Publications

401.

Albaugh, A., Tuckerman, M. E., and Head-Gordon, T. Combining iteration-free polarization with large time step stochastic-isokinetic integration. J. Chem. Theory Comput. 15, 2195-2205 (2019)

402.

Xu, M., He, X., Zhu, T., and Zhang, J. Z. H. A fragment quantum mechanical method for metalloproteins. J. Chem. Theory Comput. 15, 1430-1439 (2019)

403.

Jeon, J. Y., Park, S. Han, J., Maurya, S., Mohanty, A. D. Tian, D. Saikia, N., Hickner, M. A., Ryu, C. Y., Tuckerman, M. E., Paddison, S. J., Kim, Y. S., and Bae, C. Synthesis of aromatic anion exchange membranes by Friedel–Crafts bromoalkylation and cross-linking of polystyrene block copolymers. Macromolecules. 52, 2139-2147 (2019)

404.

Huang, D., Wen, W., Liu, X., Li, Y., and Zhang, J. Z. H. Computational analysis of hot spots and binding mechanism in the PD-1/PD-L1 interaction. RSC Adv. 9, 14944-14956 (2019)

405.

Zelovich, T., Long, Z., Hickner, M., Paddison, S. J., Bae, C., and Tuckerman, M. E. Ab initio molecular dynamics study of hydroxide diffusion mechanisms in nanoconfined structural mimics of anion exchange membranes. J. Phys. Chem. C. 123, 4638-4653 (2019)

406.

Liu, X., Peng, L., and Zhang, J. Z. H. Accurate and efficient calculation of protein-protein binding free energy-interaction entropy with residue type-specific dielectric constants. J. Chem. Inf. Model. 59, 272-281 (2019)

407.

Lauvergnat, D., Felker, P., Scribano, Y., Benoit, D. M., and Bačić, Z. H2, HD, and D2 in the small cage of structure II clathrate hydrate: Vibrational frequency shifts from fully coupled quantum six-dimensional calculations of the vibration-translation-rotation eigenstatesJ. Chem. Phys. 150, 154303 (2019)

408.

Bascom, G. D., Myers, C. G., and Schlick, T. Mesoscale modeling reveals formation of an epigenetically driven HOXC gene hubProc. Natl. Acad. Sci., 116, 4955-4962 (2019)

409.

Tse, C. K. M., Xu, J., Xu, L., Sheong, F. K., Wang, S., Chow, H. Y., Gao, X., Li, X., Cheung, P. P. H., Wang, D., Zhang, Y., and Huang, X. Intrinsic cleavage of RNA polymerase II adopts a nucleobase-independent mechanism assisted by transcript phosphateNature Catalysis, 2, 228-235 (2019)

410.

Lei, J., Sheng, G., Cheung, P. P. H., Wang, S., Li, Y., Gao, X., Zhang, Y., Wang, Y., and Huang, X. Two symmetric arginine residues play distinct roles in Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavageProc. Natl. Acad. Sci., 116, 845-853 (2019)

411.

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)

412.

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)

413.

Yan, Y., Wang, W., Sun, Z., Zhang, J. Z. H., and Ji, C. Protein–ligand empirical interaction components for virtual screeningJ. Chem. Inf. Model. 57, 1793–1806 (2017)

414.

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)

415.

Sun, Z. X., Wang, X. H., and Zhang, J. Z. H. BAR-based optimum adaptive sampling regime for variance minimization in alchemical transformationPhys. Chem. Chem. Phys. 19, 15005 (2017)

416.

Luo, Z., Gao, Y., Zhu, T., Zhang, J. Z. H., and Xia, F. Origins of protons in C−H bond insertion products of phenols: Proton-self-sufficient function via water molecules.  J. Phys. Chem. A. 121, 6523-6529 (2017)

417.

Liu, J., He, X., and Zhang, J. Z. H. Structure of liquid water – a dynamical mixture of tetrahedral and ‘ring-and-chain’ like structuresPhys. Chem. Chem. Phys. 19, 11931-11936 (2017)

418.

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)

419.

Li, M. and Zhang, J. Z. H. Two-bead polarizable water models combined with a two-bead multipole force field (TMFF) for coarse-grained simulation of proteins. Phys. Chem. Chem. Phys. 19, 7410-7419 (2017)

420.

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

421.

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)

422.

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)

423.

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)

424.

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)

425.

Wang, Y., Jin, X., Yu, H. S., Truhlar, D. G., and He, X. Revised M06-L functional for improved accuracy on chemical reaction barrier heights, noncovalent interactions, and solid-state physics. Proc. Natl. Acad. Sci. U.S.A. 114, 8487-8492 (2017)

426.

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)

427.

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)

428.

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

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)

431.

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)

432.

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)

433.

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)

434.

Huang, J., Mei, Y., König, G., Simmonett, A. C., Pickard IV, F. C., Wu, Q., Wang, L.-P., MacKerell Jr., A. D., Brooks, B. R., and Shao, Y. An estimation of hybrid quantum mechanical molecular mechanical polarization energies for small molecules using polarizable force-field approaches. J. Chem. Theory Comput. 13, 679-695 (2017)

435.

Duan, L., Zhu, T., Ji, C., Zhang, Q., and Zhang, J. Z. H. Direct folding simulation of helical proteins using an effective polarizable bond force fieldPhys. Chem. Chem. Phys. 19, 15273-15284 (2017)

436.

Liu, W., Jia, X., Wang, M., Li, P., Wang, X., Hu, W., Zheng, J., and Mei, Y. Calculations of the absolute binding free energies for Ralstonia solanacearum lectins bound with methyl-α-L-fucoside at molecular mechanical and quantum mechanical/molecular mechanical levels. RSC Adv. 7, 38570 (2017)

437.

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)

438.

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)

439.

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)

440.

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)

441.

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)

442.

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)

443.

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)

444.

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)

445.

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)

446.

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)

447.

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)

448.

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)

449.

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)

450.

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

Pages