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2020
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E.N. Frigini, J.J López Cascales, R.D. Porasso
Influence of Lipid Composition on the Insertion Process of Glyphosate into Membranes: A Thermodynamic Study
The Journal of Physical Chemistry B (2020)
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J.A. Vila
About the Protein Space Vastness
The Protein Journal (2020) 39, 472–475(2020)
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P.G. Ramírez, M.G. Del Pópolo, J.A. Vila, G.S. Longo
Thermodynamics of Cell Penetrating Peptides on Lipid Membranes: Sequence and Membrane Acidity Regulate Surface Binding
Physical Chemistry Chemical Physics (2020)
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J.A. Vila Harold A. Scheraga Legatum The Protein Journal (2020)
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J.A. Vila Metamorphic Proteins in Light of Anfinsen’s Dogma The Journal of Physical Chemistry Letters (2020)
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O.A Martin, J.A. Vila The Marginal Stability of Proteins: How the Jiggling and Wiggling of Atoms is Connected to Neutral Evolution Journal of Molecular Evolution (2020)
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A. Arroyuelo, O.A Martin, H.A. Scheraga, J.A. Vila Assessing the One-Bond Cα–H Spin–Spin Coupling Constants in Proteins: Pros and Cons of Different Approaches The Journal of Physical Chemistry B Article ASAP
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__________________________________________________________________ 2019 __________________________________________________________________
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E.N. Frigini, E.E. Barrera, S. Pantano, R.D. Porasso Role of Membrane Curvature on the Activation/Deactivation of Carnitine Palmitoyltransferase 1A: A Coarse Grain Molecular Dynamic Study Biochimica et Biophysica Acta (BBA) - Biomembranes (2019), 183094.
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A.A. Icazatti, J.M. Loyola, I. Szleifer, J.A. Vila, O.A. Martin Classification of RNA backbone conformations into rotamers using 13C′ chemical shifts: exploring how far we can go PeerJ. 2019.
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O.A. Martin, Y. Vorobjev, H.A. Scheraga, J.A. Vila Outline of an experimental design aimed to detect protein A mirror image in solution PeerJ. 2019.
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G. Baldi, S. Schauman, M. Texeira, S. Marinaro, O.A. Martin, P. Gandini, E.G. Jobbágy Nature representation in South American protected areas: country contrasts and conservation priorities PeerJ. 2019.
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J.A. Vila Forecasting the upper bound free energy difference between protein native-like structures Physica A: Statistical Mechanics and its Applications (2019) 533, 122053.
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P.G. Ramírez, M.G. Del Pópolo, J.A. Vila, I.Szleifer, G.S. Longo Adsorption and insertion of polyarginine peptides into membrane pores: The trade-off between electrostatics, acid-base chemistry and pore formation energy Journal of Colloid and Interface Science (2019) 552, 701-711
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R. Kumar, C. Carroll, A. Hartikainen, O.A. Martin ArviZ a unified library for exploratory analysis of Bayesian models in Python Journal of Open Source Software (2019) ,4(33), 1143.
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__________________________________________________________________ 2018 __________________________________________________________________
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A.A. Icazatti, O.A. Martin, M. Villegas, I. Szleifer and J.A. Vila; 13Check_RNA: A tool to evaluate 13C chemical shifts assignments of RNA. Bioinformatics (2018), bty470
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C. