A. van der Vaart

发表

Multiple scaling replica exchange for the conformational sampling of biomolecules in explicit water.

H. Kamberaj, A. van der Vaart, 2007, The Journal of chemical physics.

The unfolding action of GroEL on a protein substrate.

Jianpeng Ma, Martin Karplus, M. Karplus, 2004, Biophysical journal.

Coupled binding-bending-folding: The complex conformational dynamics of protein-DNA binding studied by atomistic molecular dynamics simulations.

A. van der Vaart, 2015, Biochimica et biophysica acta.

Interaction energy decomposition in protein-protein association: a quantum mechanical study of barnase-barstar complex.

Kenneth M Merz, Valentin Gogonea, K. Merz, 2007, Biophysical chemistry.

An optimized replica exchange molecular dynamics method.

Hiqmet Kamberaj, H. Kamberaj, A. van der Vaart, 2009, The Journal of chemical physics.

Extracting the causality of correlated motions from molecular dynamics simulations.

H. Kamberaj, A. van der Vaart, Hiqmet Kamberaj, 2009, Biophysical journal.

Simulation of liquid water using semiempirical Hamiltonians and the divide and conquer approach.

K. Merz, A. van der Vaart, G. Monard, 2005, The journal of physical chemistry. A.

Fast semiempirical calculations for nuclear magnetic resonance chemical shifts: a divide-and-conquer approach.

K. Merz, A. van der Vaart, E. Brothers, 2004, The Journal of chemical physics.

Anisotropy of B-DNA Groove Bending.

A. van der Vaart, Ning Ma, 2016, Journal of the American Chemical Society.

Importance of domain closure for the autoactivation of ERK2.

Alexander D. MacKerell, Taiji Oashi, Paul Shapiro, 2011, Biochemistry.

Minimum free energy pathways and free energy profiles for conformational transitions based on atomistic molecular dynamics simulations.

Martin Karplus, M. Karplus, A. van der Vaart, 2007, The Journal of chemical physics.

Calculation of conformational free energies by confinement simulations in explicit water with implicit desolvation

A. van der Vaart, F. Villemot, Alfredo Peguero-Tejada, 2018 .

The natural DNA bending angle in the lac repressor headpiece-O1 operator complex is determined by protein-DNA contacts and water release.

Daniel A. Barr, A. van der Vaart, 2012, Physical chemistry chemical physics : PCCP.

Cy3-DNA stacking interactions strongly depend on the identity of the terminal basepair.

A. van der Vaart, Justin Spiriti, M. Levitus, 2011, Biophysical journal.

Linear scaling molecular orbital calculations of biological systems using the semiempirical divide and conquer method

S. L. Dixon, Valentin Gogonea, K. Merz, 2000, J. Comput. Chem..

Assessment of Mutational Effects on Peptide Stability through Confinement Simulations.

G. Tiana, G. Colombo, E. Moroni, 2016, The journal of physical chemistry letters.

De Novo Left-Handed Synthetic Peptidomimetic Foldamers.

A. van der Vaart, L. Wojtas, Jianfeng Cai, 2018, Angewandte Chemie.

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.

A. van der Vaart, Geoffrey M. Gray, 2015, Biochemistry.

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).

P. Jurutka, J. Ziller, A. van der Vaart, 2016, Journal of medicinal chemistry.

Phosphorylation induced cochaperone unfolding promotes kinase recruitment and client class-specific Hsp90 phosphorylation

L. Neckers, A. van der Vaart, K. Beebe, 2018, Nature Communications.

Modulation of protein stability by O-glycosylation in a designed Gc-MAF analog.

Justin Spiriti, Giovanna Ghirlanda, A. van der Vaart, 2008, Biophysical chemistry.

Secondary Structure Adopted by the Gly-Gly-X Repetitive Regions of Dragline Spider Silk

A. van der Vaart, R. Lewis, Chengchen Guo, 2016, International journal of molecular sciences.

Hydrogen-Bonding-Driven 3D Supramolecular Assembly of Peptidomimetic Zipper.

A. van der Vaart, Peng Sang, L. Wojtas, 2018, Journal of the American Chemical Society.

Uracil-DNA glycosylase efficiency is modulated by substrate rigidity

A. van der Vaart, Wade D. Van Horn, M. Levitus, 2022, bioRxiv.

Photophysical and dynamical properties of doubly linked Cy3-DNA constructs.

A. van der Vaart, M. Levitus, Elana M. S. Stennett, 2014, The journal of physical chemistry. B.

One-Bead-Two-Compound Thioether Bridged Macrocyclic γ-AApeptide Screening Library against EphA2.

A. van der Vaart, Peng Sang, Chunpu Li, 2017, Journal of medicinal chemistry.

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).

