Publications

1.

Wang, Y., Liu, J., Li, J., and He, X. Fragment-based quantum mechanical calculation of protein–protein binding affinities. J. Comput. Chem. 39, 1617-1628 (2018)

2.

Cai, Y., Fu, I., Geacintov, N. E., Zhang, Y., and Broyde, S. Synergistic effects of H3 and H4 nucleosome tails on structure and dynamics of a lesion-containing DNA: Binding of a displaced lesion partner base to the H3 tail for GG-NER recognitionDNA Repair. 65, 73-78 (2018)

3.

Qiu, L., Shen, C., Song, J.Zhang, Y., and Zhang, J. Z. H. Functional loop dynamics of the S-component of ECF transporter FolTMol. Phys. 116, 2613-2621 (2018)

4.

Zhu, T., Wu, C., Song, J., Reimers, J. R., and Li, Y. Polarization effect within a protein crystal: A molecular dynamics simulation studyChem. Phys. Lett. 706, 303-307 (2018)

5.

Song, J., Qiu, L., and Zhang, J. Z. H. An efficient method for computing excess free energy of liquidSci. China Chem. 61, 135-140 (2018)

6.

Bačić, Z. Perspective: Accurate treatment of the quantum dynamics of light molecules inside fullerene cages: Translation-rotation states, spectroscopy, and symmetry breaking. J. Chem. Phys. 149, 100901 (2018)

7.

Bascom, G. D. and Schlick, T. Chromatin fiber folding directed by cooperative histone tail acetylation and linker histone binding. Biophys. J. 114, 2376-2385 (2018)

8.

Cuendet, M. A., Margul, D. T., Schneider, E., Vogt-Maranto, L., and Tuckerman, M. E. Endpoint-restricted adiabatic free energy dynamics approach for the exploration of biomolecular conformational equilibria. J. Chem. Phys. 149, 072316 (2018)

9.

Gao, Y., Zhu T., Zhang, C. M., Zhang, J. Z. H., and Mei, Y. Comparison of the unfolding and oligomerization of human prion protein under acidic and neutral environments by molecular dynamics simulationsChem. Phys. Lett. 706, 594-600 (2018)

10.

Silletta, E. V., Tuckerman, M. E., and Jerschow, A. Unusual protont transfer kinetics in water at the temperature of maximum density. Phys. Rev. Lett. 121, 076001 (2018)

11.

Xu, M., Zhu, T., and Zhang, J. Z. H. A force balanced fragmentation method for ab initio molecular dynamic simulation of proteinFront. Chem. 6, 189 (2018)

12.

Sun, X., Zhang, P., Lai, Y., Williams, K. L., Cheung, M. S., Dunietz, B. D., and Geva, E. Computational study of charge-transfer dynamics in the carotenoid–porphyrin–C60 molecular triad solvated in explicit tetrahydrofuran and its spectroscopic signature. J. Phys. Chem. C. 122, 11288-11299 (2018)

13.

Cong, Y., Li, Y., Jin, K., Zhong, S., Zhang, J. Z. H., Li, H., and Duan, L. Exploring the reasons for decrease in binding affinity of HIV-2 against HIV-1 protease complex using interaction entropy under polarized force field. Front. Chem. 6, 380 (2018)

14.

Chen, J., Duan, L., Ji, C., and Zhang, J. Z. H. Computational study of PCSK9-EGFA complex with effective polarizable bond force field. Front. Mol. Biosci. 4, 101 (2018)

15.

Zhou, Y., Liu, X., Zhang, Y., Peng, L. and Zhang, J. Z. H. Residue-specific free energy analysis in ligand bindings to JAK2. Mol. Phys. 116, 2633-2641 (2018)

16.

Li, Y., Wang, X., Ren, L., Cao, X., Ji, C., Xia, F., and Zhang, J. Z. H. Electrostatic polarization effect on cooperative aggregation of full length human islet amyloid. J. Chem. Inf. Model.  58, 1587-1595 (2018)

17.

Sun, H., Duan, L., Chen, F., Liu, H., Wang, Z., Pan, P., Zhu, F., Zhang, J. Z. H., and Hou, T. Assessing the performance of MM/PBSA and MM/GBSA methods. 7. Entropy effects on the performance of end-point binding free energy calculation approaches. Phys. Chem. Chem. Phys. 20, 14450-14460 (2018)

18.

