Publications

Hu, Z., Sun, Z., and Sun, H. Simulation of negative ion photoelectron spectroscopy using a nuclear ensemble approach: Implications from a nuclear vibration effect. J. Phys. Chem. A. 125, 6621–6628 (2021)

Li, N., Gao, Y., Qiu, F., and Zhu, T. Benchmark force fields for the molecular dynamic simulation of G-quadruplexes. Molecules. 26, 5379 (2021)

Rogal, J., & Tuckerman, M. E. (2021). Pathways in Classification Space: Machine Learning as a Route to Predicting Kinetics of Structural Transitions in Atomic Crystals. In Multiscale Dynamics Simulations (pp. 312-348).

Zhao, Y., Miao, Y., Zhi, F., Pan, Y., Zhang, J., Yang, X., Zhang, J. Z. H., and Zhang, L. Rational design of pepsin for enhanced thermostability via exploiting the guide of structural weakness on stability. Front. Phys. 9, 755253 (2021)

Wang, X., Li, X., He, X., and Zhang, J. Z. H. A fixed multi-site interaction charge model for an accurate prediction of the QM/MM interactions. Phys. Chem. Chem. Phys. 23, 21001-21012 (2021)

Li, Z. and Zhang, J. Z. H. Quantitative analysis of ACE2 binding to coronavirus spike proteins: SARS-CoV-2 vs. SARS-CoV and RaTG13. Phys. Chem. Chem. Phys. 23, 13926-13933 (2021)

Zeng, J., Weng, J., Zhang, Y., Xia, F., Cui, Q., and Xu, X. Conformational features of Ras: Key hydrogen-bonding interactions of Gln61 in the intermediate state during GTP hydrolysis. J. Phys. Chem. B. 125, 8805–8813 (2021)

Huai, Z., Tong, Z., Mei, Y., and Mo, Y. Theoretical study of the spectral differences of the Fenna–Matthews–Olson protein from different species and their mutants. J. Phys. Chem. B. 125, 8313–8324 (2021)

Pan, X., Wang, H., Li, C., Zhang, J. Z. H., and Ji, C. MolGpka: A web server for small molecule pKa prediction using a graph-convolutional neural network. J. Chem. Inf. Model. 61, 3159–3165 (2021)

Kaplan, M., Wang, Y., Chreifi, G., Zhang, L., Chang, Y.-W., and Jensen, G. J. Programmed flagellar ejection in caulobacter crescentus leaves PL-subcomplexes. J. Mol. Biol. 433, 1670042 (2021)

Li, M., Lu, W.C., and Zhang, J. Z. H. Ultra-coarse-graining modeling of liquid water. J. Chem. Phys. 154, 224506 (2021)

Cong, Y., Feng, Y., Ni, H., Zhi, F., Miao, Y., Fang, B., Zhang, L., and Zhang, J. Z. H. Anchor-Locker binding mechanism of the coronavirus spike protein to human ACE2: Insights from computational analysis. J. Chem. Inf. Model. 61, 3529–3542 (2021)

Wen, W., Huang, D., Bao, J., Zhang, J. Z. H. Residue-specific binding mechanisms of PD-L1 to its monoclonal antibodies by computational alanine scanning. Phys. Chem. Chem. Phys. 23, 15591-15600 (2021)

Felker, P. M., Liu, Y., Li, J., and Bačić, Z. DCl–H₂O, HCl–D₂O, and DCl–D₂O dimers: Inter- and intramolecular vibrational states and frequency shifts from fully coupled quantum calculations on a full-dimensional neural network potential energy surface. J. Phys. Chem. A. 125, 6437–6449 (2021)

Zhao, X., Zhang, P., Li, Y., Wu, S., Li, F., Wang, Y., Liang, S., He, X., Zeng, Y., and Liu, Z. Glucose–lipopeptide conjugates reveal the role of glucose modification position in complexation and the potential of malignant melanoma therapy. J. Med. Chem. 64, 11483–11495 (2021)

Shen, C., Jin, X., Glover, J. W., and He, X. Accurate prediction of absorption spectral shifts of proteorhodopsin using a fragment-based quantum mechanical method. Molecules. 26, 4486 (2021)

Xu, M., Zhu, T., and Zhang, J. Z. H. Automatically constructed neural network potentials for molecular dynamics simulation of zinc proteins. Front. Chem. 9, 692200 (2021)

