Dominy, Brian

Graduate Student

Positions

2018 - Associate Dean of the Graduate School, Clemson University
2011 - Associate Professor, Clemson University
2016 - 2018 Interim Associate Dean for Academic Affairs, Clemson University
2005 - 2011 Assistant Professor, Clemson University
2001 - 2005 Postdoctoral Fellow, Harvard University

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Doctoral Dissertation

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academic article
- Xia, B., Liu, Y., Guevara, J., Li, J., Jilich, C., Yang, Y., Wang, L. J., Dominy, B. N., Cao, W. Correlated mutation in the evolution of catalysis in uracil DNA glycosylase superfamily Scientific Reports 2017 7 DOI:10.1038/srep45978 PMID:28397787 PMCID:PMC5387724
- Lee, D. H., Liu, Y., Lee, H. W., Xia, B., Brice, A. R., Park, S. H., Balduf, H., Dominy, B. N., Cao, W. A structural determinant in the uracil DNA glycosylase superfamily for the removal of uracil from adenine/uracil base pairs Nucleic Acids Research 2015 43:1081-1089 DOI:10.1093/nar/gku1332 PMID:25550433 PMCID:PMC4333384
- Xia, B., Liu, Y., Li, W., Brice, A. R., Dominy, B. N., Cao, W. Specificity and catalytic mechanism in family 5 uracil DNA glycosylase Journal of Biological Chemistry 2014 289:18413-18426 DOI:10.1074/jbc.M114.567354 PMID:24838246 PMCID:PMC4140252
- Brice, A. R., Dominy, B. N. Examining electrostatic influences on base-flipping: a comparison of TIP3P and GB solvent models Communications in Computational Physics 2013 13:223-237 DOI:10.4208/cicp.210711.121011s
- Date, M. S., Dominy, B. N. Modeling the influence of salt on the hydrophobic effect and protein fold stability Communications in Computational Physics 2013 13:90-106 DOI:10.4208/cicp.290711.121011s
- Singh, M. K., Dominy, B. N. The evolution of cefotaximase activity in the TEM β-lactamase Journal of Molecular Biology 2012 415:205-220 DOI:10.1016/j.jmb.2011.10.041 PMID:22075446
- Lee, H. W., Dominy, B. N., Cao, W. New family of deamination repair enzymes in uracil-DNA glycosylase superfamily Journal of Biological Chemistry 2011 286:31282-31287 DOI:10.1074/jbc.M111.249524 PMID:21642431 PMCID:PMC3173141
- Singh, M. K., Streu, K., McCrone, A. J., Dominy, B. N. The evolution of catalytic function in the HIV-1 protease Journal of Molecular Biology 2011 408:792-805 DOI:10.1016/j.jmb.2011.02.031 PMID:21376058
- Brice, A. R., Dominy, B. N. Analyzing the robustness of the MM/PBSA free energy calculation method: application to DNA conformational transitions Journal of Computational Chemistry 2011 32:1431-1440 DOI:10.1002/jcc.21727 PMID:21284003
- Lee, H. W., Brice, A. R., Wright, C. B., Dominy, B. N., Cao, W. Identification of Escherichia coli mismatch-specific uracil DNA glycosylase as a robust xanthine DNA glycosylase Journal of Biological Chemistry 2010 285:41483-41490 DOI:10.1074/jbc.M110.150003 PMID:20852254 PMCID:PMC3009874
- Singh, M. K., Dominy, B. N. Thermodynamic resolution: how do errors in modeled protein structures affect binding affinity predictions? Proteins-Structure Function and Bioinformatics 2010 78:1613-1617 DOI:10.1002/prot.22691 PMID:20201067
- Mi, R., Dong, L., Kaulgud, T., Hackett, K. W., Dominy, B. N., Cao, W. Insights from Xanthine and Uracil DNA Glycosylase Activities of Bacterial and Human SMUG1: Switching SMUG1 to UDG Journal of Molecular Biology 2009 385:761-778 DOI:10.1016/j.jmb.2008.09.038 PMID:18835277
- Dominy, B. N. Molecular recognition and binding free energy calculations in drug development Current Pharmaceutical Biotechnology 2008 9:87-95 DOI:10.2174/138920108783955155 PMID:18393865
- Sun, Y., Dominy, B. N., Latour, R. A. Comparison of solvation-effect methods for the simulation of peptide interactions with a hydrophobic surface Journal of Computational Chemistry 2007 28:1883-1892 DOI:10.1002/jcc.20716 PMID:17405115
- Dominy, B. N., Minoux, H., Brooks III, C. L. An electrostatic basis for the stability of thermophilic proteins Proteins-Structure Function and Bioinformatics 2004 57:128-141 DOI:10.1002/prot.20190 PMID:15326599
- Dominy, B. N., Shakhnovich, E. I. Native atom types for knowledge-based potentials: application to binding energy prediction Journal of Medicinal Chemistry 2004 47:4538-4558 DOI:10.1021/jm0498046 PMID:15317465
- Liu, Z., Dominy, B. N., Shakhnovich, E. I. Structural mining: self-consistent design on flexible protein-peptide docking and transferable binding affinity potential Journal of the American Chemical Society 2004 126:8515-8528 DOI:10.1021/ja032018q PMID:15238009
- Dominy, B. N., Perl, D., Schmid, F. X., Brooks III, C. L. The effects of ionic strength on protein stability: the cold shock protein family Journal of Molecular Biology 2002 319:541-554 DOI:10.1016/s0022-2836(02)00259-0 PMID:12051927
- Dominy, B. N., Brooks III, C. L. Identifying native-like protein structures using physics-based potentials Journal of Computational Chemistry 2002 23:147-160 DOI:10.1002/jcc.10018
- Dominy, B. N. Parameterization and application of an implicit solvent model for macromolecules Molecular Simulation 2000 24:259-274 DOI:10.1080/08927020008022375
- Dominy, B. N., Brooks III, C. L. Methodology for protein-ligand binding studies: application to a model for drug resistance, the HIV/FIV protease system Proteins-Structure Function and Genetics 1999 36:318-331 DOI:10.1002/(SICI)1097-0134(19990815)36:3<318::AID-PROT6>3.0.CO;2-K PMID:10409825
- Mohanty, D., Dominy, B. N., Kolinski, A., Brooks III, C. L., Skolnick, J. Correlation between knowledge-based and detailed atomic potentials: application to the unfolding of the GCN4 leucine zipper Proteins-Structure Function and Genetics 1999 35:447-452 DOI:10.1002/(SICI)1097-0134(19990601)35:4<447::AID-PROT8>3.0.CO;2-O PMID:10382672
- Dominy, B. N., Brooks III, C. L. Development of a generalized born model parametrization for proteins and nucleic acids Journal of Physical Chemistry B 1999 103:3765-3773 DOI:10.1021/jp984440c
- Vieth, M., Hirst, J. D., Dominy, B. N., Daigler, H., Brooks III, C. L. Assessing search strategies for flexible docking Journal of Computational Chemistry 1998 19:1623-1631