Jain, S., Bayrak, C. S., Petingi, L., and Schlick, T. Dual graph partitioning highlights a small group of pseudoknot-containing RNA submotifs. Genes. 9, 371 (2018)

19.

Schlick, T. Adventures with RNA graphs. Methods. 143, 16-33, 2018

20.

Wang, J., Cao, H., Zhang, J. Z. H., and Qi, Y. Computational protein design with deep learning neural networks. Sci. Rep. 8, 6349 (2018)

21.

Li, Y., Zhang, Y., Großerüschkamp, F., Stephan, S., Cui, Q., Kötting, C., Xia, F., and Gerwert, K. Specific substates of Ras to interact with GAPs and effectors: Revealed by theoretical simulations and FTIR experiments. J. Phys. Chem. Lett. 9, 1312-1317 (2018)

22.

Liu, X., Peng, L., Zhou, Y., Zhang, Y, and Zhang, J. Z. H. Computational alanine scanning with interaction entropy for protein–ligand binding free energies. J. Chem. Theory Comput. 14, 1772-1780 (2018)

23.

Qiu, L., Yan, Y., Sun, Z., Song, J., and Zhang, J. Z. H. Interaction entropy for computational alanine scanning in protein–protein binding. Wiley Interdiscip. Rev. Comput. Mol. Sci. 8, e1342 (2018)

24.

Liu, J., Swails, J., Zhang, J. Z. H., He, X., and Roitberg, A. E. A coupled ionization-conformational equilibrium is required to understand the properties of ionizable residues in the hydrophobic interior of staphylococcal nuclease. J. Am. Chem. Soc. 140, 1639–1648 (2018)

25.

Ji, L., Luo, Z., Zhang, Y., Wang, R., Ji, Y., Xia, F., Gao, G. Imidazolium ionic liquids/organic bases: Efficient intermolecular synergistic catalysts for the cycloaddition of  CO and epoxides under atmospheric pressure. Molecular Catalysis. 446, 124-130 (2018)

26.

Wang, P., Liu, L., Luo, Z., Zhou, Q., Lu, Y., Xia, F., and Liu, Y. Combination of transition metal Rh-catalysis and tautomeric catalysis through a bi-functional ligand for one-pot tandem methoxycarbonylation-aminolysis of olefins towards primary amides. J. Catal. 361, 230-237 (2018)

27.

Bačić, Z., Xu, M., and Felker, P. M. Coupled translation-rotation dynamics of H2 and H2O inside C60: Rigorous quantum treatment. Adv. Chem. Phys. 163, 195-216 (2018)

28.

Wang, X., Tu, X., Zhang, J. Z. H., and Sun, Z. BAR-based optimum adaptive sampling regime for variance minimization in alchemical transformation: the nonequilibrium stratification. Phys. Chem. Chem. Phys. 20, 2009-2021 (2018)

29.

Powers, A., Scribano, Y., Lauvergnat, D., Mebe, E., Benoit, D. M., and Bačić, Z. The effect of the condensed-phase environment on the vibrational frequency shift of a hydrogen molecule inside clathrate hydrates. J. Chem. Phys. 148, 144304 (2018)

30.

Gao, B., Jiang, S., Wang, L., Zhang, L., Wei, D. Energy and conformation determine the enantioselectivity of enzyme. Biochem. Eng. J. 129, 106-112 (2018)

31.

Jin, X., Zhu, T., Zhang, J. Z. H., and He, X. Automated fragmentation QM/MM calculation of NMR chemical shifts for protein-ligand complexes. Front. Chem. 6, 150 (2018)

32.

Tuckerman M. and Ceperley, D. Preface: Special topic on nuclear quantum effectsJ. Chem. Phys. 148, 102001 (2018) 

33.

Chen, P.-Y., and Tuckerman, M. E. Molecular dynamics based enhanced sampling of collective variables with very large time stepsJ. Chem. Phys. 148, 024106 (2018)

34.

Cendagorta, J. R., Bačić, Z., and Tuckerman, M. E. An open-chain imaginary-time path-integral sampling approach to the calculation of approximate symmetrized quantum time correlation functionsJ. Chem. Phys. 148, 102340 (2018)

35.

Liu, J., He, X., Zhang, J. Z. H., and Qi, L.-W. Hydrogen-bond structure dynamics in bulk water: Insights from ab initio simulations with coupled cluster theory. Chem. Sci. 9, 2065-2073 (2018)

36.

