Curriculum Vitae Wei Yang February 16, 2013 General Information University address: Institute of Molecular Biophysics Chemistry & Biochemistry College of Arts & Sciences 418 Kasha Laboratory of Biophysics Florida State University Tallahassee, Florida 32306-4380 Phone: 850-645-6884; Fax: 850-644-7244 E-mail address: [email protected]Web site: www.sb.fsu.edu/~yang Professional Preparation 2001 Doctor of Philosophy, State University of New York At Stony Brook. Major: Computational Chemistry. Supervisor: Dale G. Drueckhammer. Yang, W. (2001). Computational Approaches to Molecular Recognition and Bioorganic Reactions. (Doctoral dissertation, State University of New York At Stony Brook). Retrieved from ProQuest Dissertations & Theses Database, AAT 3044977. 1997 Bachelor of Science, Tsinghua University, Beijing. Major: Chemistry. Supervisor: Muzhen Liao. Yang, W. (1997). Ab Initio Calculation Study of Fulgide. (Bachelor's thesis, Tsinghua University, Beijing). Retrieved from Dissertations and Theses Databases of Tsinghua University. Postdegree Education and Training 2001–2005 Post-doctoral fellow, Harvard University, Cambridge, MA. Computational Biophysics, Department of Chemistry and Chemical Biology.
Transcript
Curriculum Vitae
Wei Yang
February 16, 2013
General Information
University address: Institute of Molecular Biophysics
Chemistry & Biochemistry College of Arts & Sciences 418 Kasha Laboratory of Biophysics Florida State University Tallahassee, Florida 32306-4380 Phone: 850-645-6884; Fax: 850-644-7244
E-mail address: [email protected] Web site: www.sb.fsu.edu/~yang Professional Preparation 2001 Doctor of Philosophy, State University of New York At Stony Brook. Major:
Computational Chemistry. Supervisor: Dale G. Drueckhammer.
Yang, W. (2001). Computational Approaches to Molecular Recognition and Bioorganic Reactions. (Doctoral dissertation, State University of New York At Stony Brook). Retrieved from ProQuest Dissertations & Theses Database, AAT 3044977.
1997 Bachelor of Science, Tsinghua University, Beijing. Major: Chemistry.
Supervisor: Muzhen Liao.
Yang, W. (1997). Ab Initio Calculation Study of Fulgide. (Bachelor's thesis, Tsinghua University, Beijing). Retrieved from Dissertations and Theses Databases of Tsinghua University.
Postdegree Education and Training 2001–2005 Post-doctoral fellow, Harvard University, Cambridge, MA.
Computational Biophysics, Department of Chemistry and Chemical Biology.
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Professional Experience 2011–present Associate Professor, Department of Chemistry and Biochemistry & Institute
of Molecular Biophysics, Florida State University. 2008–2011 Assistant Professor, Chemistry & Biochemistry and Institute of Molecular
Biophysics, College of Arts & Sciences, Florida State University. Contributing to the mission of the university through excellence in scholarly research, teaching, and service.
2005–2008 Assistant Professor, Chemistry & Biochemistry, Institute of Molecular
Biophysics, and School of Computational Science, Florida State University. Contributing to the mission of the university through excellence in scholarly research, teaching, and service.
