Arjan van der Vaart - Related publications

2006-2009 Chemistry Arizona State University, Tempe, AZ, United States 
 2009- Chemistry University of South Florida, Tampa, FL, United States 
General Biophysics, Biochemistry
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Fernandes DD, Neale C, Gomes GW, Li Y, Malik A, Pandey A, Orazietti AP, Wang X, Ye L, Scott Prosser R, Gradinaru CC. Ligand modulation of the conformational dynamics of the A adenosine receptor revealed by single-molecule fluorescence. Scientific Reports. 11: 5910. PMID 33723285 DOI: 10.1038/s41598-021-84069-0   
2021 Fernandes DD, Neale C, Gomes GW, Li Y, Malik A, Pandey A, Orazietti AP, Wang X, Ye L, Scott Prosser R, Gradinaru CC. Ligand modulation of the conformational dynamics of the A adenosine receptor revealed by single-molecule fluorescence. Scientific Reports. 11: 5910. PMID 33723285 DOI: 10.1038/s41598-021-84069-0   
2021 Sikkema HR, Poolman B. In silico method for selecting residue pairs for single-molecule microscopy and spectroscopy. Scientific Reports. 11: 5756. PMID 33707507 DOI: 10.1038/s41598-021-85003-0   
2021 King E, Qi R, Li H, Luo R, Aitchison E. Estimating the Roles of Protonation and Electronic Polarization in Absolute Binding Affinity Simulations. Journal of Chemical Theory and Computation. PMID 33764050 DOI: 10.1021/acs.jctc.0c01305   
2021 Di Rienzo L, Miotto M, Bò L, Ruocco G, Raimondo D, Milanetti E. Characterizing Hydropathy of Amino Acid Side Chain in a Protein Environment by Investigating the Structural Changes of Water Molecules Network. Frontiers in Molecular Biosciences. 8: 626837. PMID 33718433 DOI: 10.3389/fmolb.2021.626837   
2021 Nath P, Goyal A. Structure and dynamics analysis of multi-domain putative β-1,4-glucosidase of family 3 glycoside hydrolase (PsGH3) from Pseudopedobacter saltans. Journal of Molecular Modeling. 27: 106. PMID 33694107 DOI: 10.1007/s00894-021-04721-4   
2021 Barge S, Jade D, Gosavi G, Talukdar NC, Borah J. In-silico screening for identification of potential inhibitors against SARS-CoV-2 transmembrane serine protease 2 (TMPRSS2). European Journal of Pharmaceutical Sciences : Official Journal of the European Federation For Pharmaceutical Sciences. 162: 105820. PMID 33775827 DOI: 10.1016/j.ejps.2021.105820   
2021 Miller EB, Murphy RB, Sindhikara D, Borrelli KW, Grisewood MJ, Ranalli F, Dixon SL, Jerome S, Boyles NA, Day T, Ghanakota P, Mondal S, Rafi SB, Troast DM, Abel R, et al. Reliable and Accurate Solution to the Induced Fit Docking Problem for Protein-Ligand Binding. Journal of Chemical Theory and Computation. PMID 33779166 DOI: 10.1021/acs.jctc.1c00136   
2021 Ludwig J, Smith J, Pfaendtner J. Analyzing the Long Time-Scale Dynamics of Uremic Toxins Bound to Sudlow Site II in Human Serum Albumin. The Journal of Physical Chemistry. B. PMID 33715376 DOI: 10.1021/acs.jpcb.1c00221   
2021 Liu B, Shi H, Al-Hashimi HM. Developments in solution-state NMR yield broader and deeper views of the dynamic ensembles of nucleic acids. Current Opinion in Structural Biology. 70: 16-25. PMID 33836446 DOI: 10.1016/   
2021 Hernandes IS, Da Silva HC, Dos Santos HF, De Almeida WB. Unveiling the Molecular Structure of Antimalarial Drugs Chloroquine and Hydroxychloroquine in Solution through Analysis of H NMR Chemical Shifts. The Journal of Physical Chemistry. B. PMID 33760611 DOI: 10.1021/acs.jpcb.1c00609   