Song, J., Qiu, L., and Zhang, J. Z. H. An efficient method for computing excess free energy of liquidScience China Chemistry, 61, 135-140 (2018)  

37.

Glover, W. J., Mori, T., Schuurman, M. S., Boguslavskiy, A. E., Schalk, O., Stolow, A., and Martínez, T. J. Excited state non-adiabatic dynamics of the smallest polyene, trans 1,3-butadiene. II. Ab initio multiple spawning simulations. J. Chem. Phys. 148, 164303 (2018)

38.

Hagras, M. A. and Glover, W. J. Polarizable embedding for excited-state reactions: Dynamically weighted polarizable QM/MM. J. Chem. Theory Comput. 14, 2137-2144 (2018)

39.

Felker, P. M. and Bačić, Z. Accurate quantum calculations of translation-rotation eigenstates in electric-dipole-coupled H2O@ C60 assemblies. Chem. Phys. L. 683, 172–178 (2017)

40.

Rooklin, D., Modell, A. E., Li, H., Berdan, V., Arora, P. S., and Zhang, Y. Targeting unoccupied surfaces on protein–protein interfaces. J. Am. Chem. Soc., 139, 15560–15563 (2017)

41.

Felker, P. M. and Bačić, Z. Accurate quantum calculations of translation-rotation eigenstates in electric-dipole-coupled H 2 O@C 60 assemblies. Chem. Phys. Lett. 683, 172-178 (2017)

42.

Jiang, M., Zhang, L., Wang, F., Zhang, J., Liu, G., Gao, B., and Wei, D. Novel application of magnetic protein: Convenient one-step purification and immobilization of proteins. Sci. Rep. 7, 13329 (2017)

43.

Wang, Y., Wang, X., Truhlar, D. G., and He, X. How well can the M06 suite of functionals describe the electron densities of Ne, Ne6+, and Ne8+? J. Chem. Theory Comput. 13, 6068-6077 (2017)

44.

Wang, X., Zhang, J. Z. H., and He, X. Ab initio quantum mechanics/molecular mechanics molecular dynamics simulation of CO in the heme distal pocket of myoglobinChin. J. Chem. Phys. 30, 705-716 (2017)

45.

Zhang, Y. and He, X. Reaction mechanisms of CO oxidation on cationic, neutral, and anionic X-O-Cu (X = Au, Ag) clustersChem. Phys. Lett. 686, 116-123 (2017)

46.

Wang, Y., Liu, J., Zhang, L., He, X., Zhang, J. Z. H. Computational search for aflatoxin binding proteins. Chem. Phys. Lett. 685, 1-8 (2017)

47.

Li, P., Jia, X., Wang, M., and Mei, Y. Comparison of accuracy and convergence rate between equilibrium and nonequilibrium alchemical transformations for calculation of relative binding free energyChin. J. Chem. Phys. 30, 789−799 (2017)

48.

Huang, M., Luo, Z., Zhu, T., Chen, J., Zhang, J. Z., and Xia, F. A theoretical study of the substituent effect on reactions of amines, carbon dioxide and ethylene oxide catalyzed by binary ionic liquidsRSC Adv. 7, 51521-51527 (2017) 

49.

Sun, Z., Wang, X., and Zhang, J. Z. H. Protonation-dependent base flipping in the catalytic triad of a small RNAChem. Phys. Lett. 684, 239-244 (2017)

50.

Sun, Z., Zhu, T., Wang, X., Mei, Y., and Zhang, J. Z. H. Optimization of convergence criteria for fragmentation methodsChem. Phys. Lett. 687, 163-170 (2017)

51.

Liu, F., Yang, Z., Yu, Y., Mei, Y., and Houk, K. N. Bimodal Evans–Polanyi relationships in dioxirane oxidations of sp3 C–H: Non-perfect synchronization in generation of delocalized radical intermediatesJ. Am. Chem. Soc. 139, 16650-16656 (2017)

52.

Jain, S. and Schlick, T. F-RAG: Generating atomic coordinates from RNA graphs by fragment assembly. J. Mol. Biol. 429, 3587-3605 (2017)

53.

