Publications

301.

Burnham, C. J., Futera, Z., Bačić, Z., and English, N. J. Hydrogen intramolecular stretch redshift in the electrostatic environment of type II clathrate hydrates from Schrödinger equation treatment. Appl. Sci. 10, 8504 (2020)

302.

Hu, W., Li, P., Wang, J.-N., Xue, Y., Mo, Y., Zheng, J., Pan, X., Shao, Y., Mei, Y. Accelerated computation of free energy profile at ab initio quantum mechanical/molecular mechanics accuracy via a semiempirical reference potential. 3. Gaussian smoothing on density-of-states. J. Chem. Theory Comput. 16, 6814–6822 (2020)

303.

Song, H., Vogt-Maranto, L., Wiscons, R., Matzger, A. J., and Tuckerman, M. E. Generating cocrystal polymorphs with information entropy driven by molecular dynamics-based enhanced sampling. J. Phys. Chem. Lett. 11, 9751–9758 (2020)

304.

Abreu, C. R. A. and Tuckerman, M. E. Molecular dynamics with very large time steps for the calculation of solvation free energiesJ. Chem. Theory Comput. 16, 7314–7327 (2020)

305.

Bao, J., He, X., and Zhang, J. Z. H. Development of a new scoring function for virtual screening: APBScoreJ. Chem. Inf. Model. 60, 6355–6365 (2020)

306.

Cendagorta, J. R., Shen, H., Bačić, Z., and Tuckerman, M. E. Enhanced sampling path integral methods using neural network potential energy surfaces with application to diffusion in hydrogen hydratesAdv. Theory Simul. 4, 2000258 (2020)

307.

Zha, J., Zhang, Y., Xia, K., Gräter, F., and Fei Xia. Coarse-grained simulation of mechanical properties of single microtubules with micrometer length. Front. Biosci. 7, 632122 (2020)

308.

Zhang, B., Ma, Y., Jin, X., Wang, Y., Suo, B., He, X., and Jin, Z. GridMol2. 0: Implementation and application of linear‐scale quantum mechanics methods and molecular visualization. Int. J. Quantum Chem. 120, e26402 (2020)

309.

Shan, J., Pan, X., Wang, X., Xiao, X., and Ji, C. FragRep: A web server for structure-based drug design by fragment replacement. J. Chem. Inf. Model. 60, 5900–5906 (2020)

310.

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)

311.

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)

312.

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)

313.

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)

314.

Sun, Z., Wang, X., and Zhang, J. Z. H. Determination of binding affinities of 3-Hydroxy-3-Methylglutaryl Coenzyme A reductase inhibitors from free energy calculation. Chem. Phys. Lett. 723, 1-10 (2019)

315.

Wang, X., Tu, X., Deng, B., Zhang, J. Z. H., and Sun, Z. BAR-based optimum adaptive steered MD for configurational sampling. J. Comput. Chem. 40, 1270-1289 (2019)

316.

Huang, D., Qi, Y., Song, J., and Zhang, J. Z. H. Calculation of hot spots for protein-protein interaction in p53/PMI-MDM2/MDMX complexes. J. Comput. Chem. 40, 1045-1056 (2019)

317.

Chen, J., Pang, L., Wang, W., Wang, L., Zhang, J. Z. H., and Zhu, T. Decoding molecular mechanism of inhibitor bindings to CDK2 using molecular dynamics simulations and binding free energy calculationsJ. Biomol. Struct. Dyn. 1-15 (2019)

318.

Yang, Y., He, L., Bao, J., Qi, Y., and Zhang, J. Z. H. Computational analysis for residue-specific CDK2-inhibitor bindings. Chinese Journal of Chemical Physics. 32, 134-142 (2019)

319.

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)

320.

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)

321.

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)

322.

Zhao, P., Cao, H., Chen, Y., and Zhu, T. Insights into the binding mechanisms of inhibitors of MDM2 based on molecular dynamics simulations and binding free energy calculations. Chem. Phys. Lett. 728, 94-101 (2019)

323.

Perišić, O., Portillo-Ledesma, S, and Schlick, T. Sensitive effect of linker histone binding mode and subtype on chromatin condensation. Nucleic Acids Res. 47, 4948-4957 (2019)

324.

Liu, W., Li, P., and Mei, Y. Discovery of SBF1 as an allosteric inhibitor targeting the PIF-pocket of 3-phosphoinositide-dependent protein kinase-1. J. Mol. Model. 25, 187 (2019)

325.

Tong, Z., Huai, Z., Mei, Y., and Mo, Y. Influence of the protein environment on the electronic excitation of chromophores in the phycoerythrin 545 light-harvesting complex: A combined MD-QM/MM method with polarized protein-specific charge scheme. J. Phys. Chem. B. 123, 2040-2049 (2019)

326.

Liu, W., Dai, X., Jih, J., Chan, K., Trang, P., Yu, X., Balogun, R., Mei, Y., Liu, F., Zhou, Z. H. Atomic structures and deletion mutant reveal different capsid-binding patterns and functional significance of tegument protein pp150 in murine and human cytomegaloviruses with implications for therapeutic development. PLOS Pathog. 15, e1007615 (2019)

327.

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)

328.

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)

329.

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)

330.

Felker, P. M. and  Bačić, Z. Weakly bound molecular dimers: Intramolecular vibrational fundamentals, overtones, and tunneling splittings from full-dimensional quantum calculations using compact contracted bases of intramolecular and low-energy rigid-monomer intermolecular eigenstatesJ. Chem. Phys. 151, 024305 (2019)

331.