2021 Kumar R, Kumar R, Tanwar P. drug designing for COVID-19: an approach of high-throughput virtual screening, molecular, and essential dynamics simulations. Journal of Biomolecular Structure & Dynamics. 1-15. PMID 33715592 DOI: 10.1080/07391102.2021.1897681   
2021 Wang B, Su Z, Wu Y. Computational Assessment of Protein-Protein Binding Affinity by Reverse Engineering the Energetics in Protein Complexes. Genomics, Proteomics & Bioinformatics. PMID 33838354 DOI: 10.1016/j.gpb.2021.03.004   
2021 Norn C, Wicky BIM, Juergens D, Liu S, Kim D, Tischer D, Koepnick B, Anishchenko I, , Baker D, Ovchinnikov S. Protein sequence design by conformational landscape optimization. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33712545 DOI: 10.1073/pnas.2017228118   
2021 Vittorio S, Gitto R, Adornato I, Russo E, De Luca L. In Silico Strategy for Targeting the mTOR Kinase at Rapamycin Binding Site by Small Molecules. Molecules (Basel, Switzerland). 26. PMID 33669763 DOI: 10.3390/molecules26041103   
2021 Ma N, Nivedha AK, Vaidehi N. Allosteric Communication Regulates Ligand-Specific GPCR Activity. The Febs Journal. PMID 33738925 DOI: 10.1111/febs.15826   
2021 Shao G, Bao J, Pan X, He X, Qi Y, Zhang JZH. Computational Analysis of Residue-Specific Binding Free Energies of Androgen Receptor to Ligands. Frontiers in Molecular Biosciences. 8: 646524. PMID 33778009 DOI: 10.3389/fmolb.2021.646524   
2021 Gopi S, Lukose B, Naganathan AN. Diverse Native Ensembles Dictate the Differential Functional Responses of Nuclear Receptor Ligand-Binding Domains. The Journal of Physical Chemistry. B. PMID 33818099 DOI: 10.1021/acs.jpcb.1c00972   
2021 Feng X, Li F, Ding M, Zhang R, Shi T, Jiang W. Molecular dynamic simulation: Structural insights of multi-stranded curdlan in aqueous solution. Carbohydrate Polymers. 261: 117844. PMID 33766340 DOI: 10.1016/j.carbpol.2021.117844   
2021 Dawson WM, Lang EJM, Rhys GG, Shelley KL, Williams C, Brady RL, Crump MP, Mulholland AJ, Woolfson DN. Structural resolution of switchable states of a de novo peptide assembly. Nature Communications. 12: 1530. PMID 33750792 DOI: 10.1038/s41467-021-21851-8   
2021 Huai Z, Yang H, Sun Z. Binding thermodynamics and interaction patterns of human purine nucleoside phosphorylase-inhibitor complexes from extensive free energy calculations. Journal of Computer-Aided Molecular Design. PMID 33759016 DOI: 10.1007/s10822-021-00382-w   
2021 Dandekar BR, Ahalawat N, Mondal J. Reconciling Conformational Heterogeneity and Substrate Recognition in Cytochrome P450. Biophysical Journal. PMID 33675756 DOI: 10.1016/j.bpj.2021.02.040   
2021 Dias D'Andréa É, Sebastian Retel J, Diehl A, Schmieder P, Oschkinat H, Ricardo Pires J. NMR structure and dynamics of Q4DY78, a conserved kinetoplasid-specific protein from Trypanosoma cruzi. Journal of Structural Biology. 107715. PMID 33705979 DOI: 10.1016/j.jsb.2021.107715   
2021 Al-Thiabat MG, Saqallah FG, Gazzali AM, Mohtar N, Yap BK, Choong YS, Wahab HA. Heterocyclic Substitutions Greatly Improve Affinity and Stability of Folic Acid towards FRα. an In Silico Insight. Molecules (Basel, Switzerland). 26. PMID 33670773 DOI: 10.3390/molecules26041079   
2021 Mulligan VK, Workman S, Sun T, Rettie S, Li X, Worrall LJ, Craven TW, King DT, Hosseinzadeh P, Watkins AM, Renfrew PD, Guffy S, Labonte JW, Moretti R, Bonneau R, et al. Computationally designed peptide macrocycle inhibitors of New Delhi metallo-β-lactamase 1. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33723038 DOI: 10.1073/pnas.2012800118   
