Brian N. Dominy - Publications

Affiliations: 
Chemistry Clemson University, Clemson, SC, United States 
Area:
Biochemistry, General Biophysics, Physical Chemistry

24 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2017 Xia B, Liu Y, Guevara J, Li J, Jilich C, Yang Y, Wang L, Dominy BN, Cao W. Correlated Mutation in the Evolution of Catalysis in Uracil DNA Glycosylase Superfamily. Scientific Reports. 7: 45978. PMID 28397787 DOI: 10.1038/srep45978  0.4
2015 Lee DH, Liu Y, Lee HW, Xia B, Brice AR, Park SH, Balduf H, Dominy BN, Cao W. A structural determinant in the uracil DNA glycosylase superfamily for the removal of uracil from adenine/uracil base pairs. Nucleic Acids Research. 43: 1081-9. PMID 25550433 DOI: 10.1093/nar/gku1332  1
2014 Xia B, Liu Y, Li W, Brice AR, Dominy BN, Cao W. Specificity and catalytic mechanism in family 5 uracil DNA glycosylase. The Journal of Biological Chemistry. 289: 18413-26. PMID 24838246 DOI: 10.1074/jbc.M114.567354  1
2013 Date MS, Dominy BN. Modeling the influence of salt on the hydrophobic effect and protein fold stability Communications in Computational Physics. 13: 90-106. DOI: 10.4208/cicp.290711.121011s  1
2013 Brice AR, Dominy BN. Examining electrostatic influences on base-flipping: A comparison of TIP3P and GB solvent models Communications in Computational Physics. 13: 223-237. DOI: 10.4208/cicp.210711.121011s  1
2012 Singh MK, Dominy BN. The evolution of cefotaximase activity in the TEM β-lactamase. Journal of Molecular Biology. 415: 205-20. PMID 22075446 DOI: 10.1016/j.jmb.2011.10.041  1
2011 Lee HW, Dominy BN, Cao W. New family of deamination repair enzymes in uracil-DNA glycosylase superfamily. The Journal of Biological Chemistry. 286: 31282-7. PMID 21642431 DOI: 10.1074/jbc.M111.249524  1
2011 Singh MK, Streu K, McCrone AJ, Dominy BN. The evolution of catalytic function in the HIV-1 protease. Journal of Molecular Biology. 408: 792-805. PMID 21376058 DOI: 10.1016/j.jmb.2011.02.031  1
2011 Brice AR, Dominy BN. Analyzing the robustness of the MM/PBSA free energy calculation method: application to DNA conformational transitions. Journal of Computational Chemistry. 32: 1431-40. PMID 21284003 DOI: 10.1002/jcc.21727  1
2010 Lee HW, Brice AR, Wright CB, Dominy BN, Cao W. Identification of Escherichia coli mismatch-specific uracil DNA glycosylase as a robust xanthine DNA glycosylase. The Journal of Biological Chemistry. 285: 41483-90. PMID 20852254 DOI: 10.1074/jbc.M110.150003  1
2010 Singh MK, Dominy BN. Thermodynamic resolution: how do errors in modeled protein structures affect binding affinity predictions? Proteins. 78: 1613-7. PMID 20201067 DOI: 10.1002/prot.22691  1
2009 Mi R, Dong L, Kaulgud T, Hackett KW, Dominy BN, Cao W. Insights from xanthine and uracil DNA glycosylase activities of bacterial and human SMUG1: switching SMUG1 to UDG. Journal of Molecular Biology. 385: 761-78. PMID 18835277 DOI: 10.1016/j.jmb.2008.09.038  1
2008 Dominy BN. Molecular recognition and binding free energy calculations in drug development. Current Pharmaceutical Biotechnology. 9: 87-95. PMID 18393865 DOI: 10.2174/138920108783955155  1
2007 Sun Y, Dominy BN, Latour RA. Comparison of solvation-effect methods for the simulation of peptide interactions with a hydrophobic surface. Journal of Computational Chemistry. 28: 1883-92. PMID 17405115 DOI: 10.1002/jcc.20716  1
2004 Dominy BN, Minoux H, Brooks CL. An electrostatic basis for the stability of thermophilic proteins. Proteins. 57: 128-41. PMID 15326599 DOI: 10.1002/prot.20190  1
2004 Dominy BN, Shakhnovich EI. Native atom types for knowledge-based potentials: application to binding energy prediction. Journal of Medicinal Chemistry. 47: 4538-58. PMID 15317465 DOI: 10.1021/jm0498046  1
2004 Liu Z, Dominy BN, Shakhnovich EI. Structural mining: self-consistent design on flexible protein-peptide docking and transferable binding affinity potential. Journal of the American Chemical Society. 126: 8515-28. PMID 15238009 DOI: 10.1021/ja032018q  1
2002 Dominy BN, Perl D, Schmid FX, Brooks CL. The effects of ionic strength on protein stability: the cold shock protein family. Journal of Molecular Biology. 319: 541-54. PMID 12051927 DOI: 10.1016/S0022-2836(02)00259-0  1
2002 Dominy BN, Brooks CL. Identifying native-like protein structures using physics-based potentials. Journal of Computational Chemistry. 23: 147-60. PMID 11913380 DOI: 10.1002/jcc.10018  1
2000 Dominy BN. Parameterization and application of an implicit solvent model for macromolecules Molecular Simulation. 24: 259-274.  1
1999 Dominy BN, Brooks CL. Methodology for protein-ligand binding studies: application to a model for drug resistance, the HIV/FIV protease system. Proteins. 36: 318-31. PMID 10409825 DOI: 10.1002/(SICI)1097-0134(19990815)36:3<318::AID-PROT6>3.0.CO;2-K  1
1999 Mohanty D, Dominy BN, Kolinski A, Brooks CL, Skolnick J. Correlation between knowledge-based and detailed atomic potentials: Application to the unfolding of the GCN4 leucine zipper Proteins: Structure, Function and Genetics. 35: 447-452. PMID 10382672 DOI: 10.1002/(SICI)1097-0134(19990601)35:4<447::AID-PROT8>3.0.CO;2-O  1
1999 Dominy BN, Brooks CL. Development of a generalized born model parametrization for proteins and nucleic acids Journal of Physical Chemistry B. 103: 3765-3773.  1
1998 Vieth M, Hirst JD, Dominy BN, Daigler H, Brooks CL. Assessing search strategies for flexible docking Journal of Computational Chemistry. 19: 1623-1631.  1
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