Honors, Awards, and Prizes Innovator Award, Florida State University (2011). Innovator Award, Florida State University (2010). Innovator Award, Florida State University (2009). Hewlett-Packard Outstanding Junior Faculty Award in Computational Chemistry, American
Chemical Society (2008). Ralph E. Powe Junior Faculty Enhancement Award, Oak Ridge Associated Universities (2007). First-Year Assistant Professor Award, Florida State University (2006). Current Membership in Professional Organizations Editorial Board of PMC: Biophysics
Teaching Courses Taught Enzyme Structures and Functions ((BCH5505)) General Chemistry I (CHM1045) Honors General Chemistry I (CHM1050) General Chemistry I (CHM1045) General Chemistry I (CHM1045) Physical Chemistry I (CHM4410) Molecular Dynamics: Algorithms and Applications (ISC5225) Honors General Chemistry I (CHM1050) Molecular Dynamics: Algorithms and Applications (ISC5225) Honors General Chemistry I (CHM1050)
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New Course Development Molecular Dynamics: Algorithms and Applications (2007) Curriculum Development Comprehensive introduction to molecular dynamics simulation algorithms and their
corresponding applications in molecular sciences (2007) Doctoral Committee Chair Nelson, J. D., graduate. (2010). Computational and Experimental Exploration of
Conformational Changes in Nucleic Acids Associated Biomolecular Functions. Carbone, I., graduate. (2009). Computational Approaches to Long Timescale Biomolecular
Space Random Walk and the Wang-Landau Recursion. Master's Committee Member Dubey, S., graduate. (2008). Nelson, J. D., graduate. (2007). Bachelor's Committee Member Lockamy, T., graduate. (2011). O'Neil, E., graduate. (2006). Burns, J., student. Fajer, M., student. [NSF Fellowship] Hart, A., student. [Hoffman Scholarship in Chemistry, 2012] Martinez, M., student. McCullers, M., student. Noud, K., student. Patel, D., student. Pepitone, J., student. Pikaard, B., student. Roberti, M., student. Stribling, D., student. [Goldwater Scholarship 2012; Johnsen Scholarship in Chemistry 2011;
Undergraduate Research and Creative Activity Awards 2011, 2012] Teves, K., student. Vickers, C., student. Vijapura, N., student.
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Wunch, M., student. Cartabuke, M., student. (2013). Supervision of Student Research Not Related to Thesis or Dissertation Gohil, A. (Jun 2008–present).
National Science Foundation REU Undergraduate Student.
Research and Original Creative Work Program of Research and/or Focus of Original Creative Work Developing and applying novel generalized ensemble sampling techniques to understand long timescale functions of biomolecules.
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. Yang, W., 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.
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.
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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.
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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.
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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.
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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, 20227-20232.
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.
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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
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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.
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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.
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# 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.
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.
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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.
Refereed Reviews Yang, W., Cui, Q., Min, D., & Li, H. Z. (2010). QM/MM alchemical free energy simulations:
Challenges and recent developments. Annual Reports in Computational Chemistry, 6, 51-62.
This review is upon an invitation due to the pioneering contributions of the corresponding author, W. Yang, on the topic of QM/MM alchemical free energy simulations. Practical QM/MM alchemical free energy simulation has been a long-sought target in computational chemistry. Due to the efforts by the authors and others, practically accurate and efficient QM/MM alchemical free energy simulation methods are possible. The present review summarizes recent developments related to this topic. Q. Cui from Madison is a collaborator of W. Yang on the related efforts. D. Min and H. Z. Li were postdoctoral fellows in the Yang lab.
Brooks, B. R. E. (2009). CHARMM: The biomolecular simulation program. Journal of
Computational Chemistry, 30, 1545-1614.
This invited report reviews the underlying theories and methods in the biomolecular simulation program CHARMM. The CHARMM program is developed jointly by the research groups led by the involved authors. The authors do not directly collaborate but individually contribute their developments through the CHARMM manager, Dr. Won. The Yang group has been actively developing the free energy simulation and the sampling portions of this program in the recent years.
Yang, W., Nymeyer, H., Zhou, H. X., Berg, B. A., & Bruschweiler, R. (2008). Quantitative
computer simulations of biomolecules: A snapshot. Journal of Computational Chemistry, 29, 668-672.
This paper reviews the research topics covered in a recent quantitative computational biophysics workshop that was co-organized by the authors. W. Yang was responsible for reviewing the topics related to the sampling enhancement and free energy simulation. R. Brüschweiler was the senior author who designed the review.
Nonrefereed Reviews Zheng, L., Li, H., & Yang, W. (2008). Towards accurate predictions of binding affinities: The
simulated scaling based free energy methods. The Proceedings of Computational Biophysics to Systems Biology, 40, 57-63.
This chapter reviews the simulated scaling free energy simulation method and introduces its derivatives, especially when the systems are treated by QM/MM potentials. L. Zheng and H. Li were postdoctoral fellows in the Yang group. This review chapter was invited by NIC-Directors for the fact that W. Yang was a plenary speaker of the workshop on "Computational Biophysics to Systems Biology".
