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Dominy, Brian
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Dominy, Brian

Graduate Student
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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

Websites

  • Doctoral Dissertation
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Publications

recent publications
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  • Publications without PubMed PMIDs

  • 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
    • degree-related publication 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
    • degree-related publication 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
    • degree-related publication 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
    • degree-related publication Dominy, B. N. Parameterization and application of an implicit solvent model for macromolecules Molecular Simulation  2000 24:259-274  DOI:10.1080/08927020008022375
    • degree-related publication 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
    • degree-related publication 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
    • degree-related publication 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
    • degree-related publication 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
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Background

education and training

  • Ph.D. in Biology, Scripps Research 1995 - 2001
  • B.S. in Biology, Chemistry, Computer Science, Carnegie Mellon University 1991 - 1995

advisee of

  • graduate advising relationship

    • Brooks III, Charles L., Ph.D.  candidacy, 1996 - 2001
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Contact

full name

  • Brian Neil Dominy

geographic location

  • Scripps California 

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