University colleagues, collaborated by supervising C. Lakner in performing evolutionary analysis. It was featured in PLoS Biology, Chemistry & Chemical Engineering News, Computing Life of National Institute of General Medical Science etc.
Min, D., Li, H., Berg, B. A., Fenley, M. O., & Yang, W. (2008). Efficient sampling of ion motions in molecular dynamics simulations on DNA: Variant Hamiltonion replica exchange strategy. Chemical Physics Letters, 454, 391-395.
This paper reports a replica exchange based sampling method to efficiently simulate diffusion ions around highly-charged systems like DNA. D. Min and H. Li were postdoctoral fellows in the Yang group. B. A. Berg and M. O. Fenley are colleagues of W. Yang; they contributed to this work by providing useful suggestions.
Min, D., & Yang, W. (2008). A divide-and-conquer strategy to improve diffusion sampling in generalized ensemble simulations. Journal of Chemical Physics, 128, 094106 (7 pages).
This paper reports a novel generalized ensemble strategy to improve the sampling of the complex events where multiple energetic barriers exist in separate domains. D. Min was a postdoctoral fellow of the Yang group. It was selected by Virtual Journal of Biological Physics Research.
Min, D., & Yang, W. (2008). Energy difference space random walk to achieve fast free energy calculations. Journal of Chemical Physics, 128, 019102 (4 pages).
This paper reports a novel enhanced sampling based free energy simulation method, by which the involved collective motions can be easily achieved. D. Min was a postdoctoral fellow of the Yang group. It was selected by Virtual Journal of Biological Physics Research.
Yang, W., Nymeyer, H., Zhou, H.-X., Berg, B. A., & Brüschweiler, R. (2008). Quantitative computer simulations of biomolecules: A snapshot. J. Comput. Chem, 29, 668-672.
Zheng, L., Carbone, I. O., Berg, B. A., & Yang, W. (2008). A hybrid recursion method to robustly ensure efficiency in the simulated scaling based free energy simulations. Journal of Chemical Physics, 129, 034105 (7 pages).
This paper reports an improved version of the simulated scaling free energy simulation method; in this improvement, two recursion strategies were effectively combined. L. Zheng was a postdoctoral fellow and I. Carbone was a graduate student in the Yang group. B. A. Berg, a colleague of W. Yang, provided useful suggestions. It was selected by Virtual Journal of Biological Physics Research.
Zheng, L., Chen, M., & Yang, W. (2008). Random walk in orthogonal space to achieve efficient free energy simulation of complex systems. Proceedings of the National Academy of Sciences USA, 51, 20227-2023
This paper reports a significant algorithm breakthrough in free energy simulation; by speeding up environmental relaxations, orders of magnitude of sampling efficiency improvement can be gained. L. Zheng and M. Chen were postdoctoral fellows in the Yang group. It was selected by Faculty1000 as “a technical breakthrough”. It has been cited 21 times.
Zheng, L., & Yang, W. (2008). Essential energy space random walks to accelerate molecular dynamics simulations: Convergence improvements via an adaptive-length self-healing strategy. Journal of Chemical Physics, 129, 014105 (9 pages).
This paper reports an improved version of the essential energy space random walk method to accelerate molecular dynamics simulations; in this improvement, recursion can be effectively performed in the equilibrium regime. L. Zheng was a postdoctoral fellow in the Yang group. It was selected by Virtual Journal of Biological Physics Research.
Zheng, L., & Yang, W. (2008). On the simulated scaling based free energy simulations: Adaptive optimization of the scaling parameter intervals. Journal of Chemical Physics, 129, 124107 (5 pages).
This paper reports a further enhanced version of the simulated scaling free energy simulation method; in this improvement, a numerical scheme was designed to automatically optimize the scaling parameter intervals. L. Zheng was a postdoctoral fellow in the Yang group. It was selected by Virtual Journal of Biological Physics Research.and JCP: BioChemical Physics.
Berg, B. A., & Yang, W. (2007). Efficient numerical calculation of the combinatorial entropy of partially ordered ice. Journal of Chemical Physics, 127, 024502 (6 pages).
This paper reports a novel application of the multi-canonical ensemble Monte Carlo method in the calculation of the combinatorial entropy of partially ordered water clusters, which could be pivotal in biomolecular functions. The senior author, B. A. Berg, who is a colleague of W. Yang, designed the overall research; B. A. Berg and W. Yang performed the research. It was selected by Virtual Journal of Biological Physics Research.