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Presentations
Invited Keynote and Plenary Presentations at Conferences
For invited keynote and plenary presentations at conferences, 100.0% were international in scope. Yang, W. (presented 2008, July). Quantitative Alchemical Free Energy Simulations: Are We
There Yet. Plenary presentation at the Gordon Research Conference on "Computational Chemistry: New Computational Tools For 21st Century Chemistry", the Gordon Research Conference Organization, Mount Holyoke College, MA. (International)
Yang, W. (presented 2008, May). Advancing Drug and Protein Binding Affinity Predications
via Generalized Ensemble Based Methods. Plenary presentation at the conference on "From Computational Biophysics to Systems Biology" 2008, John von Neumann Institute for Computing (NIC), Juelich, Germany. (International)
Invited Keynote and Plenary Presentations at Symposia
For invited keynote and plenary presentations at symposia, 100.0% were international in scope. Yang, W. (presented 2009, June). Quantitative Biomolecular Simulation: An Emerging
Technique for Protein Engineering. Plenary presentation in Zhihe Rao (Chair), Life Science and Frontier of Biotechnology Symposium. Symposium conducted at the meeting of 2009 International Conference for Bioeconomy, Tianjin, P. R. China. (International)
Invited Presentations at Conferences
For invited presentations at conferences, 100.0% were international in scope. Yang, W. (presented 2013, July). Orthogonal Space Sampling to Achieve Long Timescale
Dynamics. Presentation at Telluride Workshop on "Protein Electrostatics", Telluride Workshop Organization, Telluride, CO. (International)
Yang, W. (presented 2013, June). Orthogonal Space Sampling to Achieve Long Timescale
Dynamics. Presentation at Kavli Institute Workshop on "Advanced Molecular Simulation Methods in the Physical Sciences", Kavli Institute for Theoretical Physics, Beijing. (International)
Yang, W. (presented 2013, June). Orthogonal Space Sampling to Achieve Long Timescale
Dynamics. Presentation at Snowmass Workshop on "Free Energy Calculations", Snowmass Workshop Organization, Snowmass, CO. (International)
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Yang, W. (presented 2013, March). Orthogonal Space Sampling to Achieve Long Timescale Dynamics. Presentation at Telluride Workshop on "Membrane Biophysics", Telluride Workshop Organization, Telluride, CO. (International)
Yang, W. (presented 2012, August). High-order generalized ensemble sampling methods.
Presentation at E. Elexov (Chair), Solvation Dynamics and Modeling, National American Chemical Society Meeting, Philadelphia, PA. (International)
Yang, W. (presented 2012, June). Orthogonal Space Sampling for Free Energy Simulations.
Presentation at Presentation at the CECAM Workshop on "Free Energy Simulations", CECAM Workshop Organization, Paris, FR. (International)
Yang, W. (presented 2011, June). Orthogonal Space Sampling for Free Energy Simulations.
Presentation at Telluride Workshop on "Free Energy Simulations", Telluride Workshop Organization, Telluride, CO. (International)
Yang, W. (presented 2011, June). Orthogonal Space Sampling for Free Energy Simulations.
Presentation at Telluride Workshop on "Protein Electrostatics", Telluride Workshop Organization, Telluride, CO. (International)
Yang, W. (presented 2010, June). Higher-Order Generalized Ensemble Sampling Methods to
Accelerate Molecular Dynamics Simulations. Presentation at the Telluride Workshop on "Protein Landscape and Network", the Telluride Workshop Organization, Telluride, CO. (International)
Yang, W. (presented 2010, June). Higher-Order Generalized Ensemble Sampling Methods to
Accelerate Molecular Dynamics Simulations. Presentation at the Telluride Workshop on "Sampling Enhancement Methods", the Telluride Workshop Organization, Telluride, CO. (International)
Yang, W. (presented 2010, June). Higher-Order Generalized Ensemble Sampling Methods to
Accelerate Molecular Dynamics Simulations. Presentation at the Telluride Workshop on "Reaction Path and Order Parameter Determination Methods", the Telluride Workshop Organization, Telluride, CO. (International)
Yang, W. (presented 2010, May). A Solution to the Drug Binding Prediction Challenge: The
Generalized Ensemble Approach. Presentation at Free Energy Methods in Drug Discovery - Going the 'Last Mile', Vertex Pharmaceuticals and Stanford Computational Biology Center, Cambridge, MA. (International)
Zheng, L. Q., & Yang, W. (presented 2009, July). The orthogonal space random walk based
free energy simulation approach to predict the pKa values. Presentation at the Telluride Workshop on "Protein Electrostatics", the Telluride Workshop Organization, Telluride, CO. (International)
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Yang, W. (presented 2008, July). The Generalized Ensemble Based Free Energy Simulation Methods. Presentation at the Telluride Workshop on "Sampling Enhancement Methods", the Telluride Workshop Organization, Telluride, CO. (International)
Yang, W. (presented 2007, February). The Replica Exchange Based Free Energy Simulation
Methods. Presentation at the Quantitative Computational Biophysics Workshop, School of Computational Science and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL. (International)
Yang, W. (presented 2005, August). A Perspective on Quantitative Biomolecular Simulations.