Tinnin, J., Aksu, H., Tong, Z., Zhang, P., Geva, E., Dunietz, B. D., Sun, X., and Cheung, M. S. CTRAMER: An open-source software package for correlating interfacial charge transfer rate constants with donor/acceptor geometries in organic photovoltaic materials. J. Chem. Phys. 154, 214108 (2021)

T. Schlick, “Isabella Karle: A Crystallography Pioneer”, DNA Cell Biol. June 14, 2021. doi: 10.1089/dna.2021.0372.

Zelovich, T. and Tuckerman, M. E. OH− and H3O+ Diffusion in model AEMs and PEMs at low hydration: Insights from ab initio molecular dynamics. Membranes. 11, 355 (2021)

Lv, Y., Luo, S., Huang, K., Wang, H., Dong, S., Cong, Y., Zhang, J. Z. H., and Duan, L. Investigating effects of bridging water on the binding of neuraminidase−ligands using computational alanine scanning combined with interaction entropy method. J. Mol. Liq. 336, 116214 (2021)

Luo, S., Huang, K., Zhao, X., Cong, Y., Zhang, J. Z. H., and Duan, L. Inhibition mechanism and hot-spot prediction of nine potential drugs for SARS-CoV-2 Mpro by large-scale molecular dynamic simulations combined with accurate binding free energy calculations. Nanoscale. 13, 8313-8332 (2021)

Cao, L., Zeng, J., Xu, M., Chin, C.-H., Zhu, T., and Zhang, J. Z. H. Fragment-based ab initio molecular dynamics simulation for combustion. Molecules. 26, 3120 (2021)

Han, Y., He, L., Qi, Y., Zhao, Y., Pan, Y., Fang, B., Li, S., Zhang, J. Z. H., and Zhang, L. Identification of three new compounds that directly target human serine hydroxymethyltransferase 2. Chem. Biol. Drug Des. 97, 221-230 (2021)

Wang, F., Hu, Z., Wang, X. B., Sun, Z., and Sun, H. Assessment of DFT methods for the prediction of detachment energies and electronic structures of complex and multiply charged anions. Comput. Theor. Chem. 1202, 113295 (2021)

Yusufova, N., Kloetgen, A., Teater, M., Osunsade, A., Camarillo, J. M., Chin, C. R., Doane, A. S., Venters, B. J., Portillo-Ledesma, S., Conway, J., Phillip, J. M., Elemento, O., Scott, D. W., Béguelin, W., Licht, J. D., Kelleher, N. L., Staudt, L. M., Skoultchi, A. I., Keogh, M.-C., Apostolou, E., Mason, C. E., Imielinski, M., Schlick, T., David, Y., Tsirigos, A., Allis, C. D., Soshnev, A. A., Cesarman, E., and Melnick, A. M. Histone H1 loss drives lymphoma by disrupting 3D chromatin architecture. Nature. 589, 299-305 (2021)

Gómez-García, P. A., Portillo-Ledesma, S., Neguembor, M. V., Pesaresi, M., Oweis, W., Rohrlich, T., Wieser, S., Meshorer, E., Schlick, T., Cosma, M. P., Lakadamyali, M. Mesoscale modeling and single-nucleosome tracking reveal remodeling of clutch folding and dynamics in stem cell differentiation. Cell Rep. 34, 108614 (2021)

Schlick, T., Portillo-Ledesma, S., Myers, C. G., Beljak, L., Chen, J., Dakhel, S., Darling, D., Ghosh, S., Hall, J., Jan, M., Liang, E., Saju, S., Vohr, M., Wu, C., Xu, Y., Xue, E. Biomolecular modeling and simulation: A prospering multidisciplinary field. Annu. Rev. Biophys. 50, 267-301 (2021)

Schlick, T. and Bishop, T. C. MGO on the go: Multiscale genome symposium-annual biophysical society meeting 2021. Biophys. Rev. 13, 309–310 (2021)

Schlick, T. and Portillo-Ledesma, S. Biomolecular modeling thrives in the age of technology. Nat. Comput. Sci. 1, 321-331 (2021)

Bao, J., He, X., and Zhang, J. Z. H. DeepBSP—a machine learning method for accurate prediction of protein–ligand docking structures. Chem. Inf. Model. 61, 2231–2240 (2021)

Long, B., Wang, Y., Xia, Y., He, X., Bao, J. L., and Truhlar, D. G. Atmospheric kinetics: Bimolecular reactions of carbonyl oxide by a triple-level strategy. J. Am. Chem. Soc. 143, 8402–8413 (2021)