Fajer, M. I., Li, H., Yang, W., & Fajer, P. G. (2007). Mapping electron paramagnetic resonance spin label conformations by the simulated scaling method. Journal of the American Chemical Society, 129, 13840-13846.
This paper reports an enhanced sampling based simulation study of the electron paramagnetic resonance spin conformations in various locations of the target proteins; this paper demonstrated the powerful sampling capability of the simulated scaling technique earlier developed in the Yang lab. M. Fajer was a summer research undergraduate; H. Li was a postdoctoral fellow in the Yang lab; the senior author, P. G. Fajer and W. Yang designed this research.
Li, H. Z., & Yang, W. (2007). Forging the missing link in free energy estimations: λ-WHAM in thermodynamic integration, overlap histogramming, and free energy perturbation. Chemical Physics Letters, 440, 155-159.
This theoretical paper unravels a historical mystery: why different rigorous free energy estimators have varied efficiency and proposes a numerical method to optimize their efficiency. H. Li was a postdoctoral fellow in the Yang group.
Li, H., Fajer, M., & Yang, W. (2007). Simulated scaling method for efficient localized conformational sampling and simultaneous “alchemical” free energy simulation: A general method for MM, QM, and QM/MM simulations. Journal of Chemical Physics, 126, 024106 (12 pages).
It reports one of the first computational methods to enhance the sampling efficiency for the purpose of free energy simulation, which is an essential technique for computational drug and protein designs. H. Li was a postdoctoral fellow of the Yang group and M. Fajer was a summer undergraduate student. It was selected by JCP: BioChemical Physics and Virtual Journal of Biological Physics Research. It was a top monthly downloaded paper and has been cited 24 times.
Li, H., Min, D., Liu, Y., & Yang, W. (2007). Essential energy space random walk via energy space metadynamics method to accelerate molecular dynamics simulations. Journal of Chemical Physics, 127, 094101 (8 pages).
This paper reports a novel accelerated molecular dynamics simulation technique; it is especially powerful for the biomolecular events occurring in a localized region. H. Li and D. Min were postdoctoral fellows and Y. Liu was a graduated student in the Yang group. It was selected by Virtual Journal of Biological Physics Research and it was a top 3 monthly downloaded paper. It has been cited 11 times.
Li, H., Min, D., Shore, S. G., Lipscomb, W. G., & Yang, W. (2007). Nature of “hydrogen bond” of diborane-benzene: covalent, electrostatic, or dispersive. Inorganic Chemistry, 46, 3956-3959.
This paper reports a computational analysis of the nature of the diborane-benzene interaction, which could be mistakenly believed as a hydrogen bond. H. Li and D. Min were postdoctoral fellows in the Yang group. The co-corresponding author, W. G. Lipscomb, is a collaborator at Harvard, who received his Nobel Prize for the contribution to Boron chemistry. The experimental collaborator, S. G. Shore, from Ohio State University provided the structural model of the diborane-benzene complex, which was captured in his experiments.
Li, H., & Yang, W. (2007). Sampling enhancement for the simulations based on the quantum mechanical potentials: A general algorithm and its extension for free energy calculation on the rugged energy surfaces. Journal of Chemical Physics, 126, 114104 (7 pages).
It reports the first general algorithm to enhance the sampling for the simulation of complex systems when they are treated by quantum mechanical potentials. H. Li was a postdoctoral fellow in the Yang group. It was selected by Virtual Journal of Biological Physics Research and has been cited 11 times.
Min, D., Li, H., Li, G., Bitetti-Putzer, R., & Yang, W. (2007). Synergistic approach to improve “alchemical” free energy calculations on rugged energy surfaces. Journal of Chemical Physics, 126, 144109 (12 pages).
It reports a “parallel computing” based synergistic method to enhance the sampling for free energy simulation, which is an essential technique for computational drug and protein designs. D. Min, H. Li, G. Li were postdoctoral fellows in the Yang group and R. Bitetti-Putzer was an outside collaborator. It has been cited 15 times.
Min, D., Liu, Y., Carbone, I., & Yang, W. (2007). On the convergence improvement in the metadynamics simulations: A Wang-Landau recursion approach. Journal of Chemical Physics, 126, 194104 (7 pages).