Jung, J., Nishima, W., Daniels, M., Bascom, G., Kobayashi, C., Adedoyin, A., Wall. M., Lappala, A., Phillips, D., Fischer, W., Tung, C.-S., Schlick, T., Sugita, Y., and Sanbonmatsu,  K. Y. Scaling molecular dynamics beyond 100,000 processor cores for large‐scale biophysical simulationsJ. Comp. Chem. 40, 1919-1930 (2019)

332.

Jain, S., Saju, S., Petingi, L., and Schlick, T. An extended dual graph library and partitioning algorithm applicable to pseudoknotted RNA structuresMethods. 162-163, 74-84 (2019)

333.

Portillo-Ledesma, S. and Schlick, T. Bridging chromatin structure and function over a range of experimental spatial and temporal scales by molecular modelingWIREs Comput. Mol. Sci. e1434 (2019)

334.

L. Petingi and T. Schlick, "Graph-Theoretic Partitioning of RNAs and Classification of Pseudoknots'', In: I. Holmes, C. Martín-Vide, M. Vega-Rodríguez, Editors, Algorithms for Computational Biology (AlCoB 2019), Lec. Notes in Comp. Sci. (LNCS) 11488: 68-79 (2019) 

335.

Xu, M., Felker, P. M., Mamone, S., Horsewill, A. J., Rols, S., Whitby, R. J., and Bačić, Z. The endofullerene HF@C60: Inelastic neutron scattering spectra from quantum simulations and experiment, validity of the selection rule, and symmetry breakingJ. Phys. Chem. Lett. 10, 5365−5371 (2019)

336.

Felker, P. M., Lauvergnat, D., Scribano, Y., Benoit, D. M., and Bačić, Z. Intramolecular stretching vibrational states and frequency shifts of (H2)2 confined inside the large cage of clathrate hydrate from an eight-dimensional quantum treatment using small basis setsThe Journal of Chemical Physics151, 124311 (2019)

337.

Wang, T., Su, X., Zhang, X., Huang, W., Huang, L., Zhang, X., Sun, X., Luo, Y., and Zhang, G. A combinatory approach towards the design of organic polymer luminescent materials. J. Mater. Chem. C. 7, 9917-9925 (2019)

338.

Mulvihill, E., Schubert, A., Sun, X., Dunietz, B. D., and Geva, E. A modified approach for simulating electronically nonadiabatic dynamics via the generalized quantum master equationJ. Chem. Phys. 150, 034101 (2019)

339.

Liu, X., Zhao, Y., and Zhang, J. Z. H. Molecular mechanism of ligand bindings to Zika virus at SAM site. Chem. Phys. Lett. 735, 136771 (2019)

340.

Chen, J., Gao, H., Ding, T., Ji, L., Zhang, J. Z. H., Gao, G., and Xia, F. Mechanistic studies of CO2 cycloaddition reaction catalyzed by amine-functionalized ionic liquids. Front Chem. 7, 615 (2019)

341.

Duan, G., Ji, C., and Zhang, J. Z. H. A force consistent method for electrostatic energy calculation in fluctuating charge model. J. Chem. Phys. 151, 094105 (2019)

342.

Wang, E., Sun, H., Wang, J., Wang, Z., Liu, H., Zhang, J. Z. H., and Hou, T. End-point binding free energy calculation with MM/PBSA and MM/GBSA: Strategies and applications in drug design. Chem. Rev. 119, 9478-9508 (2019)

343.

Duan, L., Guo, X., Cong, Y., Feng, G., Li, Y., and Zhang, J. Z. H. Accelerated molecular dynamics simulation for helical proteins folding in explicit water. Front Chem. 7, 540 (2019)

344.

Xu, M., Zhu, T., and Zhang, J. Z. H. Molecular dynamics simulation of zinc ion in water with an ab initio based neural network potential. J. Phys. Chem. A. 123, 6587-6595 (2019)

345.

Chen, J., Wang, X., Pang, L., Zhang, J. Z. H., and Zhu, T. Effect of mutations on binding of ligands to guanine riboswitch probed by free energy perturbation and molecular dynamics simulations. Nucleic Acids Res. 47, 6618-6631 (2019)

346.

Cao, H., Wang, J., He, L., Qi, Y., and Zhang, J. Z. H. DeepDDG: Predicting the stability change of protein point mutations using neural networks. J. Chem. Inf. Model. 59, 1508-1514 (2019)

347.

Sun, Z., Wang, X., Zhang, J. Z. H., and He, Q. Sulfur-substitution-induced base flipping in the DNA duplex. Phys. Chem. Chem. Phys. 21, 14923-14940 (2019)

348.

Xiao, Z., Cong, Y., Huang, K., Zhong, S., Zhang, J. Z. H., and Duan, L. Drug-resistance mechanisms of three mutations in anaplastic lymphoma kinase against two inhibitors based on MM/PBSA combined with interaction entropy. Phys. Chem. Chem. Phys. 21, 20951-20964 (2019)

349.

Chen, J., Yin, B., Pang, L., Wang, W., Zhang, J. Z. H., and Zhu, T. Binding modes and conformational changes of FK506-binding protein 51 induced by inhibitor bindings: insight into molecular mechanisms based on multiple simulation technologiesJ. Biomol. Struct. Dyn. 1-15 (2019)

350.

Li, P., Liu, F., Shao, Y., and Mei, Y. Computational insights into endo/exo selectivity of the Diels-Alder reaction in explicit solvent at ab initio quantum mechanical/molecular mechanical level. J. Phys. Chem. B. 123, 5131-5138 (2019)

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