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 energies. J. 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: APBScore. J. 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 hydrates. Adv. 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 phosphate. Nature 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 cleavage. Proc. 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 hub. Proc. 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 eigenstates. J. 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 calculations. J. 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 eigenstates. J. 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 simulations. J. 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 structures. Methods. 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 modeling. WIREs 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 breaking. J. 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 sets. The Journal of Chemical Physics, 151, 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 equation. J. 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 technologies. J. 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)
|
|