P. Jurutka, J. Ziller, T. Groy, 2009, Journal of medicinal chemistry.

Using Photoacoustic Calorimetry to Study the cis- to trans- Photoisomerization of the [Ru(II)(2,2’-bipyridine)2(H2O)2]2+ Complex in Aqueous Solution

A. van der Vaart, A. Karolak, R. Larsen, 2016 .

Right-Handed Helical Foldamers Consisting of De Novo d-AApeptides.

A. van der Vaart, L. Wojtas, Hai Xu, 2017, Journal of the American Chemical Society.

Orthogonal Halogen-Bonding-Driven 3D Supramolecular Assembly of Right-Handed Synthetic Helical Peptides.

A. van der Vaart, L. Wojtas, Xiaopeng Li, 2019, Angewandte Chemie.

Molecular Dynamics Simulations of 5-Hydroxycytosine Damaged DNA.

A. van der Vaart, A. Karolak, 2016, The journal of physical chemistry. B.

New developments in applying quantum mechanics to proteins.

K M Merz, K. Merz, A. van der Vaart, 2001, Current opinion in structural biology.

H. Kamberaj, A. van der Vaart, 2009, Biophysical journal.

[KCl] Dependence of B-DNA Groove Bending Anisotropy.

A. van der Vaart, Ning Ma, 2017, The journal of physical chemistry. B.

DNA Bending through Roll Angles Is Independent of Adjacent Base Pairs.

A. van der Vaart, Justin Spiriti, 2012, The journal of physical chemistry letters.

DNA Binding and Bending by Sac7d is Stepwise

A. van der Vaart, Justin Spiriti, 2013, Chembiochem : a European journal of chemical biology.

BII stability and base step flexibility of N6-adenine methylated GATC motifs.

A. van der Vaart, A. Karolak, 2015, Biophysical chemistry.

Rational discovery of antimetastatic agents targeting the intrinsically disordered region of MBD2

G. Alterovitz, V. Uversky, H. Won, 2019, Science Advances.

Protein structural transitions and their functional role

Jianpeng Ma, Wei Yang, Martin Karplus, 2005, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.

Importance of local interactions for the stability of inhibitory helix 1 in apo Ets-1.

Aleksandra Karolak, A. van der Vaart, A. Karolak, 2012, Biophysical chemistry.

Secondary structure of peptides mimicking the Gly-rich regions of major ampullate spidroin protein 1 and 2.

A. van der Vaart, Geoffrey M. Gray, Brittany Thiessen, 2022, Biophysical chemistry.

Phosphorylation induced cochaperone unfolding promotes kinase recruitment and client class-specific Hsp90 phosphorylation

L. Neckers, A. van der Vaart, K. Beebe, 2018, Nature Communications.

Mechanism of the calcium-induced trans-cis isomerization of a non-prolyl peptide bond in Clostridium histolyticum collagenase.

Justin Spiriti, A. van der Vaart, Justin Spiriti, 2010, Biochemistry.

Free Energy Coupling between DNA Bending and Base Flipping

A. van der Vaart, Ning Ma, Arjan van der Vaart, 2017, J. Chem. Inf. Model..

Molecular dynamics simulations and molecular flooding studies of the retinoid X-receptor ligand binding domain

A. van der Vaart, Ning Ma, C. Wagner, 2017, Journal of Molecular Modeling.

Analysis of differential secondary effects of novel rexinoids: select rexinoid X receptor ligands demonstrate differentiated side effect profiles

P. Jurutka, A. van der Vaart, Ning Ma, 2015, Pharmacology research & perspectives.

Gaussian-mixture umbrella sampling.

Martin Karplus, Paul Maragakis, M. Karplus, 2009, The journal of physical chemistry. B.

Conformational free energy differences of large solvated systems with the focused confinement method.

A. van der Vaart, Paul B. Orndorff, Kaiba Li, 2020, Journal of chemical theory and computation.

Calculation of conformational free energies with the focused confinement method.

A. van der Vaart, Paul B. Orndorff, Sang T Le Phan, 2019, Journal of chemical theory and computation.

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-hydroxyphe

P. Jurutka, J. Ziller, A. van der Vaart, 2013, Journal of medicinal chemistry.

Pairwise decomposition of residue interaction energies using semiempirical quantum mechanical methods in studies of protein-ligand interaction.

Kevin E. Riley, Lance M. Westerhoff, Kenneth M Merz, 2005, Journal of the American Chemical Society.

DNA Bending through Large Angles Is Aided by Ionic Screening.

M. Thorpe, H. Kamberaj, A. van der Vaart, 2012, Journal of chemical theory and computation.

Simulation of conformational transitions by the restricted perturbation-targeted molecular dynamics method.

Martin Karplus, M. Karplus, A. van der Vaart, 2005, The Journal of chemical physics.

Computer Simulations of the Retinoid X Receptor: Conformational Dynamics and Allosteric Networks.

A. van der Vaart, Ning Ma, Geoffrey M. Gray, 2017, Current topics in medicinal chemistry.