Year |
Citation |
Score |
2017 |
Jia Z, Ackroyd C, Han T, Agrawal V, Liu Y, Christensen K, Dominy B. Effects from metal ion in tumor endothelial marker 8 and anthrax protective antigen: BioLayer Interferometry experiment and molecular dynamics simulation study. Journal of Computational Chemistry. 38: 1183-1190. PMID 28437008 DOI: 10.1002/Jcc.24768 |
0.338 |
|
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 |
0.456 |
|
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 |
0.746 |
|
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 |
0.739 |
|
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 |
0.519 |
|
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 |
0.739 |
|
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 |
0.493 |
|
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 |
0.471 |
|
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 |
0.525 |
|
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 |
0.731 |
|
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 |
0.736 |
|
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 |
0.505 |
|
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 |
0.49 |
|
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 |
0.392 |
|
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 |
0.506 |
|
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 |
0.566 |
|
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 |
0.583 |
|
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 |
0.514 |
|
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 |
0.566 |
|
2000 |
Dominy BN. Parameterization and application of an implicit solvent model for macromolecules Molecular Simulation. 24: 259-274. DOI: 10.1080/08927020008022375 |
0.365 |
|
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 |
0.531 |
|
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 |
0.563 |
|
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. DOI: 10.1021/Jp984440C |
0.58 |
|
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. |
0.367 |
|
1998 |
Vieth M, Hirst JD, Dominy BN, Daigler H, Brooks CL. Assessing search strategies for flexible docking Journal of Computational Chemistry. 19: 1623-1631. DOI: 10.1002/(Sici)1096-987X(19981115)19:14<1623::Aid-Jcc8>3.0.Co;2-L |
0.487 |
|
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