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Arjan van der Vaart - Publications

Affiliations: 
2006-2009 Chemistry Arizona State University, Tempe, AZ, United States 
 2009- Chemistry University of South Florida, Tampa, FL, United States 
Area:
General Biophysics, Biochemistry
Website:
http://chemistry.usf.edu/faculty/vandervaart/
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29 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
2023 Orndorff PB, van der Vaart A. Register-Shifted Structures in Base-Flipped Uracil-Damaged DNA. Journal of the American Chemical Society. 145: 16350-16354. PMID 37478299 DOI: 10.1021/jacs.3c05890  0.314
2023 Orndorff PB, van der Vaart A. Systematic assessment of the flexibility of uracil damaged DNA. Journal of Biomolecular Structure & Dynamics. 1-11. PMID 37261803 DOI: 10.1080/07391102.2023.2217683  0.337
2023 Orndorff PB, Poddar S, Owens AM, Kumari N, Ugaz BT, Amin S, Van Horn WD, van der Vaart A, Levitus M. Uracil-DNA glycosylase efficiency is modulated by substrate rigidity. Scientific Reports. 13: 3915. PMID 36890276 DOI: 10.1038/s41598-023-30620-0  0.324
2017 Ma N, van der Vaart A. Free Energy Coupling between DNA Bending and Base Flipping. Journal of Chemical Information and Modeling. 57: 2020-2026. PMID 28696686 DOI: 10.1021/acs.jcim.7b00215  0.419
2017 Ma N, van der Vaart A. [KCl] Dependence of B-DNA Groove Bending Anisotropy. The Journal of Physical Chemistry. B. 121: 5322-5330. PMID 28481093 DOI: 10.1021/acs.jpcb.7b01957  0.366
2017 Peguero-Tejada A, van der Vaart A. Biasing Simulations of DNA Base Pair Parameters with Application to Propellor Twisting in AT/AT, AA/TT, and AC/GT Steps and Their Uracil Analogs. Journal of Chemical Information and Modeling. 57: 85-92. PMID 27976883 DOI: 10.1021/acs.jcim.6b00660  0.344
2016 Ma N, van der Vaart A. Anisotropy of B-DNA Groove Bending. Journal of the American Chemical Society. 138: 9951-8. PMID 27435602 DOI: 10.1021/jacs.6b05136  0.421
2016 Karolak A, van der Vaart A. Molecular Dynamics Simulations of 5-Hydroxycytosine Damaged DNA. The Journal of Physical Chemistry. B. 120: 42-8. PMID 26654566 DOI: 10.1021/acs.jpcb.5b09250  0.354
2015 Gray GM, van der Vaart A. Importance of β2-β3 Loop Motion for the Increased Binding and Decreased Selectivity of the ΔLL Mutant of the Human Papillomavirus Type 6 E2 Protein. Biochemistry. 54: 4918-26. PMID 26169609 DOI: 10.1021/acs.biochem.5b00433  0.333
2015 van der Vaart A. Coupled binding-bending-folding: The complex conformational dynamics of protein-DNA binding studied by atomistic molecular dynamics simulations. Biochimica Et Biophysica Acta. 1850: 1091-8. PMID 25161164 DOI: 10.1016/j.bbagen.2014.08.009  0.44
2014 Karolak A, van der Vaart A. Enhanced sampling simulations of DNA step parameters. Journal of Computational Chemistry. 35: 2297-304. PMID 25303338 DOI: 10.1002/jcc.23751  0.359
2014 Chung YH, van der Vaart A. RevErbα preferentially deforms DNA by induced fit. Chembiochem : a European Journal of Chemical Biology. 15: 643-6. PMID 24677802 DOI: 10.1002/cbic.201300557  0.395
2014 Stennett EM, Ma N, van der Vaart A, Levitus M. Photophysical and dynamical properties of doubly linked Cy3-DNA constructs. The Journal of Physical Chemistry. B. 118: 152-63. PMID 24328104 DOI: 10.1016/J.Bpj.2013.11.448  0.355
2013 Spiriti J, van der Vaart A. DNA binding and bending by Sac7d is stepwise. Chembiochem : a European Journal of Chemical Biology. 14: 1434-7. PMID 23853062 DOI: 10.1002/Cbic.201300264  0.712