2021 Zhuang Y, Bureau HR, Lopez C, Bucher R, Quirk S, Hernandez R. Energetics and structure of alanine-rich α-helices via Adaptive Steered Molecular Dynamics (ASMD). Biophysical Journal. PMID 33775636 DOI: 10.1016/j.bpj.2021.03.017   
2021 Freiberger MI, Wolynes PG, Ferreiro DU, Fuxreiter M. Frustration in Fuzzy Protein Complexes Leads to Interaction Versatility. The Journal of Physical Chemistry. B. 125: 2513-2520. PMID 33667107 DOI: 10.1021/acs.jpcb.0c11068   
2021 Sagar A, Jeffries CM, Petoukhov MV, Svergun DI, Bernadó P. Comment on the Optimal Parameters to Derive Intrinsically Disordered Protein Conformational Ensembles from Small-Angle X-ray Scattering Data Using the Ensemble Optimization Method. Journal of Chemical Theory and Computation. PMID 33725442 DOI: 10.1021/acs.jctc.1c00014   
2021 Khamari L, Pramanik U, Shekhar S, Mohanakumar S, Mukherjee S. Thermal Reversibility and Structural Stability in Lysozyme Induced by Epirubicin Hydrochloride. Langmuir : the Acs Journal of Surfaces and Colloids. PMID 33703900 DOI: 10.1021/acs.langmuir.1c00179   
2021 Fogarty CA, Fadda E. Oligomannose -Glycans 3D Architecture and Its Response to the FcγRIIIa Structural Landscape. The Journal of Physical Chemistry. B. PMID 33661628 DOI: 10.1021/acs.jpcb.1c00304   
2021 Ganotra GK, Nunes-Alves A, Wade RC. A Protocol to Use Comparative Binding Energy Analysis to Estimate Drug-Target Residence Time. Methods in Molecular Biology (Clifton, N.J.). 2266: 171-186. PMID 33759127 DOI: 10.1007/978-1-0716-1209-5_10   
2021 Zia MK, Siddiqui T, Ahsan H, Khan FH. Characterization of the binding between anti-tumor drug 5-fluorouracil and human alpha-2-macroglobulin: spectroscopic and molecular docking analyses. Journal of Biomolecular Structure & Dynamics. 1-11. PMID 33798029 DOI: 10.1080/07391102.2021.1905550   
2021 Fischer TF, Schoeder CT, Zellmann T, Stichel J, Meiler J, Beck-Sickinger AG. Cyclic Analogues of the Chemerin C-Terminus Mimic a Loop Conformation Essential for Activating the Chemokine-like Receptor 1. Journal of Medicinal Chemistry. PMID 33705662 DOI: 10.1021/acs.jmedchem.0c01804   
2021 Zou J, Xiao S, Simmerling C, Raleigh DP. Quantitative Analysis of Protein Unfolded State Energetics: Experimental and Computational Studies Demonstrate That Non-Native Side-Chain Interactions Stabilize Local Native Backbone Structure. The Journal of Physical Chemistry. B. PMID 33779182 DOI: 10.1021/acs.jpcb.0c08922   
2021 Weng YL, Naik SR, Dingelstad N, Lugo MR, Kalyaanamoorthy S, Ganesan A. Molecular dynamics and in silico mutagenesis on the reversible inhibitor-bound SARS-CoV-2 main protease complexes reveal the role of lateral pocket in enhancing the ligand affinity. Scientific Reports. 11: 7429. PMID 33795718 DOI: 10.1038/s41598-021-86471-0   
2021 Mohanty AK, Choudhary S, Kaushik JK, Fisher AJ. Crystal structure of BRP39, a signaling glycoprotein expressed during mammary gland apoptosis at 2.6 Å resolution. Journal of Structural Biology. 107737. PMID 33838225 DOI: 10.1016/j.jsb.2021.107737   
2021 Kaddouri Y, Abrigach F, Ouahhoud S, Benabbes R, El Kodadi M, Alsalme A, Al-Zaqri N, Warad I, Touzani R. Synthesis, characterization, reaction mechanism prediction and biological study of mono, bis and tetrakis pyrazole derivatives against Fusarium oxysporum f. sp. Albedinis with conceptual DFT and ligand-protein docking studies. Bioorganic Chemistry. 110: 104696. PMID 33652343 DOI: 10.1016/j.bioorg.2021.104696   
