Steven K. Burger, Ph.D. - Publications

Affiliations: 
2007 Chemistry Duke University, Durham, NC 
Area:
quantum mechanical simulations of biological systems and nanostructures

28 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
2014 Mohammed AA, Burger SK, Ayers PW. Drug release by pH-responsive molecular tweezers: atomistic details from molecular modeling. Journal of Computational Chemistry. 35: 1545-51. PMID 24962869 DOI: 10.1002/jcc.23652  1
2014 Burger SK, Ayers PW, Schofield J. Efficient parameterization of torsional terms for force fields. Journal of Computational Chemistry. 35: 1438-45. PMID 24831846 DOI: 10.1002/jcc.23636  1
2013 Burger SK, Schofield J, Ayers PW. Quantum mechanics/molecular mechanics restrained electrostatic potential fitting. The Journal of Physical Chemistry. B. 117: 14960-6. PMID 24176005 DOI: 10.1021/jp409568h  1
2013 Burger SK, Cisneros GA. Efficient optimization of van der Waals parameters from bulk properties. Journal of Computational Chemistry. 34: 2313-9. PMID 23828265 DOI: 10.1002/jcc.23376  1
2013 Kraskouskaya D, Drewry JA, Duodu E, Burger S, Eaton J, Cisneros GA, Gunning PT. Exploring the structural determinants of selective phosphopeptide recognition using bivalent metal-coordination complexes Medchemcomm. 4: 289-292. DOI: 10.1039/c2md20342a  1
2012 Burger SK, Lacasse M, Verstraelen T, Drewry J, Gunning P, Ayers PW. Automated Parametrization of AMBER Force Field Terms from Vibrational Analysis with a Focus on Functionalizing Dinuclear Zinc(II) Scaffolds. Journal of Chemical Theory and Computation. 8: 554-62. PMID 26596604 DOI: 10.1021/ct2007742  1
2012 Drewry JA, Duodu E, Mazouchi A, Spagnuolo P, Burger S, Gradinaru CC, Ayers P, Schimmer AD, Gunning PT. Phosphopeptide selective coordination complexes as promising SRC homology 2 domain mimetics. Inorganic Chemistry. 51: 8284-91. PMID 22784241 DOI: 10.1021/ic3008393  1
2012 Lou M, Burger SK, Gilpin ME, Gawuga V, Capretta A, Berti PJ. Transition state analysis of enolpyruvylshikimate 3-phosphate (EPSP) synthase (AroA)-catalyzed EPSP hydrolysis. Journal of the American Chemical Society. 134: 12958-69. PMID 22765279 DOI: 10.1021/ja304339h  1
2012 Lou M, Gilpin ME, Burger SK, Malik AM, Gawuga V, Popović V, Capretta A, Berti PJ. Transition state analysis of acid-catalyzed hydrolysis of an enol ether, enolpyruvylshikimate 3-phosphate (EPSP). Journal of the American Chemical Society. 134: 12947-57. PMID 22765168 DOI: 10.1021/ja3043382  1
2012 Drewry JA, Burger S, Mazouchi A, Duodu E, Ayers P, Gradinaru CC, Gunning PT. Src homology 2 domain proteomimetics: Developing phosphopeptide selective receptors Medchemcomm. 3: 763-770. DOI: 10.1039/c2md20052j  1
2011 Liu Y, Burger SK, Ayers PW, Vöhringer-Martinez E. Computational study of the binding modes of caffeine to the adenosine A2A receptor. The Journal of Physical Chemistry. B. 115: 13880-90. PMID 21970461 DOI: 10.1021/jp2022049  1
2011 Bain AD, Baron M, Burger SK, Kowalewski VJ, Rodríguez MB. Interconversion study in 1,4-substituted six-membered cyclohexane-type rings. Structure and dynamics of trans-1,4-dibromo-1,4-dicyanocyclohexane. The Journal of Physical Chemistry. A. 115: 9207-16. PMID 21786756 DOI: 10.1021/jp205375f  1
2011 Burger SK, Ayers PW. A parameterized, continuum electrostatic model for predicting protein pKa values. Proteins. 79: 2044-52. PMID 21557315 DOI: 10.1002/prot.23019  1