Presentation at the Telluride Workshop on "Biomolecular Vibrational Dynamics", the Telluride Workshop Organization, Telluride, CO. (International)
Invited Presentations at Symposia
For invited presentations at symposia, 68.8% were international, 31.3% were regional in scope. Yang, W. (presented 2012, May). Generalized Ensemble Path Simulation Methods. In A. van
der Vaart. (Chair), the Computational Chemistry Symposium. Presentation at the meeting of Florida American Chemical Society Regional Meeting, Tampa, FL. (Regional)
Yang, W. (presented 2012, May). Orthogonal Space Sampling for Biomolecular simulations.
In R. Prabhakar (Chair), the Biochemistry Symposium. Presentation at the meeting of Florida American Chemical Society Regional Meeting, Tampa, FL. (Regional)
Yang, W. (presented 2012, February). Orthogonal Space Sampling for Free Energy
Simulations. In Sanibel Symposium. Presentation at the meeting of Sanibel Symposium Organization, St. Simons Island, GA. (International)
Yang, W. (presented 2011, June). Orthogonal Space Sampling for Free Energy Simulations. In
Telluride Workshop on "Protein Electrostatics". Presentation at the meeting of Telluride Workshop Organization, Telluride, CO. (International)
Yang, W. (presented 2010, August). High-order generalized ensemble sampling methods. In J.
W. Chu (Chair), Multiscale Modeling and Simulation. Presentation at the meeting of the National American Chemical Society Meeting, Boston, MA. (International)
Yang, W. (presented 2010, May). High-order generalized ensemble sampling in biomolecular
simulations. In R. Prabhakar (Chair), the Biochemistry Symposium. Presentation at the meeting of the Florida American Chemical Society Regional Meeting, Tampa, FL. (Regional)
Yang, W. (presented 2010, March). High-order generalized ensemble sampling methods. In D.
Agrafiotis (Chair), Advanced Sampling method symposium. Presentation at the meeting
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of the National American Chemical Society Meeting, San Francisco, CA. (International)
Zheng, L., & Yang, W. (presented 2010, March). High-order generalized ensemble free energy
simulation methods. In U. H. E. Hansmann (Chair), the Generalized ensemble simulation symposium. Presentation at the meeting of the National American Chemical Society Meeting, San Francisco, CA. (International)
Yang, W. (presented 2009, August). An emerging perspective in free energy simulation of
protein interactions. In G. Hummer (Chair), the Protein Function and Dynamics Symposium. Presentation at the meeting of the National American Chemical Society Meeting, Washington DC. (International)
Yang, W. (presented 2009, May). An emerging perspective in free energy simulation of protein
interactions. In R. Prabhakar (Chair), the Biochemistry Symposium. Presentation at the meeting of the Florida American Chemical Society Regional Meeting, Orlando, FL. (Regional)
Yang, W. (presented 2008, August). Computer guided protein engineering: Free energy
simulation approaches. In A. Lugovskoy (Chair), the Biophysical & Biomolecular Symposium. Presentation at the meeting of the National American Chemical Society Meeting, Philadelphia, PA. (International)
Yang, W. (presented 2008, May). Energy Landscapes of Protein Dynamic Domains:
Generalized Ensemble Based Models. In R. Prabhakar (Chair), the Biochemistry Symposium. Presentation at the meeting of the Florida American Chemical Society Regional Meeting, Orlando, FL. (Regional)
Yang, W. (presented 2008, April). Problem oriented sampling design via the replica exchange
strategy. In S. W. Rick (Chair), Replica Exchange: New Methods and Applications to Protein Folding and other Large Systems. Presentation at the meeting of the National American Chemical Society Meeting, New Orleans, LA. (International)
