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Andreas Vitalis, Ph.D. - Publications

Affiliations: 
2009 Biology & Biomedical Sciences (Molecular Biophysics) Washington University, Saint Louis, St. Louis, MO 
Area:
Medical Biophysics
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37 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
2020 Cocina F, Vitalis A, Caflisch A. SAPPHIRE-based clustering. Journal of Chemical Theory and Computation. PMID 32905698 DOI: 10.1021/Acs.Jctc.0C00604  0.32
2020 Marchand JR, Knehans T, Caflisch A, Vitalis A. An ABSINTH-Based Protocol for Predicting Binding Affinities Between Proteins and Small Molecules. Journal of Chemical Information and Modeling. PMID 32897071 DOI: 10.1021/Acs.Jcim.0C00558  0.344
2019 Bacci M, Caflisch A, Vitalis A. On the removal of initial state bias from simulation data. The Journal of Chemical Physics. 150: 104105. PMID 30876362 DOI: 10.1063/1.5063556  0.387
2018 Esposito C, Vitalis A. Precise estimation of transfer free energies for ionic species between similar media. Physical Chemistry Chemical Physics : Pccp. PMID 30328430 DOI: 10.1039/C8Cp05331F  0.356
2017 Bacci M, Langini C, Vymětal J, Caflisch A, Vitalis A. Focused conformational sampling in proteins. The Journal of Chemical Physics. 147: 195102. PMID 29166086 DOI: 10.1063/1.4996879  0.375
2017 Bacci M, Vymětal J, Mihajlovic M, Caflisch A, Vitalis A. Amyloid β Fibril Elongation by Monomers Involves Disorder at the Tip. Journal of Chemical Theory and Computation. PMID 28870064 DOI: 10.1021/Acs.Jctc.7B00662  0.469
2017 Langini C, Caflisch A, Vitalis A. The ATAD2 Bromodomain Binds Different Acetylation Marks on the Histone H4 in Similar Fuzzy Complexes. The Journal of Biological Chemistry. PMID 28798233 DOI: 10.1074/Jbc.M117.786350  0.394
2016 Arnon ZA, Vitalis A, Levin A, Michaels TC, Caflisch A, Knowles TP, Adler-Abramovich L, Gazit E. Dynamic microfluidic control of supramolecular peptide self-assembly. Nature Communications. 7: 13190. PMID 27779182 DOI: 10.1038/Ncomms13190  0.357
2015 Blöchliger N, Caflisch A, Vitalis A. Weighted Distance Functions Improve Analysis of High-Dimensional Data: Application to Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. 11: 5481-92. PMID 26574336 DOI: 10.1021/Acs.Jctc.5B00618  0.391
2015 Holehouse AS, Garai K, Lyle N, Vitalis A, Pappu RV. Quantitative assessments of the distinct contributions of polypeptide backbone amides versus side chain groups to chain expansion via chemical denaturation. Journal of the American Chemical Society. 137: 2984-95. PMID 25664638 DOI: 10.1021/Ja512062H  0.791
2015 Bacci M, Vitalis A, Caflisch A. A molecular simulation protocol to avoid sampling redundancy and discover new states. Biochimica Et Biophysica Acta. 1850: 889-902. PMID 25193737 DOI: 10.1016/J.Bbagen.2014.08.013  0.348
2014 Blöchliger N, Vitalis A, Caflisch A. High-resolution visualisation of the states and pathways sampled in molecular dynamics simulations. Scientific Reports. 4: 6264. PMID 25179558 DOI: 10.1038/Srep06264  0.376
2014 Vitalis A, Pappu RV. A simple molecular mechanics integrator in mixed rigid body and dihedral angle space. The Journal of Chemical Physics. 141: 034105. PMID 25053299 DOI: 10.1063/1.4887339  0.534
2014 Vitalis A, Caflisch A. Equilibrium sampling approach to the interpretation of electron density maps. Structure (London, England : 1993). 22: 156-67. PMID 24316403 DOI: 10.1016/J.Str.2013.10.014  0.367
2014 Holehouse AS, Lyle N, Vitalis A, Thirumalai D, Pappu RV. Parsing the Contributions of Polypeptide Backbones and Sidechains to Denaturation in Concentrated Aqueous Solutions of Urea and Guanidinium Chloride Biophysical Journal. 106: 484a. DOI: 10.1016/J.Bpj.2013.11.2731  0.772
2013 Blöchliger N, Vitalis A, Caflisch A. A scalable algorithm to order and annotate continuous observations reveals the metastable states visited by dynamical systems Computer Physics Communications. 184: 2446-2453. DOI: 10.1016/J.Cpc.2013.06.009  0.35
2012 Vitalis A, Caflisch A. Efficient Construction of Mesostate Networks from Molecular Dynamics Trajectories. Journal of Chemical Theory and Computation. 8: 1108-20. PMID 26593370 DOI: 10.1021/Ct200801B  0.351
2012 Vitalis A, Caflisch A. 50 Years of Lifson-Roig Models: Application to Molecular Simulation Data. Journal of Chemical Theory and Computation. 8: 363-73. PMID 26592894 DOI: 10.1021/Ct200744S  0.446