This paper reports a solution to the convergence problem in a popular free energy simulation method, the metadynamics algorithm and shows that the proposed method allows more robust and efficient free energy calculations. D. Min was a postdoctoral fellow and Y. Liu & I. Carbone were graduate students in the Yang group. It was selected by Virtual Journal of Biological Physics Research and has been cited 12 times.
Min, D., Song, X., Li, H., & Yang, W. (2007). “In-line attack” conformational effect plays a modest role in an enzyme-catalyzed RNA cleavage: A free energy simulation study. Nucleic Acids Research, 35, 4001-4006.
This paper reports a free energy simulation study of the “in-line attack” conformational effect, which was long believed to the major driving force in the enzymatic catalysis of the phosphate cleavage; this study shows that this effect only plays a modest role in an enzyme-catalyzed RNA cleavage. D. Min was a postdoctoral fellow in the Yang group. The experimental collaborator, H. Li, is a colleague of W. Yang and provided the structural model and her biological insights for this study. X. Song was a postdoctoral fellow in the Li group, who solved the enzyme-RNA complex structure.
Oruganti, S., Zhang, Y., Li, H., Robinson, H., Terns, R. M., Terns, M. P., Yang, W., & Li, H. (2007). Alternative conformations of the Archael Nop56/58-fibrillarin complex imply induced-fit assembly of box C/D RNPs. Journal of Molecular Biology, 371, 1141-1150.
This paper reports possible alternative functional conformations of the Archael Nop56/58-fibrillarin complex during the formation of biologically essential assembly of box C/D RNPs based on new X-ray structures and computational analysis. The Yang group (H. Li, a postdoctoral fellow in the Yang group and W. Yang) were involved by providing the computational analysis and showed that the conformations solved earlier and presently are linked by a motion, which is energetically the most efficient. The senior author, H. Li, a colleague of W. Yang, designed the overall research and her lab members (S. Oruganti, Y. Zhang) and other biological collaborators (H. Robinson, R. M. Terns, and M. P. Terns) performed the experimental studies.
Wang, J., Zheng, X., Yang, Y., Drueckhammer, D., Yang, W., Verkhivker, G., & Wang, E. (2007). Quantifying intrinsic specificity: A potential complement to affinity in drug screening. Physical Review Letters, 99, 198101 (4 pages).
This paper reports a novel theory to quantify intrinsic specificity of a drug ligand when it may possibly bind many protein targets. The senior author, J. Wang, who is a W. Yang’ collaborator at Stony Brook, designed the overall research. W. Yang contributed to this work by designing a part of the numerical scheme. Other group members (X. Zheng & Y. Yang) and collaborators (D. Drueckhammer, G. Verkhivker, and E. Wang) of J. Wang were also involved in the performance of this research. It was selected by Virtual Journal of Biological Physics Research.
Yang, W., & Berg, B. A. (2007). Numerical calculation of the combinatorial entropy of partially ordered ice. J. Chem. Phys, 127, 024502.
Yang, W., & Li, H. (2007). 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. J. Chem. Phys, 126, 114104.
Yang, W., Li, H., & Fajer, M. (2007). Simulated scaling method for efficient localized conformational sampling and simultaneous “alchemical” free energy simulation: A general method for MM, QM, and QM/MM simulations. J. Chem. Phys, 126, 024106.
Yang, W., Oliva, C., Rodriguez, A., & González, M. (2007). A QM/MM study of the reaction mechanism of the hepatitis C virus NS3 protease with the NS5A/5B substrate. Proteins: Struc. Func. Bioinf, 66, 444-455.
Li, H., Li, G., Berg, B. A., & Yang, W. (2006). Finite reservoir replica exchange method to enhance sampling on rugged energy surfaces. Journal of Chemical Physics, 125, 144902 (5 pages).
An improved algorithm was developed to further enhance the sampling power of the classical replica exchange method. H. Li and G. Li were the postdoctoral fellows of the Yang group and the co-corresponding author, B. A. Berg, is the FSU colleague of W. Yang. It was selected by Virtual Journal of Biological Physics Research and has been cited 16 times.
Yang, W., Bitetti-Putzer, R., Dinner, A. R., & Karplus, M. (2006). Conformational sampling via a self-regulating effective energy surface. J. Chem. Phys, 124, 174901-174915.