2021 Choi YK, Cao Y, Frank M, Woo H, Park SJ, Yeom MS, Croll TI, Seok C, Im W. Structure, Dynamics, Receptor Binding, and Antibody Binding of the Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein in a Viral Membrane. Journal of Chemical Theory and Computation. PMID 33689337 DOI: 10.1021/acs.jctc.0c01144   
2021 Cao TQ, Kim JA, Woo MH, Min BS. SARS-CoV-2 main protease inhibition by compounds isolated from Luffa cylindrica using molecular docking. Bioorganic & Medicinal Chemistry Letters. 127972. PMID 33753260 DOI: 10.1016/j.bmcl.2021.127972   
2021 Liu D, Mao Y, Gu X, Zhou Y, Long D. Unveiling the "invisible" druggable conformations of GDP-bound inactive Ras. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33836610 DOI: 10.1073/pnas.2024725118   
2021 Niu C, Du Y, Kaltashov IA. Towards better understanding of the heparin role in NETosis: feasibility of using native mass spectrometry to monitor interactions of neutrophil elastase with heparin oligomers. International Journal of Mass Spectrometry. 463. PMID 33692650 DOI: 10.1016/j.ijms.2021.116550   
2021 Ortet PC, Muellers SN, Viarengo-Baker LA, Streu K, Szymczyna BR, Beeler AB, Allen KN, Whitty A. Recapitulating the Binding Affinity of Nrf2 for KEAP1 in a Cyclic Heptapeptide, Guided by NMR, X-ray Crystallography, and Machine Learning. Journal of the American Chemical Society. PMID 33683866 DOI: 10.1021/jacs.0c09799   
2021 Turan HT, Meuwly M. Spectroscopy, Dynamics, and Hydration of -Nitrosylated Myoglobin. The Journal of Physical Chemistry. B. PMID 33724027 DOI: 10.1021/acs.jpcb.0c10353   
2021 Turan HT, Meuwly M. Spectroscopy, Dynamics, and Hydration of -Nitrosylated Myoglobin. The Journal of Physical Chemistry. B. PMID 33724027 DOI: 10.1021/acs.jpcb.0c10353   
2021 Crean RM, Biler M, van der Kamp MW, Hengge AC, Kamerlin SCL. Loop Dynamics and Enzyme Catalysis in Protein Tyrosine Phosphatases. Journal of the American Chemical Society. PMID 33661624 DOI: 10.1021/jacs.0c11806   
2021 Aljoundi A, El Rashedy A, Soliman MES. Distinguishing the optimal binding mechanism through reversible and irreversible inhibition analysis of HSP72 protein in cancer therapy. Computers in Biology and Medicine. 132: 104301. PMID 33751994 DOI: 10.1016/j.compbiomed.2021.104301   
2021 Vuorio J, Škerlová J, Fábry M, Veverka V, Vattulainen I, Řezáčová P, Martinez-Seara H. N-Glycosylation can selectively block or foster different receptor-ligand binding modes. Scientific Reports. 11: 5239. PMID 33664400 DOI: 10.1038/s41598-021-84569-z   
2021 Shakya A, Chikhale RV, Bhat HR, Alasmary FA, Almutairi TM, Ghosh SK, Alhajri HM, Alissa SA, Nagar S, Islam MA. Pharmacoinformatics-based identification of transmembrane protease serine-2 inhibitors from Morus Alba as SARS-CoV-2 cell entry inhibitors. Molecular Diversity. PMID 33786727 DOI: 10.1007/s11030-021-10209-3   
2021 Li C, Chen S, Huang T, Zhang F, Yuan J, Chang H, Li W, Han W. Conformational Changes of Glutamine 5'-Phosphoribosylpyrophosphate Amidotransferase for Two Substrates Analogue Binding: Insight from Conventional Molecular Dynamics and Accelerated Molecular Dynamics Simulations. Frontiers in Chemistry. 9: 640994. PMID 33718330 DOI: 10.3389/fchem.2021.640994   
2021 Singh AN, Yethiraj A. Liquid-Liquid Phase Separation As the Second Step of Complex Coacervation. The Journal of Physical Chemistry. B. PMID 33735576 DOI: 10.1021/acs.jpcb.0c07349