2012 Radhakrishnan A, Vitalis A, Mao AH, Steffen AT, Pappu RV. Improved atomistic Monte Carlo simulations demonstrate that poly-L-proline adopts heterogeneous ensembles of conformations of semi-rigid segments interrupted by kinks. The Journal of Physical Chemistry. B. 116: 6862-71. PMID 22329658 DOI: 10.1021/Jp212637R  0.773
2011 Convertino M, Vitalis A, Caflisch A. Disordered binding of small molecules to Aβ(12-28). The Journal of Biological Chemistry. 286: 41578-88. PMID 21969380 DOI: 10.1074/Jbc.M111.285957  0.413
2011 Vitalis A, Pappu RV. Assessing the contribution of heterogeneous distributions of oligomers to aggregation mechanisms of polyglutamine peptides. Biophysical Chemistry. 159: 14-23. PMID 21530061 DOI: 10.1016/J.Bpc.2011.04.006  0.596
2011 Radhakrishnan A, Vitalis A, Mao AH, Steffen AT, Pappu RV. Accurate Atomistic Modeling of Conformational Equilibria of Proline-Rich Sequences Biophysical Journal. 100: 378a-379a. DOI: 10.1016/J.Bpj.2010.12.2254  0.77
2010 Vitalis A, Caflisch A. Micelle-like architecture of the monomer ensemble of Alzheimer's amyloid-β peptide in aqueous solution and its implications for Aβ aggregation. Journal of Molecular Biology. 403: 148-65. PMID 20709081 DOI: 10.1016/J.Jmb.2010.08.003  0.459
2010 Wyczalkowski MA, Vitalis A, Pappu RV. New estimators for calculating solvation entropy and enthalpy and comparative assessments of their accuracy and precision. The Journal of Physical Chemistry. B. 114: 8166-80. PMID 20503993 DOI: 10.1021/Jp103050U  0.683
2010 Mao AH, Crick SL, Vitalis A, Chicoine CL, Pappu RV. Net charge per residue modulates conformational ensembles of intrinsically disordered proteins. Proceedings of the National Academy of Sciences of the United States of America. 107: 8183-8. PMID 20404210 DOI: 10.1073/Pnas.0911107107  0.756
2010 Williamson TE, Vitalis A, Crick SL, Pappu RV. Modulation of polyglutamine conformations and dimer formation by the N-terminus of huntingtin. Journal of Molecular Biology. 396: 1295-309. PMID 20026071 DOI: 10.1016/J.Jmb.2009.12.017  0.774
2009 Vitalis A, Pappu RV. Methods for Monte Carlo simulations of biomacromolecules. Annual Reports in Computational Chemistry. 5: 49-76. PMID 20428473 DOI: 10.1016/S1574-1400(09)00503-9  0.573
2009 Vitalis A, Lyle N, Pappu RV. Thermodynamics of beta-sheet formation in polyglutamine. Biophysical Journal. 97: 303-11. PMID 19580768 DOI: 10.1016/J.Bpj.2009.05.003  0.762
2009 Vitalis A, Pappu RV. ABSINTH: a new continuum solvation model for simulations of polypeptides in aqueous solutions. Journal of Computational Chemistry. 30: 673-99. PMID 18506808 DOI: 10.1002/Jcc.21005  0.653
2009 Mao A, Vitalis A, Pappu RV. How Does Charge Content Modulate Conformational Equilibria of Intrinsically Disordered Proteins? An Illustration Using Protamines Biophysical Journal. 96: 220a. DOI: 10.1016/J.Bpj.2008.12.1920  0.782
2009 Vitalis A, Pappu RV. Introducing A Software Package For The Simulation Of Biomacromolecules Using The ABSINTH Implicit Solvation Model Biophysical Journal. 96: 303a. DOI: 10.1016/J.Bpj.2008.12.1508  0.59
2008 Vitalis A, Wang X, Pappu RV. Atomistic simulations of the effects of polyglutamine chain length and solvent quality on conformational equilibria and spontaneous homodimerization. Journal of Molecular Biology. 384: 279-97. PMID 18824003 DOI: 10.1016/J.Jmb.2008.09.026  0.665
2008 Pappu RV, Wang X, Vitalis A, Crick SL. A polymer physics perspective on driving forces and mechanisms for protein aggregation. Archives of Biochemistry and Biophysics. 469: 132-41. PMID 17931593 DOI: 10.1016/J.Abb.2007.08.033  0.747
2007 Vitalis A, Wang X, Pappu RV. Quantitative characterization of intrinsic disorder in polyglutamine: insights from analysis based on polymer theories. Biophysical Journal. 93: 1923-37. PMID 17526581 DOI: 10.1529/Biophysj.107.110080  0.674
2006 Wang X, Vitalis A, Wyczalkowski MA, Pappu RV. Characterizing the conformational ensemble of monomeric polyglutamine. Proteins. 63: 297-311. PMID 16299774 DOI: 10.1002/Prot.20761  0.768
2005 Borrelli KW, Vitalis A, Alcantara R, Guallar V. PELE:  Protein Energy Landscape Exploration. A Novel Monte Carlo Based Technique. Journal of Chemical Theory and Computation. 1: 1304-11. PMID 26631674 DOI: 10.1021/Ct0501811  0.348
2004 Vitalis A, Baker NA, McCammon JA. ISIM: A program for grand canonical Monte Carlo simulations of the ionic environment of biomolecules Molecular Simulation. 30: 45-61. DOI: 10.1080/08927020310001597862  0.355
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