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/

48 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
2018 Bachman AB, Keramisanou D, Xu W, Beebe K, Moses MA, Vasantha Kumar MV, Gray G, Noor RE, van der Vaart A, Neckers L, Gelis I. Phosphorylation induced cochaperone unfolding promotes kinase recruitment and client class-specific Hsp90 phosphorylation. Nature Communications. 9: 265. PMID 29343704 DOI: 10.1038/s41467-017-02711-w  0.01
2017 Shi Y, Challa S, Sang P, She F, Li C, Gray GM, Nimmagadda A, Teng P, Odom T, Wang Y, van der Vaart A, Li Q, Cai J. One-Bead-Two-Compound Thioether Bridged Macrocyclic γ-AApeptide Screening Library against EphA2. Journal of Medicinal Chemistry. 60: 9290-9298. PMID 29111705 DOI: 10.1021/Acs.Jmedchem.7B01280  1
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  1
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  1
2017 Teng P, Ma N, Cerrato DC, She F, Odom T, Wang X, Ming LJ, van der Vaart A, Wojtas L, Xu H, Cai J. Right-Handed Helical Foldamers Consisting of De Novo d-AApeptides. Journal of the American Chemical Society. 139: 7363-7369. PMID 28480699 DOI: 10.1021/Jacs.7B03007  1
2017 Gray GM, Ma N, Wagner CE, van der Vaart A. Molecular dynamics simulations and molecular flooding studies of the retinoid X-receptor ligand binding domain. Journal of Molecular Modeling. 23: 98. PMID 28251414 DOI: 10.1007/s00894-017-3260-9  1
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  0.01
2017 van der Vaart A, Lorkowski A, Ma N, Gray GM. Computer Simulations of the Retinoid X Receptor: Conformational Dynamics and Allosteric Networks. Current Topics in Medicinal Chemistry. 17: 731-741. PMID 27320334  1
2016 Gray GM, van der Vaart A, Guo C, Jones J, Onofrei D, Cherry BR, Lewis RV, Yarger JL, Holland GP. Secondary Structure Adopted by the Gly-Gly-X Repetitive Regions of Dragline Spider Silk. International Journal of Molecular Sciences. 17. PMID 27918448 DOI: 10.3390/Ijms17122023  1
2016 Heck MC, Wagner CE, Shahani PH, MacNeill M, Grozic A, Darwaiz T, Shimabuku M, Deans DG, Robinson NM, Salama SH, Ziller JW, Ma N, van der Vaart A, Marshall PA, Jurutka PW. Modeling, Synthesis, and Biological Evaluation of Potential Retinoid X Receptor (RXR)-Selective Agonists: Analogues of 4-[1-(3,5,5,8,8-Pentamethyl-5,6,7,8-tetrahydro-2-naphthyl)ethynyl]benzoic Acid (Bexarotene) and 6-(Ethyl(5,5,8,8-tetrahydronaphthalen-2-yl)amino)nicotinic Acid (NEt-TMN). Journal of Medicinal Chemistry. 59: 8924-8940. PMID 27592633 DOI: 10.1021/Acs.Jmedchem.6B00812  1
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  1
2016 Villemot F, Capelli R, Colombo G, van der Vaart A. Balancing Accuracy and Cost of Confinement Simulations by Interpolation and Extrapolation of Confinement Energies. Journal of Chemical Theory and Computation. 12: 2779-89. PMID 27120438 DOI: 10.1021/acs.jctc.5b01183  1
2016 Capelli R, Villemot F, Moroni E, Tiana G, van der Vaart A, Colombo G. Assessment of Mutational Effects on Peptide Stability through Confinement Simulations. The Journal of Physical Chemistry Letters. 7: 126-30. PMID 26678679 DOI: 10.1021/acs.jpclett.5b02221  1
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  1
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  1
2015 Marshall PA, Jurutka PW, Wagner CE, van der Vaart A, Kaneko I, Chavez PI, Ma N, Bhogal JS, Shahani P, Swierski JC, MacNeill M. Analysis of differential secondary effects of novel rexinoids: select rexinoid X receptor ligands demonstrate differentiated side effect profiles. Pharmacology Research & Perspectives. 3: e00122. PMID 26038698 DOI: 10.1002/prp2.122  1
2015 Karolak A, van der Vaart A. BII stability and base step flexibility of N6-adenine methylated GATC motifs. Biophysical Chemistry. 203: 22-7. PMID 26004863 DOI: 10.1016/j.bpc.2015.05.001  1
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  0.01
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  1
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  1
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: 10.1021/jp410976p  1
