Refereed Journal Articles Published or In Press (Research at FSU)  



Note: The overall citation of the articles produced at FSU (2006-now) is 102.

(28) Min, D., Harris, W., Chen, M., Zheng, L., Lv, C., and Yang, W. 2009. QM/MM alchemical free energy simulation comes of age: An orthogonal space random walk based approach. J. Phys. Chem. B submitted

(27)Ye, X., Luo, R., and Yang, W. 2009. Roles of boundary conditions in DNA simulations: Analysis of ion distributions with the finite-difference Poisson-Boltzmann method. Biophys. J. in press. (26) Chen, M. and Yang, W. 2009. On-the-path random walk to efficiently optimize minimum free energy path. J. Comp. Chem. 30:1649-1653.

(25)Zheng, L., Chen, M., and 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. J. Chem. Phys. 130:234105. Selected by JCP: BioChemical Physics; Selected by Virtual Journal of Biological Physics Research.

(24) Brooks, B. R., Brooks, C. L. III, MacKerell, A. D. Jr., Nilsson, L., Petrella, R. J., Roux, B., Won, Y., Archontis, G., Bartels, C., Boresch, S., Caflisch, A., Caves, L., Cui, Q., Dinner, A. R., Feig, M., Fischer, S., Gao, J., Hodoscek, M., Im, W., Kuczera, K., Lazaridis, T., Ma, J., Ovchinnikov, V., Paci, E., Pastor, R. W., Post, C. P., Pu, J. Z., Schaefer, M., Tidor, B., Venable, R. M., Woodcock, H. L., Wu, X., Yang, W., York, D. M. and Karplus, M. 2009. CHARMM: The Biomolecular Simulation Program. J. Comp. Chem. 30:1545-1614.

(23)Nguyen, L. T., Yang, W., Wang, Q., and 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.

(22)Zheng, L., Chen, M., and Yang, W. 2008. Random walk in orthogonal space to achieve efficient free energy simulation of complex systems. Proc. Natl. Acad. Sci. USA 51:20227-20232. Selected by Faculty1000

(21)Min, D., Josephine, H., Li, H., Lakner, C., Swofford, D., Naylor, G. P., Hedstrom, L., and Yang, W. 2008. An enzymatic atavist revealed in dual pathways for water activation. PLoS Biology 6:1802-1810. Featured in PLoS Biology; Featured in Chemistry & Chemical Engineering News; Featured in Computing Life of National Institute of General Medical Science and other online media.

(20)Zheng, L. and Yang, W. 2008. On the simulated scaling based free energy simulations: Adaptive optimization of the scaling parameter intervals. J. Chem. Phys. 129:124107. Selected by JCP: BioChemical Physics; Selected by Virtual Journal of Biological Physics Research.

(19)Zheng, L. and Yang, W. 2008. Essential energy space random walks to accelerate molecular dynamics simulations: Convergence improvements via an adaptive-length self-healing strategy. J. Chem. Phys. 129:014105. Selected by Virtual Journal of Biological Physics Research.

(18)Zheng, L., Berg, B. A., and Yang, W. 2008. A hybrid recursion method to robustly ensure efficiency in the simulated scaling based free energy simulations. J. Chem. Phys. 129:034105. Selected by Virtual Journal of Biological Physics Research.

(17)Min, D. and Yang, W. 2008. Energy difference space random walk to achieve fast free energy calculations. J. Chem. Phys. (Communication) 128:19102. Selected by Virtual Journal of Biological Physics Research.

(16)Min, D., Li, H., Berg, B. A., Fenley, M. O., and Yang, W. 2008. Efficient sampling of ion motions in molecular dynamics simulations on DNA: Variant Hamiltonion replica exchange strategy. Chem. Phys. Lett. 454:391-395.

(15)Min, D. and Yang, W. 2008. A divide-and-conquer strategy to improve diffusion sampling in generalized ensemble simulations. J. Chem. Phys. 128:094106. Selected by Virtual Journal of Biological Physics Research.

(14)Yang, W., Nymeyer, H., Zhou, H.-X., Berg, B. A., and Brüschweiler, R. 2008. Quantitative computer simulations of biomolecules: A snapshot. J. Comp. Chem. 29:668-672.

(13)Berg, B. A. and Yang, W. 2007. Efficient numerical calculation of the combinatorial entropy of partially ordered ice. J. Chem. Phys. 127:024502. Selected by Virtual Journal of Biological Physics Research.

(12)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. Phys. Rev. Lett. 99:198101. Selected by Virtual Journal of Biological Physics Research.

(11)Fajer, M. I., Li, H., Yang, W., and Fajer, P. G. 2007. Mapping electron paramagnetic resonance spin label conformations by the simulated scaling method. J. Am. Chem. Soc. 129:13840-13846.

(10)Li, H., Min, D., Li, Y., and Yang, W. 2007. Essential energy space random walk via energy space metadynamics method to accelerate molecular dynamics simulations. J. Chem. Phys. 127:094101. Selected by Virtual Journal of Biological Physics Research; The top 3 monthly downloaded paper.

(9)Oruganti, S., Zhang, Y., Li, H., Robinson, H., Terns, R. M., Terns M. P., Yang, W., and Li, H. 2007. Alternative conformations of the Archael Nop56/58-fibrillarin complex imply induced-fit assembly of box C/D RNPs. J. Mol. Biol. 371: 1141-1150.

