|
501. |
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)
|
|
|
502. |
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 lesion. Biochemistry. 56, 1963-1973 (2017)
|
|
|
503. |
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)
|
|
|
504. |
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)
|
|
|
505. |
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)
|
|
|
506. |
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)
|
|
|
507. |
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)
|
|
|
508. |
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)
|
|
|
509. |
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)
|
|
|
510. |
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)
|
|
|
511. |
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)
|
|
|
512. |
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)
|
|
|
513. |
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)
|
|
|
514. |
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)
|
|
|
515. |
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)
|
|
|
516. |
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)
|
|
|
517. |
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)
|
|
|
518. |
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)
|
|
|
519. |
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)
|
|
|
520. |
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)
|
|
|
521. |
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)
|
|
|
522. |
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)
|
|
|
523. |
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)
|
|
|
524. |
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)
|
|
|
525. |
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)
|
|
|
526. |
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)
|
|
|
527. |
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)
|
|
|
528. |
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)
|
|
|
529. |
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)
|
|
|
530. |
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)
|
|
|
531. |
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)
|
|
|
532. |
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)
|
|
|
533. |
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)
|
|
|
534. |
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)
|
|
|
535. |
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)
|
|
|
536. |
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)
|
|
|
537. |
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)
|
|
|
538. |
Ozer, G., Luque, A., and Schlick, T. The chromatin fiber: Multiscale problems and approaches. Curr. Opin. Struct. Biol. 31, 124-139 (2015)
|
|
|
539. |
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)
|
|
|
540. |
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)
|
|
|
541. |
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)
|
|
|
542. |
Song, J., Li Y., Ji, C., and Zhang, J. Z. H. Functional loop dynamics of the streptavidin-biotin complex. Sci. Rep. 5, 7906 (2015)
|
|
|
543. |
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)
|
|
|
544. |
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)
|
|
|
545. |
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)
|
|
|
546. |
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)
|
|
|
547. |
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)
|
|
|
548. |
Shimshovitz, A., Bačić, Z., and Tannor, D. J. The von Neumann basis in non-Cartesian coordinates: Application to floppy triatomic molecules. J. Chem. Phys. 141, 2341061 (2014)
|
|
|
549. |
Freudenthal, B. D., Beard, W. A., Perera, L., Shock, D. D., Kim, T., Schlick, T., and Wilson, S. H. Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide. Nature. 517, 635–639 (2015)
|
|
|
550. |
Samanta, A., Tuckerman, M. E., Yu, T. Q. Weinan, E. Microscopic mechanisms of equilibrium melting of a solid. Science. 346, 729-732 (2014)
|
|
