## VM2 applications

F. Molani, S. Webb, and A.E. Cho (2023) “Combining QM/MM Calculations with Classical Mining Minima to Predict Protein−Ligand Binding Free Energy” Journal of Chemical Theory and Computation. DOI:10.1021/acs.jcim.2c01637

G. C. Schröder, W. B. O’Dell, S. P. Webb, P. K. Agarwal and F. Meilleur (2022) “Capture of activated dioxygen intermediates at the copper-active site of a lytic polysaccharide monooxygenase.” Chemical Science, Edge Article, **13**, 13303. DOI:10.1039/d2sc05031e

P. Xu, T. Sattasathuchana, E. Guidez, S. P. Webb, K. Montgomery, H. Yasini, I. F. M. Pedreira, and M. S. Gordon (2021) “Computation of host–guest binding free energies with a new quantum mechanics based mining minima algorithm.” Journal of Chemical Physics **154**:104122. DOI:10.1063/5.0040759 PDF

W. Chen, X. Ren, C-E.A. Chang (2018). “Discovery of CDK8/CycC Ligands with a New Virtual Screening Tool.” ChemMedChem. DOI:10.1002/cmdc.201800559 Preprint

W. Chen, L. Sun, Z. Tang, Z.A. Ali, B.M. Wong, and C-E.A. Chang (2018). “An MM and QM Study of Biomimetic Catalysis of Diels-Alder Reactions Using Cyclodextrins.” Catalysts **8**(12), 51. DOI:10.3390/catal8020051

W. You, Y. M. M. Huang, S. Kizhake, A. Natarajan and C-E. A. Chang (2016) “Characterization of Promiscuous Binding of Phosphor Ligands to Breast-Cancer-Gene 1 (BRCA1) C-Terminal (BRCT): Molecular Dynamics, Free Energy, Entropy and Inhibitor Design.” PLoS Comput Biol. **12: **e1005057. DOI:10.1371/journal.pcbi.1005057

Huang, Y. M. M., W. Chen, M. J. Potter, and C.-E. Chang (2012). “Insights from Free-Energy Calculations: Protein Conformational Equilibrium, Driving Forces, and Ligand-Binding Modes.” Biophysical Journal **103**(2): 342-351. DOI: 10.1016/j.bpj.2012.05.046

Chen, W., M. K. Gilson, S. P. Webb, and M. J. Potter (2010). “Modeling Protein-Ligand Binding by Mining Minima.” Journal of Chemical Theory and Computation **6**(11): 3540-3557. DOI: 10.1021/ct100245n

## VM2 background references

Chang, C.-E., M. J. Potter, and M. K. Gilson (2003). “Calculation of molecular configuration integrals.” J. Phys. Chem. B **107**: 1048-1055. DOI: 10.1021/jp027149c

Chang, C.-E. and M. K. Gilson (2003). “Tork: Conformational analysis method for molecules and complexes.” Journal of Computational Chemistry **24**(16): 1987-1998. DOI: 10.1002/jcc.10325

Chen, W., C.-E. Chang, and M. K. Gilson ( 2004). “Calculation of Cyclodextrin Binding Affinities: Energy, Entropy, and Implications for Drug Design ” Biophysical Journal **87**: 3035-3049. DOI: 10.1529/biophysj.104.049494

Gilson, M. K., J. A. Given, B. L. Bush, and A. McCammon (1997). “The statistical-thermodynamic basis for computation of binding affinities: A critical review.” Biophys. J. **72**: 1047-1069. DOI: 10.1016/S0006-3495(97)78756-3

Gilson, M. K., J. A. Given, and M. S. Head (1997). “A New Class of Models for Computing Receptor-Ligand Binding Affinities.” Chem. & Biol. **4**: 87-92. DOI: 10.1016/S1074-5521(97)90251-9

Gilson, M. K., The Binding Data Base (http://www.bindingdb.org), Skaggs School of Pharmacy & Pharmaceutical Sciences (2013).

Head, M. S., J. A. Given, and M. K. Gilson (1997). “Mining Minima: Direct computation of conformational free energy.” J. Phys. Chem. **101**: 1609-1618. DOI: 10.1021/jp963817g

Luo, R., L. David, and M. K. Gilson (2002). “Accelerated Poisson-Boltzmann calculations for static and dynamic systems.” Journal of Computational Chemistry **23**(13): 1244-1253. DOI: 10.1002/jcc.10120

Potter, M. J. and M. K. Gilson (2002). “Coordinate Systems and the Calculation of Molecular Properties.” The journal of physical chemistry. A **106**(3): 563-566. DOI: 10.1021/jp0135407

Qiu, D., P. S. Shenkin, F. P. Hollinger, and W. C. Still (1997). “The GB/SA continuum model for solvation. a fast analytical method for the calculation of approximate born radii.” J. Phys. Chem. **101**(16): 3005-3014. DOI: 10.1021/jp961992r