2012 Spiriti J, Kamberaj H, de Graff AM, Thorpe MF, van der Vaart A. DNA Bending through Large Angles Is Aided by Ionic Screening. Journal of Chemical Theory and Computation. 8: 2145-56. PMID 26593845 DOI: 10.1021/Ct300177R  0.717
2012 Spiriti J, van der Vaart A. DNA Bending through Roll Angles Is Independent of Adjacent Base Pairs. The Journal of Physical Chemistry Letters. 3: 3029-33. PMID 26292244 DOI: 10.1021/Jz301227Y  0.719
2012 Karolak A, van der Vaart A. Importance of local interactions for the stability of inhibitory helix 1 in apo Ets-1. Biophysical Chemistry. 165: 74-8. PMID 22494801 DOI: 10.1016/j.bpc.2012.03.007  0.301
2012 Barr D, van der Vaart A. The natural DNA bending angle in the lac repressor headpiece-O1 operator complex is determined by protein-DNA contacts and water release. Physical Chemistry Chemical Physics : Pccp. 14: 2070-7. PMID 22234444 DOI: 10.1039/C2Cp23780F  0.611
2011 Barr D, Oashi T, Burkhard K, Lucius S, Samadani R, Zhang J, Shapiro P, MacKerell AD, van der Vaart A. Importance of domain closure for the autoactivation of ERK2. Biochemistry. 50: 8038-48. PMID 21842857 DOI: 10.1021/Bi200503A  0.518
2011 Spiriti J, Binder JK, Levitus M, van der Vaart A. Cy3-DNA stacking interactions strongly depend on the identity of the terminal basepair. Biophysical Journal. 100: 1049-57. PMID 21320450 DOI: 10.1016/J.Bpj.2011.01.014  0.722
2010 Spiriti J, van der Vaart A. Mechanism of the calcium-induced trans-cis isomerization of a non-prolyl peptide bond in Clostridium histolyticum collagenase. Biochemistry. 49: 5314-20. PMID 20499930 DOI: 10.1021/Bi1007047  0.668
2009 Maragakis P, van der Vaart A, Karplus M. Gaussian-mixture umbrella sampling. The Journal of Physical Chemistry. B. 113: 4664-73. PMID 19284746 DOI: 10.1021/Jp808381S  0.397
2009 Kamberaj H, van der Vaart A. Correlated motions and interactions at the onset of the DNA-induced partial unfolding of Ets-1. Biophysical Journal. 96: 1307-17. PMID 19217849 DOI: 10.1016/j.bpj.2008.11.019  0.325
2008 Spiriti J, Bogani F, van der Vaart A, Ghirlanda G. Modulation of protein stability by O-glycosylation in a designed Gc-MAF analog. Biophysical Chemistry. 134: 157-67. PMID 18329161 DOI: 10.1016/J.Bpc.2008.02.005  0.686
2007 van der Vaart A, Karplus M. Minimum free energy pathways and free energy profiles for conformational transitions based on atomistic molecular dynamics simulations. The Journal of Chemical Physics. 126: 164106. PMID 17477588 DOI: 10.1063/1.2719697  0.469
2005 Monard G, Bernal-Uruchurtu MI, van der Vaart A, Merz KM, Ruiz-López MF. Simulation of liquid water using semiempirical Hamiltonians and the divide and conquer approach. The Journal of Physical Chemistry. A. 109: 3425-32. PMID 16833679 DOI: 10.1021/Jp0459099  0.6
2005 van der Vaart A, Karplus M. Simulation of conformational transitions by the restricted perturbation-targeted molecular dynamics method. The Journal of Chemical Physics. 122: 114903. PMID 15836253 DOI: 10.1063/1.1861885  0.446
2005 Karplus M, Gao YQ, Ma J, van der Vaart A, Yang W. Protein structural transitions and their functional role. Philosophical Transactions. Series a, Mathematical, Physical, and Engineering Sciences. 363: 331-55; discussion 3. PMID 15664887 DOI: 10.1098/Rsta.2004.1496  0.494
2004 van der Vaart A, Ma J, Karplus M. The unfolding action of GroEL on a protein substrate. Biophysical Journal. 87: 562-73. PMID 15240489 DOI: 10.1529/Biophysj.103.037333  0.452
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