Yang, W. (presented 2007, August). Mapping multidimensional free energy surfaces in
biomolecular simulations. In J. P. Ma (Chair), Structural Determination, Refinement, and Modeling of Large Biomolecular Complexes. Presentation at the meeting of the National American Chemical Society Meeting, Boston, MA. (International)
Yang, W. (presented 2006, September). Free energy simulation based protein-protein binding
predictions. In J. J. Gray (Chair), Biophysical and Biomolecular Symposium: Protein-Protein Interactions. Presentation at the meeting of the National American Chemical Society Meeting, San Francisco, CA. (International)
Yang, W. (presented 2006, February). The twin-brother strategy to enhance free energy
simulation efficiency. In A. E. Roitberg (Chair), the Sanibel Symposium. Presentation at
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the meeting of The Quantum Theory Project of University of Florida, St. Simons Island, GA. (International)
Refereed Presentations at Symposia
For refereed presentations at symposia, 100.0% were international in scope. Yang, W. (presented 2008, October). The Generalized Ensemble Based Free Energy
Simulation Methods. In J. Saven (Chair), Computational modeling of biological and soft condensed matter systems. Presentation at the meeting of the International Multi-Scale Material Modeling Conference, Tallahassee, FL. (International)
Zheng, L., & Yang, W. (presented 2008, August). New paradigm for binding free energy
simulations: The simulated scaling based approaches. In W. Yang (Chair), Free Energy Simulations. Presentation at the meeting of the National American Chemical Society Meeting, Philadelphia, PA. (International)
Yang, W. (presented 2007, August). Sampling enhanced quantum mechanical potential based
free energy simulations. In J. Gao (Chair), Quantum Mechanics and Statistical Mechanics: Can One Avoid the Other. Presentation at the meeting of the National American Chemical Society Meeting, Boston, MA. (International)
Yang, W. (presented 2006, September). Enhance sampling for free energy simulations. In A. F.
Voter (Chair), Theory of Rare Events and Accelerated Dynamics. Presentation at the meeting of the National American Chemical Society Meeting, San Francisco, CA. (International)
Invited Lectures and Readings of Original Work
For invited lectures and readings of original work, 100.0% were local in scope. Yang, W. (2012, December). Orthogonal space sampling to achieve long timescale dynamics.
Delivered at Indiana University Purdue University at Indianapoli, Indiana University Purdue University at Indianapolis, Indianapolis, IN. (Local)
Yang, W. (2012, October). Orthogonal space sampling to achieve long timescale dynamics.
Delivered at Brandeis University, Brandeis University, Waltham, MA. (Local) Yang, W. (2011, November). Orthogonal space sampling to achieve long timescale dynamics.
Delivered at University of Kansas, University of Kansas, Lawrence, KS. (Local) Yang, W. (2011, October). Orthogonal space sampling to achieve long timescale dynamics.
Delivered at University of Pittsburg, University of Pittsburg, Pittsburgh, PA. (Local)
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Yang, W. (2011, March). Orthogonal space sampling to achieve long timescale dynamics. Delivered at Dalian Institute of Chemical Physics, Chinese Academy of Science, Chinese Academy of Science, Dalian, P. R. China. (Local)
Yang, W. (2010, November). Orthogonal space sampling to achieve long timescale dynamics.
Delivered at Boston University, Boston, Boston University, Boston, MA. (Local) Yang, W. (2010, November). Orthogonal space sampling to achieve long timescale dynamics.
Delivered at National Institute of Health, Bethesda, MD. (Local) Yang, W. (2010, October). Orthogonal space sampling to achieve long timescale dynamics.