Wang, T., Hu, Z., Nie, X., Huang, L., Hui, M., Sun, X., and Zhang, G. Thermochromic aggregation-induced dual phosphorescence via temperature-dependent sp3 -linked donor-acceptor electronic coupling. Nat. Commun. 12, 1364 (2021)

Chin, C.-H., Zhu, T., and Zhang, J. Z. H. Cyclopentadienyl radical formation from the reaction of excited nitrogen atoms with benzene: A theoretical study. Phys. Chem. Chem. Phys. 23, 12408-12420 (2021)

Zhao, J., Blayney, A., Liu, X., Gandy, L., Jin, W., Yan, L., Ha, J.-H., Canning, A. J., Connelly, M., Yang, C., Liu, X., Xiao, Y., Cosgrove, M. S., Solmaz, S. R., Zhang, Y., Ban, D., Chen, J., Loh, S. N., and Wang, C. EGCG binds intrinsically disordered N-terminal domain of p53 and disrupts p53-MDM2 interaction. Nat. Commun. 12, 986 (2021)

Lu, J., Xia, S., Lu, J., and Zhang, Y. Dataset construction to explore chemical space with 3D geometry and deep learning. J. Chem. Inf. Model. 61,1095-1104 (2021)

Portillo-Ledesma, S., Tsao, L. H., Wagley, M., Lakadamyali, M., Cosma, M. P., and Schlick, T. Nucleosome clutches are regulated by chromatin internal parameters. J. Mol. Biol. 433, 166701 (2021)

Yin, Y., Chen, H., and Yuan, Q. Strain-induced bandgap engineering in C₃N nanotubes. Chem. Phys. Lett. 768, 138390 (2021)

Wang, X, Yan, J., Zhang, H., Xu, Z., and Zhang, J. Z. H. An electrostatic energy-based charge model for molecular dynamics simulation. J. Chem. Phys. 154, 134107 (2021)

Chen, J., Li, N., Wang, X., Chen, J., Zhang, J. Z. H., and Zhu, T. Molecular mechanism related to the binding of fluorophores to Mango-II revealed by multiple-replica molecular dynamics simulations. Phys. Chem. Chem. Phys. 23, 10636-10649 (2021)

Brian, D. and Sun, X. Linear-response and nonlinear-response formulations of the instantaneous Marcus theory for nonequilibrium photoinduced charge transfer. J. Chem. Theory Comput. 17, 2065–2079 (2021)

Brian, D., Liu, Z., Dunietz, B. D., Geva, E., and Sun, X. Three-state harmonic models for photoinduced charge transfer. J. Chem. Phys. 154, 174105 (2021)

Zeng, J., Zhang, L., Wang, H., and Zhu, T. Exploring the chemical space of linear alkane pyrolysis via deep potential GENerator. Energy Fuels. 35, 762–769 (2021)

Duan, L., Dong, S., Huang, K., Cong, Y., Luo, S., and Zhang, J. Z. H. Computational analysis of binding free energies, hotspots and the binding mechanism of Bcl-xL/Bcl-2 binding to Bad/Bax. Phys. Chem. Chem. Phys. 23, 2025-2037 (2021)

Zhu, Q. and Schlick, T. A Fiedler vector scoring approach for novel RNA motif selection. J. Phys. Chem. B. 125,1144-1155 (2021)

Paz, A. S. P. and Glover, W. J. Diabatic many-body expansion: Development and application to charge-transfer reactions. J. Chem. Theory Comput. 17, 1497-1511 (2021)

Wang, J.-N., Liu, W., Li, P., Mo, Y., Hu, W., Zheng, J., Pan, X., Shao, Y., and Mei, Y. Accelerated computation of free energy profile at ab initio quantum mechanical/molecular mechanics accuracy via a semiempirical reference potential. 4. adaptive QM/MM. J. Chem. Theory Comput. 17, 1318-1325 (2021)

Schlick, T., Zhu, Q., Jain, S., and Yan, S. Structure-altering mutations of the SARS-CoV-2 frameshifting RNA element. Biophys. J. 120, 1040-1053 (2021)

Li, M. and Zhang, J. Z. H. Multiscale polarizable coarse-graining water models on cluster-level electrostatic dipoles. Phys. Chem. Chem. Phys. 23, 8926-8935 (2021)

Liu, Y., Cong, Y., Zhang, C., Fang, B., Pan, Y., Li, Q., You, C., Gao, B., Zhang, J. Z. H., Zhu, T., and Zhang, L. Engineering the biomimetic cofactors of NMNH for cytochrome P450 BM3 based on binding conformation refinement. RSC Adv. 11, 12036-12042 (2021)