Rao, S. S. P., Huang, S. C., Brian, G. S. H., Engreitz, J. M., Perez, E. M., Kieffer-Kwon, K. R., Sanborn, A. L., Johnstone, S. E., Bascom, G. D., Bochkov, I. D., Huang, X., Shamim, M. S., Shin, J., Turner, D., Ye, Z., Omer, A. D., Robinson, J. T., Schlick, T., Bernstein, B. E., Casellas, R., Lander, E. S., and Aiden, E. L. Cohesin loss eliminates all loop domains. Cell. 171, 305-320.e24 (2017)

54.

Felker, P.M., Vlček, V., Hietanen, I., Fitzgerald, S., Neuhauser, D. and Bačić, Z.Explaining the symmetry breaking observed in the endofullerenes H2@C60, HF@C60, and H2O@C60Phys. Chem. Chem. Phys., 19, 31274-31283 (2017)

55.

Schneider, E., Dai, L., Topper, R. Q., Drechsel-Grau, C., and Tuckerman, M. E. Stochastic neural network approach for learning high-dimensional free energy surfaces. Phys. Rev. Lett. 119, 150601 (2017)

56.

Wang, M., Li, P., Jia, X., Liu, W., Shao, Yi., Hu, W., Zheng, J., Brooks, B. R., and Mei, Y. Efficient strategy for the calculation of solvation free energies in water and chloroform at the quantum mechanical/molecular mechanical level. J. Chem. Inf. Model. 57, 2476-2489 (2017)

57.

Brockherde, F., Vogt, L., Li, L., Tuckerman, M. E., Burke, K., and Müller, K. R. Bypassing the Kohn-Sham equations with machine learning. Nat. Commun. 8, 872 (2017)

58.

Dupuis, R., Benoit, M., Tuckerman, M. E., and Méheut, M. Importance of a fully anharmonic treatment of equilibrium isotope fractionation properties of dissolved ionic species as evidenced by Li+ (aq). Acc. Chem. Res. 50, 1597-1605 (2017)

59.

Shtukenberg, A. G., Zhu, Q., Carter, D. J., Vogt, L., Hoja, J., Schneider, E., Song, H., Pokroy, B., Polishchuk, I., Tkatchenko, A., Oganov, A. R., Rohl, A. L., Tuckerman, M. E., and Kahr, B. Powder diffraction and crystal structure prediction identify four new coumarin polymorphs.  Chem. Sci. 8, 4926-4940 (2017)

60.

Sepehr, F., Liu, H., Luo, X., Bae, C., Tuckerman, M. E., Hickner, M. A., and Paddison, S. J. Mesoscale simulations of anion exchange membranes based on quaternary ammonium tethered triblock copolymers. Macromolecules. 50, 4397-4405 (2017)

61.

Bascom, G. D., Kim, T., and Schlick, T. Kilobase pair chromatin fiber contacts promoted by living-system-like DNA linker length distributions and nucleosome depletion. J. Phys. Chem. B. 121, 3882-3894 (2017)

62.

Bascom, G. and Schlick, T. Linking chromatin fibers to gene folding by hierarchical looping. Biophys. J. 112, 434-445 (2017)

63.

Rooklin, D. W., Modell, A. E., Li, H., Berdan, V., Arora, P. S., and Zhang, Y.  Targeting unoccupied surfaces on protein-protein interfacesJ. Am. Chem. Soc. DOI: 10.1021/jacs.7b05960 (2017)

64.

Mu, H., Geacintov, N. E., Min, J. H., Zhang, Y., and Broyde, S. Nucleotide excision repair lesion-recognition protein Rad4 captures a pre-flipped partner base in a benzo[a]pyrene-derived DNA lesion: How structure impacts the binding pathway. Chem. Res. Toxicol. 30, 1344-1354 (2017)

65.

Zho, C. C., Farr, E. P., Glover, W. J., and Schwartz, B. J. Temperature dependence of the hydrated electron’s excited-state relaxation. I. Simulation predictions of resonance Raman and pump-probe transient absorption spectra of cavity and non-cavity models. J. Chem. Phys. 147, 074503 (2017)

66.

Jin, X., Zhang, J. Z. H., and He, X. Full QM calculation of RNA energy using electrostatically embedded generalized molecular fractionation with conjugate caps method. J. Phys. Chem. A. 121, 2503–2514 (2017)

67.

Yan, Y., Yang, M., Ji, C., and Zhang, J. Z. H. Interaction entropy for computational alanine scanning. J. Chem. Inf. Model. 57, 1112-1122, (2017)

68.