Delivered at SUNY at Stony Brook, Stony Brook, SUNY at Stony Brook, Stony Brook, NY. (Local)
Yang, W. (2009, April). Orthogonal space random walk sampling methods. Delivered at
Michigan Technological University, Michigan Technological University, MI. (Local) Yang, W. (2009, April). Orthogonal space random walk sampling methods. Delivered at the
Oak Ridge National Laboratory, the Oak Ridge National Laboratory, TN. (Local) Yang, W. (2009, April). Orthogonal space random walk sampling methods. Delivered at
University of Texas, Austin, University of Texas, Austin, TX. (Local) Yang, W. (2009, February). Orthogonal space random walk sampling methods. Delivered at
Stanford University, Stanford University, CA. (Local) Yang, W. (2008, December). Orthogonal space random walk sampling methods. Delivered at
University of New Mexico, University of New Mexico, NM. (Local) Yang, W. (2008, November). Orthogonal space random walk sampling methods. Delivered at
University of Wisconsin, Madison, University of Maryland, Madsion, WI. (Local) Yang, W. (2008, September). Orthogonal space random walk sampling methods. Delivered at
Albert Einstein Medical College, Albert Einstein Medical College, NY. (Local) Yang, W. (2008, August). Computer guided protein engineering: Free energy simulation
approaches. Delivered at Institute of Earth Chemistry, Chinese Academy of Sciences, Guiyang, P.R. China. (Local)
Yang, W. (2008, July). Computer guided protein engineering: Free energy simulation
approaches. Delivered at Nankai University, Tianjin, P. R. China. (Local) Yang, W. (2008, June). An emerging perspective in free energy simulation of protein
interactions. Delivered at University of California at San Diego, San Diego, CA. (Local)
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Yang, W. (2008, April). An emerging perspective in free energy simulation of protein interactions. Delivered at D. E. Shaw Research Institute, Manhattan, NY. (Local)
Yang, W. (2008, April). An emerging perspective in free energy simulation of protein
interactions. Delivered at IBM Watson Research Center, York Town, NY. (Local) Yang, W. (2008, February). An emerging perspective in free energy simulation of protein
interactions. Delivered at School of Engineering, Florida State University, Tallahassee, FL. (Local)
Yang, W. (2007, November). An emerging perspective in free energy simulation of protein
interactions. Delivered at National Institute of Health, Bethesda, MD. (Local) Yang, W. (2007, November). An emerging perspective in free energy simulation of protein
interactions. Delivered at University of Tennessee, Knoxville, Knoxville, TN. (Local) Yang, W. (2007, October). An emerging perspective in free energy simulation of protein
interactions. Delivered at University of California at Irvine, Irvine, CA. (Local) Yang, W. (2007, September). An emerging perspective in free energy simulation of protein
interactions. Delivered at University of Miami, Miami, FL. (Local) Yang, W. (2007, April). An emerging perspective in free energy simulation of protein
interactions. Delivered at Biogen Idec Inc, Cambridge, MA. (Local) Yang, W. (2006, March). Advanced free energy simulations. Delivered at University of
Florida, Gainesville, FL. (Local) Yang, W. (2006, January). Advanced free energy simulations. Delivered at SUNY at Stony
Brook, Stony Brook, NY. (Local)
Contracts and Grants Contracts and Grants Funded Yang, W. (PI). (Jan 2013–Dec 2016). IMP Dehydrogenase. Funded by Brandeis University
Subcontract. Total award $240,200. Rokyta, D., & Yang, W. (co-PI). (Sep 2012–Aug 2017). Pleitotropy, Epistasis, and the
Biophysical Adaptation of ssDNA Bacteriophages. Funded by National Institute of Health/NIGMS. Total award $101,430.
Yang, W. (Sep 2012–Aug 2016). Inosine Monophosphate Dehydrogenase. Funded by National
Institute of Health/NIGMS. (R01 GM54403 (Hedstrom)). Total award $50,000.
The major goals of this project are to develop computational models that accurately recapitulate and
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quantitatively predict the catalytic properties of enzymes in the IMPDH/GMPR family. Aim 1. Develop a computational model for hydride transfer and test experimentally. Aim 2. Develop a computational model for the deamination reaction and test experimentally. Role: Co-investigator.
Yang, W. (Sep 2012–Aug 2017). Pleiotropy, Epistasis, and the Biophysical Adaptation of
ssDNA. Funded by National Institute of Health/NIGMS. (R01GM099723 (Rokyta)). Total award $22,000.
The purpose of this project is to investigate the roles of pleiotropy and epistasis in adaptive evolution using a bacteriophage experimental system. The Yang group will work with the Rokyta group on computational biophysical studies of protein stabilities. Role: Co-investigator.
Yang, W. (PI). (Jul 2012–Jun 2015). Achieving Long Timescale Sampling in Biomolecular
Simulations. Funded by National Science Foundation. Total award $633,041. Yang, W. (May 2012–Apr 2015). Achieving Long Timescale Sampling in Biomolecular
Simulations. Funded by National Science Foundation. (MCB1158284). Total award $211,014.
