## VM2 applications

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