Liu, J., Qi L., Zhang, J. Z. H., and He, X. Fragment quantum mechanical method for large-sized ion-water clusters. J. Chem. Theory Comput. 13, 2021-2034 (2017)

69.

Sun, Z., Yan, Y. N., Yang, M., and Zhang, J. Z. H. Interaction entropy for protein-protein bindingJ. Chem. Phys. 146, 124124 (2017)

70.

Gao, Y., Zhang, C., Zhang, J. Z. H., and Mei, Y. Evaluation of the coupled two-dimensional main chain torsional potential in modeling intrinsically disordered proteins. J. Chem. Inf. Model. 57, 267-274 (2017)

71.

Li, M. and Zhang, J. Z. H. Protein simulation using coarse-grained two-bead multipole force field with polarizable water models. J. Chem. Phys. 146, 065101 (2017)

72.

Duan, L. L., Zhu, T., Li, Y. C., Zhang, Q. G., and Zhang, J. Z. H. Effect of polarization on HIV-1protease and fluoro-substituted inhibitors binding energies by large scale molecular dynamics simulations. Sci. Rep. 7, 42223 (2017)

73.

Fu, I., Cai, Y., Zhang, Y., Geacintov, N. E., and Broyde, S. Nucleosome histone tail conformation and dynamics: Impacts of lysine acetylation and a nearby minor groove benzo[a]pyrene-derived lesionBiochemistry. 56, 1963-1973 (2017)

74.

Felker, P. M. and Bačić, Z. Electric-dipole-coupled H2O@C60 dimer: Translation-rotation eigenstates from twelve-dimensional quantum calculations. J. Chem. Phys. 146, 084303 (2017)

75.

Wang, C. and Zhang, Y. Improving scoring-docking-screening powers of protein-ligand scoring functions using random forest. J. Comput. Chem. 38, 169 - 177 (2017)

76.

Hou, X., Rooklin, D., Fang, H., and Zhang, Y. Resveratrol serves as a protein-substrate interaction stabilizer in human SIRT1 activation. Sci. Rep. 6, 38186 (2016)

77.

Zhou, Y., Wang, S., Li, Y., and Zhang, Y. Born-Oppenheimer ab initio QM/MM molecular dynamics simulations of enzyme reactions. Methods Enzymol. 577, 105-118 (2016)

78.

Glover, W. J. and Schwartz, B. J. Short-range electron correlation stabilizes non-cavity solvation of the hydrated electron. J. Chem. Theory Comput. 12, 5117–5131 (2016)

79.

Casey, J. R., Schwartz, B. J., and Glover W. J. Free energies of cavity and noncavity hydrated electrons near the instantaneous air/water interface. J. Phys. Chem. Lett. 7, 3192−3198 (2016)

80.

Cendagorta, J. R., Powers, A., Hele, T. J., Marsalek, O., Bačić, Z., and Tuckerman, M. E. Competing quantum effects in the free energy profiles and diffusion rates of hydrogen and deuterium molecules through clathrate hydrates. Phys. Chem. Chem. Phys. 18, 32169-32177 (2016)

81.

Felker, P. M. and Bačić, Z. Translation-rotation states of H2 in C60: New insights from a perturbation-theory treatment. J. Chem. Phys. 145, 084310 (2016)

82.

Liu, Y., Yu, Z., Zhang, J. Z. H., Liu, L., Xia, F., and Zhang, J., Origins of unique gold-catalysed chemo-and site-selective C–H functionalization of phenols with diazo compounds. Chem. Sci. 7, 1988-1995 (2016)

83.

Liu, Y., Yu, Z., Luo, Z., Zhang, J. Z. H., Liu, L., and Xia, F. Mechanistic investigation of aromatic C (sp2)–H and alkyl C (sp3)–H bond insertion by gold carbenes. J. Phys. Chem. A. 120, 1925-1932 (2016)

84.

Li, M., Zhang, J. Z. H., and Xia, F. Constructing optimal coarse-grained sites of huge biomolecules by fluctuation maximization. J. Chem. Theory Comput., 12, 2091-2100 (2016)

85.

Duan, L. L., Liu, X., and Zhang, J. Z. H. Interaction entropy: A new paradigm for highly efficient and reliable computation of protein–ligand binding free energy. J. Am. Chem. Soc. 138, 5722–5728 (2016)

86.