This project is the continuation of MCB0919983. The major goals of this project are to design novel molecular dynamics methods to more accurately sample protein conformational transitions. Specifically, the main objectives will be accomplished in two focused areas: (1) Quantitative prediction of protein electrostatic effects and understanding their coupling with protein conformational transitions; (2) Understanding how slow enzyme fluctuations prepare unique catalytic environments to activate chemical reactions.
Yang, W. (Jun 2011–May 2016). IMPDH-Targeted Antibiotics for Select Agents. Funded by
National Institute of Health/NIAID. (R01 AI093459-01 (Hedstrom)). Total award $18,625.
The major goals of this project are to develop Cryptosporidium parvum IMPDH inhibitors as broader spectrum antibiotics. The Yang group is responsible for computational docking of candidate inhibitors in the binding sites of IMPDHs. Role: Co-investigator.
Yang, W. (PI). (Jun 2011–Jul 2015). IMPDH-Targeted Antibiotics for Select Agents. Funded
by Brandeis University Subcontract from National Institute of Health. Total award $117,200.
Yang, W. (Jul 2009–Jun 2013). Achieving Long Timescale Sampling in Biomolecular
Simulations. Funded by National Science Foundation. (MCB0919983). Total award $443,588.
The major goals of this project are to design novel molecular dynamics methods to more accurately sample protein conformational transitions, specifically to understand protonation/deprotonation coupled structural changes, enable QM/MM based conformational samplings, and realize ab initio prediction of protein functional dynamics. Role: PI.
Yang, W. (Sep 2007–Jul 2011). IMP Dehydrogenase. Funded by Brandeis University
Subcontract from National Institute of Health. Total award $261,988.
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Yang, W. (PI). (Aug 2007–Jul 2009). Development of IMPDH-Targeted Drugs. Funded by Brandeis University Subcontract from National Institute of Health. Total award $75,000.
Yang, W. (PI). (Jun 2007–May 2008). Further Development of Free Energy Simulation
Methods. Funded by Oak Ridge Associated Universities. Total award $10,000. Yang, W. (PI). (Apr 2006–Dec 2007). Development and Application of Computational
Methodologies. Funded by Biogen Idec Inc. Total award $117,150. Contracts and Grants Pending Yang, W. (Aug 2021). Theoretical Analysis of Binding Selectivity and Catalysis in
Metalloenzyems. Submitted to NIH/NIGMS.
We target new QM/MM method developments to study metalloenzyme problems that involve metal sites with a high degree of structural flexibility and/or solvent accessibility. Role: Co-Investigator.
Yang, W. (Sep 2012). Accelerating Molecular Dynamics Sampling to Quantitatively
Understand Receptor-Guest Interactions. Submitted to NIH/NIGMS.
The major goals of this project are to develop novel sampling-enhanced free energy calculation tools to quantitatively predict protein-ligand, protein-protein and protein-ion interactions. Specific objectives will be accomplished in the above three areas; the third aim will be performed via the collaboration with the Ren group in Austin, who will be responsible for developing new divalent ion polarizable force field parameters. Role: PI.
Yang, W. (Jul 2010). Efficient Prediction of Potential of Mean Forces of Molecular
Transportation Across Membrane Barriers. Submitted to National Science Foundation. Yang, W. (May 2010). Biodefense by Inhibiting IMPDHs. Submitted to National Institute of
Health subcontract via Brandeis University.
Service
Florida State University FSU Department Service Member, General Chemistry Committee (2010–present). Member, Department Award Committee (2009–2010). Member, Department Web Committee (2007–2009). Member, Graduate Recruitment Committee (2006–2009).
Vita for Wei Yang
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Member, Theory Faculty Search Committee (2008). Member, Resource and Space Committee (2007–2008). Member, Faculty Evaluation Committee (2007). FSU Institute or Center Service Member, Computing Facility Advisory Committee for the Institute of Molecular Biophysics
(2007–present). Member, Executive Committee for the Institute of Molecular Biophysics (2007–2009). Member, Local Systems Committee for the School of Computational Science (2007–2008). Member, Computational Statistics Faculty Search Committee for the School of Computational
Science (2007–2008). Member, Graduate Recruitment and Curriculum Committee for the School of Computational
Science (2006–2007). FSU Program Service Coordinator, Biochemistry & Structural Biology Seminar Series (2006–2010).
