Publications

401.

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)

402.

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)

403.

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)

404.

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)

405.

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)

406.

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)

407.

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)

408.

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)

409.

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

410.

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)

411.

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)

412.

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)

413.

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)

414.

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)

415.

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)

416.

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)

417.

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)

418.

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)

419.

Yao, Z., Jiang, S., Zhang, L., Gao, B., He, X.Zhang, J. Z. H., and Wei, D. Crius: A novel fragment‐based algorithm of de novo substrate prediction for enzymesProtein Sci. 27, 1526-1534 (2018)

420.

Bačić, Z., Vlček, V., Neuhauser, D., and Felker, P. M. Effects of symmetry breaking on the translation–rotation eigenstates of H2, HF, and H2O inside the fullerene C60Faraday Discuss. 212, 547-567 (2018)

421.

Wang, M., Mei, Y., and Ryde, U. Predicting relative binding affinity using nonequilibrium QM/MM simulationsJ. Chem. Theory Comput. 14, 6613-6622 (2018)

422.

Li, P., Jia, X., Pan, X., Shao, Y., and Mei, Y. Accelerated computation of free energy profile at ab initio quantum mechanical/molecular mechanics accuracy via a semi-empirical reference potential. I. weighted thermodynamics perturbation. J. Chem. Theory Comput. 14, 5583-5596 (2018)

423.

Li, P., Liu, F., Jia, X., Shao, Y., Hu, W., Zheng, J., and Mei, Y. Efficient computation of free energy surfaces of Diels–Alder reactions in explicit solvent at ab initio QM/MM level. Molecules. 23, 2487 (2018)

424.

Liu, J., Zhang, J. Z. H., and He, X. Probing the ion-specific effects at the water/air interface and water-mediated ion pairing in sodium halide solution with ab initio molecular dynamics. J. Phys. Chem. B. 122, 10202-10209 (2018)

425.

Jain, S., Laederach, A., Ramos, S. B. V., and Schlick, T. A pipeline for computational design of novel RNA-like topologies. Nucleic Acids Res. 46, 7040–7051 (2018)

426.

Shiga, M. and Tuckerman, M. E. Finding free-energy landmarks of chemical reactions. J. Phys. Chem. Lett. 9, 6207−6214 (2018)

427.

Chen, J., Huang, M., and Xia, F. Conformer-related pathways in cycloaddition of vinylaziridines and alkynes catalyzed by rhodium(I)-complex. Chem. Phys. Lett. 713, 21-25 (2018)

428.

Mu, H., Zhang, Y., Geacintov, N. E., and Broyde, S. Lesion sensing during initial binding by yeast XPC/Rad4: Toward predicting resistance to nucleotide excision repairChem. Res. Toxicol. 31, 1260-1268 (2018)

429.

Hou, X., Rooklin, D., Yang, D., Liang, X., Li, K., Lu, J., Wang, C., Xiao, P., Zhang, Y., Sun, J., and Fang, H. Computational strategy for bound state structure prediction in structure-based virtual screening: A case study of protein tyrosine phosphatase receptor type O inhibitors. J. Chem. Inf. Model. 58, 2331-2342 (2018)

430.

Li, Y., Cong, Y., Feng, G., Zhong, S., Zhang, J. Z. H., Sun, H., and Duan, L. The impact of interior dielectric constant and entropic change on HIV-1 complex binding free energy prediction. Struct. Dyn. 5, 064101 (2018)

431.

Wang, Y., Verma, P., Jin, X., Truhlar, D. G., and He, X. Revised M06 density functional for main-group and transition-metal chemistry. Proc. Natl. Acad. Sci. U.S.A. 115, 10257–10262 (2018)

432.

Chen, J., Wang, X., Zhang, J. Z. H., and Zhu, T. Effect of Substituents in Different Positions of Aminothiazole Hinge-Binding Scaffolds on Inhibitor-CDK2 Association Probed by Interaction Entropy Method. ACS Omega. 3, 18052-18064 (2018)

433.

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)

434.

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)

435.

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)

436.

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)

437.

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)

438.

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)

439.

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)

440.

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

441.

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)

442.

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)

443.

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. 139, 15560-15563 (2017)

444.

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)

445.

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

446.

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)

447.

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)

448.

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)

449.

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)

450.

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)

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