2013 Jurutka PW, Kaneko I, Yang J, Bhogal JS, Swierski JC, Tabacaru CR, Montano LA, Huynh CC, Jama RA, Mahelona RD, Sarnowski JT, Marcus LM, Quezada A, Lemming B, Tedesco MA, ... ... van der Vaart A, et al. Modeling, synthesis, and biological evaluation of potential retinoid X receptor (RXR) selective agonists: novel analogues of 4-[1-(3,5,5,8,8-pentamethyl-5,6,7,8-tetrahydro-2-naphthyl)ethynyl]benzoic acid (bexarotene) and (E)-3-(3-(1,2,3,4-tetrahydro-1,1,4,4,6-pentamethylnaphthalen-7-yl)-4-hydroxyphenyl)acrylic acid (CD3254). Journal of Medicinal Chemistry. 56: 8432-54. PMID 24180745 DOI: 10.1021/jm4008517  1
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  1
2013 Ma N, Chung YH, van der Vaart A. Free energy simulation of helical transitions. Journal of Computational Chemistry. 34: 640-5. PMID 23125002 DOI: 10.1002/jcc.23174  1
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  1
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  1
2012 Furmick JK, Kaneko I, Walsh AN, Yang J, Bhogal JS, Gray GM, Baso JC, Browder DO, Prentice JL, Montano LA, Huynh CC, Marcus LM, Tsosie DG, Kwon JS, Quezada A, ... ... van der Vaart A, et al. Modeling, synthesis and biological evaluation of potential retinoid X receptor-selective agonists: novel halogenated analogues of 4-[1-(3,5,5,8,8-pentamethyl-5,6,7,8-tetrahydro-2-naphthyl)ethynyl]benzoic acid (bexarotene). Chemmedchem. 7: 1551-66. PMID 22927238 DOI: 10.1002/cmdc.201200319  1
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  1
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  1
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  1
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  1
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  1
2009 Wagner CE, Jurutka PW, Marshall PA, Groy TL, van der Vaart A, Ziller JW, Furmick JK, Graeber ME, Matro E, Miguel BV, Tran IT, Kwon J, Tedeschi JN, Moosavi S, Danishyar A, et al. Modeling, synthesis and biological evaluation of potential retinoid X receptor (RXR) selective agonists: novel analogues of 4-[1-(3,5,5,8,8-pentamethyl-5,6,7,8-tetrahydro-2-naphthyl)ethynyl]benzoic acid (bexarotene). Journal of Medicinal Chemistry. 52: 5950-66. PMID 19791803 DOI: 10.1021/jm900496b  1
2009 Kamberaj H, van der Vaart A. Extracting the causality of correlated motions from molecular dynamics simulations. Biophysical Journal. 97: 1747-55. PMID 19751680 DOI: 10.1016/j.bpj.2009.07.019  1
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  1
2009 Kamberaj H, van der Vaart A. An optimized replica exchange molecular dynamics method. The Journal of Chemical Physics. 130: 074906. PMID 19239315 DOI: 10.1063/1.3077857  1
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  1
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  1
2007 Kamberaj H, van der Vaart A. Multiple scaling replica exchange for the conformational sampling of biomolecules in explicit water. The Journal of Chemical Physics. 127: 234102. PMID 18154370 DOI: 10.1063/1.2806930  1
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  1
2007 Ababou A, van der Vaart A, Gogonea V, Merz KM. Interaction energy decomposition in protein-protein association: a quantum mechanical study of barnase-barstar complex. Biophysical Chemistry. 125: 221-36. PMID 16962699 DOI: 10.1016/j.bpc.2006.08.003  1
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  1
2005 Raha K, van der Vaart AJ, Riley KE, Peters MB, Westerhoff LM, Kim H, Merz KM. Pairwise decomposition of residue interaction energies using semiempirical quantum mechanical methods in studies of protein-ligand interaction. Journal of the American Chemical Society. 127: 6583-94. PMID 15869279 DOI: 10.1021/Ja042666P  1
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  1
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  1
2004 Wang B, Brothers EN, van der Vaart A, Merz KM. Fast semiempirical calculations for nuclear magnetic resonance chemical shifts: a divide-and-conquer approach. The Journal of Chemical Physics. 120: 11392-400. PMID 15268173 DOI: 10.1063/1.1752877  1
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  1
2001 Gogonea V, Suárez D, Van der Vaart A, Merz J. New developments in applying quantum mechanics to proteins Current Opinion in Structural Biology. 11: 217-223. PMID 11297931 DOI: 10.1016/S0959-440X(00)00193-7  1
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