Liu, X., Liu, J. F., Zhu, T., Zhang, L. J., He, X., and Zhang, J. Z. H. PBSA_E: A PBSA-based free energy estimator for protein–ligand binding affinity. J. Chem. Inf. Model. 56, 854-861 (2016)

87.

Li, M., Zhang, J. Z. H., and Xia, F. A new algorithm for construction of coarse-grained sites of large biomolecules. J. Comput. Chem. 37, 795–804 (2016)

88.

Jia, X. Y., Wang, M. T., Shao, Y. H., König, G., Brooks, B. R., Zhang, J. Z. H., and Mei, Y. Calculations of solvation free energy through energy reweighting from molecular mechanics to quantum mechanics. J. Chem. Theory Comput. 12, 499–511 (2016)

89.

Felker, P. M. and Bačić, Z. Communication: Quantum six-dimensional calculations of the coupled translation-rotation eigenstates of H2O@C60. J. Chem. Phys. 144, 201101 (2016)

90.

Liu, J. F., Zhang, J. Z. H., and He, X. Fragment quantum chemical approach to geometry optimization and vibrational spectrum calculation of proteins. Phys. Chem. Chem. Phys. 18, 1864-1875 (2016)

91.

Zhou, Y., Xie, D., and Zhang, Y. Amide rotation hindrance predicts proteolytic resistance of cystine-knot peptides. J. Phys. Chem. Lett. 7, 1138-1142 (2016)

92.

Fu, I., Cai, Y., Zhang, Y., Geacintov, N. E., and Broyde, S. Entrapment of a histone tail by a DNA lesion in a nucleosome suggests the lesion impacts epigenetic marking: A molecular dynamics study. Biochemistry. 55, 239 - 242 (2016)

93.

Powers, A., Marsalek, O., Xu, M., Ulivi, L., Colognesi, D., Tuckerman, M. E., and Bačić, Z. Impact of the condensed-phase environment on the translation-rotation eigenstates and spectra of a hydrogen molecule in clathrate hydrates. J. Phys. Chem. Lett. 7, 308–313 (2016)

94.

Liu, J. F., Wang, X. W., Zhang, J. Z. H., and He, X. Calculation of protein–ligand binding affinities based on a fragment quantum mechanical method. RSC Adv. 5, 107020-107030 (2015)

95.

Jia, X. Y., Mei, Y., Zhang, J. Z. H., and Mo, Y. Hybrid QM/MM study of FMO complex with polarized proteinspecific charge. Sci. Rep. 5, 17096 (2015)

96.

Liu, J. F., Zhu, T., Wang, X. W., He, X., and Zhang, J. Z. H. Quantum fragment based ab initio molecular dynamics for proteins. J. Chem. Theory Comput. 11, 5897−5905 (2015)

97.

Li, Y., Zhang, J. Z. H., and Mei, Y. Molecular dynamics simulation of protein crystal with polarized protein-specific charge. Biophys. J. 108, 160a (2015)

98.

Gao, Y., Li, Y., Zhang, J. Z. H., and Mei, Y. A coupled two-dimensional main chain torsional potential for protein dynamics. Biophys. J. 108, 159a-160a (2015)

99.

Gao, Y., Li, Y., Mou, L., Lin, B., Zhang, J. Z. H., and Mei, Y. Correct folding of an alpha-helix and a beta-hairpin using a polarized 2D torsional potential. Sci. Rep. 5, 10359 (2015)

100.

Wang, X., Zhang, J. Z. H., and He, X. Quantum mechanical calculation of electric fields and vibrational Stark shifts at active site of human aldose reductase. J. Chem. Phys. 143, 184111 (2015)

101.

Gong, W., Wu, R., and Zhang, Y. Thiol versus hydroxamate as zinc binding group in HDAC inhibition: An ab initio QM/MM molecular dynamics study. J. Comput. Chem. 36, 2228-2235 (2015)

102.

Swails, J., Zhu, T., He, X., and Case, D. A. AFNMR: Automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules. J. Biomol. NMR. 63, 125-139 (2015)

103.

Chen, J., Wang, X., Zhu, T., Zhang, Q., and Zhang, J. Z. H. A comparative insight into amprenavir resistance of mutations V32I, G48V, I50V, I54V, and I84V in HIV-1 protease based on thermodynamic integration and MM-PBSA methods. J. Chem. Inf. Model. 55, 1903–1913 (2015)

104.

