|
401. |
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)
|
|
|
402. |
Zhu, T., Wu, C., Song, J., Reimers, J. R., and Li, Y. Polarization effect within a protein crystal: A molecular dynamics simulation study. Chem. Phys. Lett. 706, 303-307 (2018)
|
|
|
403. |
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)
|
|
|
404. |
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)
|
|
|
405. |
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 enzymes. Protein Sci. 27, 1526-1534 (2018)
|
|
|
406. |
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)
|
|
|
407. |
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 field. Phys. Chem. Chem. Phys. 19, 15273-15284 (2017)
|
|
|
408. |
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)
|
|
|
409. |
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)
|
|
|
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. |
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 simulations. Chem. Phys. Lett. 706, 594-600 (2018)
|
|
|
413. |
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)
|
|
|
414. |
Xu, M., Zhu, T., and Zhang, J. Z. H. A force balanced fragmentation method for ab initio molecular dynamic simulation of protein. Front. Chem. 6, 189 (2018)
|
|
|
415. |
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)
|
|
|
416. |
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)
|
|
|
417. |
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)
|
|
|
418. |
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)
|
|
|
419. |
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)
|
|
|
420. |
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)
|
|
|
421. |
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)
|
|
|
422. |
Schlick, T. Adventures with RNA graphs. Methods. 143, 16-33, 2018
|
|
|
423. |
Wang, J., Cao, H., Zhang, J. Z. H., and Qi, Y. Computational protein design with deep learning neural networks. Sci. Rep. 8, 6349 (2018)
|
|
|
424. |
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)
|
|
|
425. |
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)
|
|
|
426. |
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)
|
|
|
427. |
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)
|
|
|
428. |
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 2 and epoxides under atmospheric pressure. Molecular Catalysis. 446, 124-130 (2018)
|
|
|
429. |
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)
|
|
|
430. |
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)
|
|
|
431. |
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)
|
|
|
432. |
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)
|
|
|
433. |
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)
|
|
|
434. |
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)
|
|
|
435. |
Tuckerman M. and Ceperley, D. Preface: Special topic on nuclear quantum effects. J. Chem. Phys. 148, 102001 (2018)
|
|
|
436. |
Chen, P.-Y., and Tuckerman, M. E. Molecular dynamics based enhanced sampling of collective variables with very large time steps. J. Chem. Phys. 148, 024106 (2018)
|
|
|
437. |
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 functions. J. Chem. Phys. 148, 102340 (2018)
|
|
|
438. |
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)
|
|
|
439. |
Song, J., Qiu, L., and Zhang, J. Z. H. An efficient method for computing excess free energy of liquid. Science China Chemistry, 61, 135-140 (2018)
|
|
|
440. |
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)
|
|
|
441. |
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)
|
|
|
442. |
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)
|
|
|
443. |
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)
|
|
|
444. |
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)
|
|
|
445. |
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 myoglobin. Chin. J. Chem. Phys. 30, 705-716 (2017)
|
|
|
446. |
Zhang, Y. and He, X. Reaction mechanisms of CO oxidation on cationic, neutral, and anionic X-O-Cu (X = Au, Ag) clusters. Chem. Phys. Lett. 686, 116-123 (2017)
|
|
|
447. |
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)
|
|
|
448. |
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 energy. Chin. J. Chem. Phys. 30, 789−799 (2017)
|
|
|
449. |
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 liquids. RSC Adv. 7, 51521-51527 (2017)
|
|
|
450. |
Sun, Z., Wang, X., and Zhang, J. Z. H. Protonation-dependent base flipping in the catalytic triad of a small RNA. Chem. Phys. Lett. 684, 239-244 (2017)
|
|