Yang, W., Li, H., Li, G., & Berg, B. A. (2006). Finite reservoir replica exchange method to enhance sampling in rugged energy surface. J. Chem. Phys, 125, 144902.
Yang, W., Banerjee, A., Karplus, M., & Verdine, G. L. (2005). Structure of hOGG1 interrogating undamaged DNA elucidates recognition of damaged DNA. Nature, 434, 612-618.
Yang, W., Gao, Y. Q., & Karplus, M. (2005). A structure-based model for synthesis and hydrolysis of ATP by F1-ATPase. Cell, 123, 195-205.
# Yang, W., Bitetti-Putzer, R., & Karplus, M. (2004). Chaperoned alchemical free energy simulations: A general method for QM, MM, and QM/MM potentials. J. Chem. Phys, 120, 9450-9453.
# Yang, W., Bitetti-Putzer, R., & Karplus, M. (2004). Free energy simulations: Use of reverse cumulative averaging to determine the equilibrated region and the time required for convergence. J. Chem. Phys, 120, 618-2628.
# Yang, W., Karplus, M., Gao, Y. Q., Ma, J., & van der Vaart, A. (2004). Protein structural transitions and their functional role. Phil. Trans.: Math. Phys. Eng. Sci, 10, 1471-2962.
# Yang, W., Bitetti-Putzer, R., & Karplus, M. (2003). Generalized ensembles serve to improve the convergence of free energy simulations. Chem. Phys. Lett, 377, 633-641.
# Yang, W., & Drueckhammer, D. G. (2003). Computational study of the citrate synthase catalyzed deprotonation of acetyl-coenzyme A and fluoroacetyl-coenzyme A: Demonstration of a layered quantum mechanical approach. J. Phys. Chem. B, 107, 5986-5994.
# Yang, W., Fromme, J. C., Bruner, S. D., Karplus, M., & Verdine, G. L. (2003). Product-assisted catalysis in base-excision DNA repair. Nature Struc. Biol, 10, 204-211.
# Yang, W., Gao, Y. Q., Cui, Q., Ma, J., & Karplus, M. (2003). The missing link between thermodynamics and structure in F1-ATPase. Proc. Natl. Acad. Sci. USA, 100, 874-879.
# Yang, W., Gao, Y. Q., Marcus, R. A., & Karplus, M. (2003). A model for the cooperative free energy transduction and kinetics of ATP hydrolysis by F1-ATPase. Proc. Natl. Acad. Sci. USA, 100, 11339-11344.
# Yang, W., & Drueckhammer, D. G. (2001). Understanding the relative acyl-transfer reactivity of oxoesters and thioesters: Computational analysis of transition state delocalization effects. J. Am. Chem. Soc, 123, 11004-11009.
# Yang, W., He, H., & Drueckhammer, D. G. (2001). Computer-guided design in molecular recognition: Design and synthesis of a glucopyranose receptor. Angew. Chem. Int. Ed, 40, 1714-1718.
# Yang, W., & Drueckhammer, D. G. (2000). Computational studies of the aminolysis of oxoesters and thioesters in aqueous solution. Org. Lett, 2, 4133-4136.
# Yang, W., Vogel, K. W., Stark, L. M., Mishra, P. K., & Drueckhammer, D. G. (2000). Investigating the role of the geminal dimethyl groups of coenzyme A: Synthesis and studies of a didemethyl analogue. Bioorg. Med. Chem, 8, 2451-2460.
# Professional activities that occurred prior to my employment at FSU.
Refereed Book Chapters
Yang, W. (2013). Specialized sampling for free energy calculations: Half of the whole story. In R. H. Zhou (Ed.), Molecular Modeling at the Atomic Detail – Methods and Applications in Quantitative Biology. Taylor & Francis.
Yang, W., Zheng, L., & Li, H. (2008). Towards accurate predictions of binding affinities: The simulated scaling based free energy methods. In U. H. E. Hansmann etc. (Ed.), The Proceedings of Computational Biophysics to Systems Biology volume 40. NIC-Directors.
Yang, W., Gao, Y. Q., & Karplus, M. (2007). Thermodynamics and kinetic analysis of F1Fo-ATP synthase. In E. B. Starikov, J. P. Lewis, and S. Tanaka (Ed.), Modern Methods of Theoretical Physical Chemistry of Biopolymers. Elsevier.