Xu, M., Ye, S., and Bačić, Z. General selection rule in the inelastic neutron scattering spectroscopy of a diatomic molecule confined inside a near-spherical nanocavity. J. Phys. Chem. Lett. 6, 3721–3725 (2015)

105.

Mu, H., Geacintov, N. E., Zhang, Y., and Broyde, S. Recognition of damaged DNA for nucleotide excision repair: A correlated motion mechanism with a mismatched cis-syn thymine dimer lesion. Biochemistry. 54, 5263-5267 (2015)

106.

Yang, J., Song, J., Zhang, J. Z. H., and Ji, C. Effect of mismatch on binding of ADAR2/GluR-2 pre-mRNA complex. J. Mol. Model. 21, 222 (2015)

107.

Rooklin, D., Wang, C., Katigbak, J., Arora, P. S., and Zhang, Y. AlphaSpace: Fragment-centric topographical mapping to target protein–protein interaction interfaces. J. Chem. Inf. Model. 55, 1585–1599 (2015)

108.

Mei, Y., Simmonett, A. C., Pickard, F. C., DiStasio, R., Brooks, B. R., and Shao, Y.  Numerical study on the partitioning of the molecular polarizability into fluctuating charge and induced atomic dipole contributions. J. Phys. Chem. A. 119, 5865–5882 (2015)

109.

Wang, X., Ji, C., and Zhang, J. Z. H. Glycosylation modulates human CD2-CD58 adhesion via conformational adjustment. J. Phys. Chem. B. 119, 6493–6501 (2015)

110.

Ozer, G., Luque, A., and Schlick, T. The chromatin fiber: Multiscale problems and approaches. Curr. Opin. Struct. Biol. 31, 124-139 (2015)

111.

Zhou J., Li M., Chen N., Wang S., Luo H., Zhang Y., and Wu, R. Computational design of a time-dependent histone deacetylase 2 selective inhibitor. ACS Chem. Biol. 10, 687-692 (2015)

112.

Gao, Y., Li, Y., Mou, L., Hu, W., Zheng, J., Zhang, J. Z. H., and Mei, Y. Coupled two-dimensional main-chain torsional potential for protein dynamics II: Performance and validation. J. Phys. Chem. B. 119, 4188–4193 (2015)

113.

Chen, M., Yu, T. Q., and Tuckerman, M. E. Locating landmarks on high-dimensional free energy surfaces. Proc. Natl. Acad. Sci. 112, 3235-3240 (2015)

114.

Song, J., Li Y., Ji, C., and Zhang, J. Z. H. Functional loop dynamics of the streptavidin-biotin complex. Sci. Rep. 5, 7906 (2015)

115.

Lei, J., Zhou, Y., Xie, D., and Zhang, Y. Mechanistic insights into a classic wonder drug-aspirin. J. Am. Chem. Soc. 137, 70-73 (2015)

116.

Ozer, G., Collepardo-Guevara, R., and Schlick, T. Forced unraveling of chromatin fibers with nonuniform linker DNA lengths. J. Phys. Condens. Matter. 27, 064113 (2015)

117.

Li, M., Zhang, J. Z. H., and Xia, F. Heterogeneous elastic network model improves description of slow motions of proteins in solution. Chem. Phys. Lett. 618, 102-107 (2015)

118.

Lei, J., Zhou, Y., Xie, D., and Zhang, Y. Mechanistic insights into a classic wonder drug-aspirin. J. Am. Chem. Soc. 137, 70–73 (2015)

119.

Sirin, G. S. and Zhang, Y. How is acetylcholinesterase phosphonylated by soman? An ab initio QM/MM molecular dynamics study. J. Phys. Chem. A. 118, 9132–9139 (2014)

120.

Yu, T. Q., Chen, P. Y., Chen, M., Samanta, A., Vanden-Eijnden, E., and Tuckerman, M. Order-parameter-aided temperature-accelerated sampling for the exploration of crystal polymorphism and solid-liquid phase transitions. J. Chem. Phys. 140, 214109 (2014)

121.

Li, M., Xu, W., Zhang, J. Z. H., and Xia, F. Combined effect of confinement and affinity of crowded environment on conformation switching of adenylate kinase. J Mol. Model. 20, 2530 (2014)

122.

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