The Profession Editor for Refereed Journals Section Editor, BMC: Biophysics (2011–present). Guest Editing for Refereed Journals Yang, W. (Ed.). (2011). [Special Issue]. Journal of Computational Chemistry. Yang, W. (Ed.). (2009, August). Free Energy Simulations: Methods and Applications [Special
Issue]. Journal of Computational Chemistry, 30.
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Editorial Board Membership(s) PMC: Biophysics (2008–2011). Guest Reviewer for Refereed Journals Biochemistry (2010–present). The Proceedings of the Pacific Symposium on Biocomputing (2009–present). PLoS Computational Biology (2009–present). Journal of Computational Chemistry (2009–present). Journal of Biological Physics (2008–present). Journal of Computational and Theoretical Nanoscience (2008–present). Journal of Chemical Information and Modeling (2008–present). Journal of Chemical Physics (2008–present). Proteins: Structure, Function, and Bioinformatics (2008–present). Biophysical Journal (2007–present). Journal of Chemical Theory and Computation (2007–present). Journal of the American Chemical Society (2006–present). Journal of Physical Chemistry A & B (2006–present). Chemical Physics Letters (2006–present). Proceedings of the National Academy of Sciences USA (2006–present). Reviewer or Panelist for Grant Applications Czech Science Foundation (2012–present). The Research Grant Council of Hong Kong (2011–present). National Science Foundation (2007–present).
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Cooperative Grants Program of U.S. Civilian Research and Development (2005–present). Service to Professional Associations Co-Organizer, Snowmass Workshop on Free Energy Simulation 2013 (2012–present).
with Andy McCammon and Benoit Roux. Co-organizer, The Telluride Workshop on "Algorithmic Developments on Sampling
Enhancement" 2012 (2010–present). Organizer, The Telluride Workshop on "Free Energy Simulation Methods" 2011
(2010–present). Immediate-Past-Chair, American Chemical Society, Florida Section (FLACS) (2009–present). Organizer, Florida Award Symposium, ACS Regional Meeting (Florida Section) FAME2009
(2009–present). Chair, American Chemical Society, Florida Section (FLACS) (2008–present). Co-Organizer, Bio and Soft Matter Symposium of MMM2008 (2008–present). Immediate-Past-Chair, American Chemical Society, Florida Section (2010–2012). Immediate-Past-Chair, American Chemical Society, Florida Section (2010–2011). Co-Organizer, Telluride Workshop on Free Energy Simulation 2011 (2010–2011). Co-Organizer, The Telluride Workshop on "Free Energy Simulation Methods" 2011
(2010–2011).
With Michael Gilson. Co-organizer, The Telluride Workshop on "Algorithmic Developments on Sampling
Enhancement" 2010 (2008–2010). Organizer, The Florida Award Symposium in Florida American Chemical Society Regional
Meeting 2009 (2010). Co-organizer, The Symposium on "Generalized ensemble simulation methods" in National
American Chemical Society Meeting, San Francisco 2010 (2009–2010). Chair, American Chemical Society, Florida Section (2009–2010).
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Organizer, The Florida Award Symposium in Florida American Chemical Society Regional Meeting 2009 (2010).
Co-organizer, The Telluride Workshop on "Algorithmic Developments on Sampling
Enhancement" 2010 (2009–2010).
With Thomas Woolf and Jianpeng Ma. Organizer, The Florida Award Symposium in Florida American Chemical Society Regional
Meeting 2009 (2009). Chair-Elect, American Chemical Society, Florida Section (2008–2009). Co-Organizer, The Symposium on "Computational modeling of biological and soft condensed
matter systems" in the International Multi-Scale Material Modeling Conference 2008 (2008).
Organizer, The Symposium on "Free energy simulation: From academic research to industrial
application" in National American Chemical Society Meeting, Philadelphia 2008 (2008).
Co-organizer, The Telluride Workshop on "Algorithmic Developments on Sampling
Enhancement" 2012 (2007–2008). Organizer, The Florida Award Symposium in Florida American Chemical Society Regional
Meeting 2009 FAME2008 (2008). The Program Co-Chair, The Florida American Chemical Society Regional Meeting 2008
FAME2008 (2007–2008). Chair-Elect-Designate, American Chemical Society, Florida Section (2007–2008). Chair-Elect, American Chemical Society, Florida Section (FLACS) (2007–2008). Organizer, The Biochemistry Symposium in the Florida American Chemical Society Regional
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