2011 Burger SK, Ayers PW. Empirical prediction of protein pKa values with residue mutation. Journal of Computational Chemistry. 32: 2140-8. PMID 21523791 DOI: 10.1002/jcc.21796  1
2011 Burger SK, Liu S, Ayers PW. Practical calculation of molecular acidity with the aid of a reference molecule. The Journal of Physical Chemistry. A. 115: 1293-304. PMID 21291187 DOI: 10.1021/jp111148q  1
2011 Burger SK, Thompson DC, Ayers PW. Quantum mechanics/molecular mechanics strategies for docking pose refinement: distinguishing between binders and decoys in cytochrome C peroxidase. Journal of Chemical Information and Modeling. 51: 93-101. PMID 21133348 DOI: 10.1021/ci100329z  1
2011 Liu Y, Burger SK, Ayers PW. Newton trajectories for finding stationary points on molecular potential energy surfaces Journal of Mathematical Chemistry. 49: 1915-1927. DOI: 10.1007/s10910-011-9864-x  1
2010 Burger SK, Ayers PW. Dual Grid Methods for Finding the Reaction Path on Reduced Potential Energy Surfaces. Journal of Chemical Theory and Computation. 6: 1490-7. PMID 26615686 DOI: 10.1021/ct100012y  1
2010 Burger SK, Ayers PW. Quasi-Newton parallel geometry optimization methods. The Journal of Chemical Physics. 133: 034116. PMID 20649317 DOI: 10.1063/1.3455719  1
2010 Burger SK, Ayers PW. Methods for finding transition states on reduced potential energy surfaces. The Journal of Chemical Physics. 132: 234110. PMID 20572692 DOI: 10.1063/1.3445772  1
2010 Liu Y, Burger SK, Dey BK, Sarkar U, Janicki MR, Ayers PW. The Fast Marching Method for Determining Chemical Reaction Mechanisms in Complex Systems Quantum Biochemistry. 171-195. DOI: 10.1002/9783527629213.ch5  1
2009 Burger SK, Liu Y, Sarkar U, Ayers PW. Moving least-squares enhanced Shepard interpolation for the fast marching and string methods. The Journal of Chemical Physics. 130: 024103. PMID 19154015 DOI: 10.1063/1.2996579  1
2008 Burger SK, Yang W. Linear-scaling quantum calculations using non-orthogonal localized molecular orbitals. Journal of Physics. Condensed Matter : An Institute of Physics Journal. 20: 294209. PMID 25076813 DOI: 10.1088/0953-8984/20/29/294209  1
2008 Hu H, Lu Z, Parks JM, Burger SK, Yang W. Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: sequential sampling and optimization on the potential of mean force surface. The Journal of Chemical Physics. 128: 034105. PMID 18205486 DOI: 10.1063/1.2816557  1
2007 Burger SK, Yang W. Sequential quadratic programming method for determining the minimum energy path. The Journal of Chemical Physics. 127: 164107. PMID 17979319 DOI: 10.1063/1.2780147  1
2006 Burger SK, Yang W. Automatic integration of the reaction path using diagonally implicit Runge-Kutta methods. The Journal of Chemical Physics. 125: 244108. PMID 17199341 DOI: 10.1063/1.2402166  1
2006 Burger SK, Yang W. A combined explicit-implicit method for high accuracy reaction path integration. The Journal of Chemical Physics. 124: 224102. PMID 16784258 DOI: 10.1063/1.2202830  1
2006 Burger SK, Yang W. Quadratic string method for determining the minimum-energy path based on multiobjective optimization. The Journal of Chemical Physics. 124: 054109. PMID 16468853 DOI: 10.1063/1.2163875  1
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