(8)Min, D., Song, X., Li, H., and Yang, W. 2007. “In-line attack” conformational effect plays a modest role in an enzyme-catalyzed RNA cleavage: A free energy simulation study. Nucl. Acids Res. 35: 4001-4006.

(7)Min, D., Liu, Y., Carbone, I., and Yang, W. 2007. On the convergence improvement in the metadynamics simulations: A Wang-Landau recursion approach. J. Chem. Phys. 126:194104. Selected by Virtual Journal of Biological Physics Research.

(6)Li, H. and Yang, W. 2007. Forging the missing link in free energy estimations: -WHAM in thermodynamic integration, overlap histogramming, and free energy perturbation. Chem. Phys. Lett. 440:155-159.

(5)Li, H., Min, D., Shore, S. G., Lipscomb, W. G., and Yang, W. 2007. Nature of “hydrogen bond” of diborane-benzene: covalent, electrostatic, or dispersive? Inorg. Chem. 46:3956-3959.

(4)Min, D., Li, H., Li, G., Bitetti-Putzer, R., and Yang, W. 2007. Synergistic approach to improve “alchemical” free energy calculations on rugged energy surfaces. J. Chem. Phys. 126:144109.

(3)Li, H. and 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. J. Chem. Phys. 126:114104. Selected by Virtual Journal of Biological Physics Research.

(2)Li, H., Fajer, M., and 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. J. Chem. Phys. 126:024106. Selected by JCP: BioChemical Physics; Selected by Virtual Journal of Biological Physics Research; The top 20 monthly downloaded paper.

(1)Li, H., Li, G., Berg, B. A., and Yang, W. 2006. Finite reservoir replica exchange method to enhance sampling on rugged energy surfaces. J. Chem. Phys. 125:144902-144906. Selected by Virtual Journal of Biological Physics Research.

             

Refereed Journal Articles Published or In Press (Prior to FSU)  



(16)Oliva, C., Rodriguez, A., González, M., and Yang, W. 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.

(15)Bitetti-Putzer, R., Dinner, A. R., Yang, W., and Karplus, M. 2006. Conformational sampling via a self-regulating effective energy surface, J. Chem. Phys. 124:174901-174915.

(14)Gao, Y. Q.*, Yang, W.*, and Karplus, M. 2005. A structure-based model for synthesis and hydrolysis of ATP by F1-ATPase, Cell 123:195-205. (* co-first author)

(13)Banerjee, A., Yang, W., Karplus, M., and Verdine, G. L. 2005. Structure of hOGG1 interrogating undamaged DNA elucidates recognition of damaged DNA. Nature 434:612-618.

(12)Karplus, M., Gao, Y. Q., Ma, J., van der Vaart, A., and Yang, W. 2004. Protein structural transitions and their functional role. Phil. Trans.: Math. Phys. Eng. Sci. 10:1471-2962.

(11)Yang, W., Bitetti-Putzer, R., and Karplus, M. 2004. Chaperoned alchemical free energy simulations: A general method for QM, MM, and QM/MM potentials. J. Chem. Phys. 120:9450-9453.

(10)Yang, W., Bitetti-Putzer, R., and 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. 120:2618-2628.

(9)Gao, Y. Q., Yang, W., Marcus, R. A., and 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.

(8)Bitetti-Putzer, R. Yang, W., and Karplus, M. 2003. Generalized ensembles serve to improve the convergence of free energy simulations. Chem. Phys. Lett. 377:633-641.

(7)Yang, W. and 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.

(6)Fromme, J. C., Bruner, S. D., Yang, W., Karplus, M., and Verdine, G. L. 2003. Product-assisted catalysis in base-excision DNA repair. Nature Struc. Biol. 10:204-211.

(5)Yang, W., Gao, Y. Q., Cui, Q., Ma, J., and Karplus, M. 2003. The missing link between thermodynamics and structure in F1-ATPase. Proc. Natl. Acad. Sci. USA 100:874-879.

(4)Yang, W. and 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.

(3)Yang, W., He, H., and Drueckhammer D. G. 2001. Computer-guided design in molecular recognition: Design of a glucopyranose receptor. Angew. Chem. Int. Ed. 40:1714-1718.

(2)Yang, W. and Drueckhammer, D. G. 2000. Computational studies of the aminolysis of Oxoesters and thioesters in aqueous solution. Org. Lett. 2:4133-4136.

(1)Vogel, K. W., Stark, L. M., Mishra, P. K., Yang, W., and Drueckhammer, D. G. 2000. Investigating the role of the geminal dimethyl groups of coenzyme A: Studies of a didemethyl analogue. Bioorg. Med. Chem. 8:2451-2460.

Invited Book Chapter Published or In Press (FSU research)  



Zheng, L., Li, H., and Yang, W.* 2008. Towards accurate predictions of binding affinities: The simulated scaling based free energy methods. in The Proceedings of Computational Biophysics to Systems Biology volume 40 (NIC-Directors). (Edited by U. H. E. Hansmann etc.)

Invited Book Chapter Published or In Press (Prior to FSU)  



Gao, Y. Q., Yang, W., and Karplus, M. 2007. Thermodynamics and kinetic analysis of F1Fo-ATP synthase. in Modern Methods of Theoretical Physical Chemistry of Biopolymers (Elsevier). (Edited by E. B. Starikov, J. P. Lewis, and S. Tanaka)

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Dr. Wei Yang 
Department of Chemistry and Biochemistry
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL 32306-4390

yyang2@fsu.edu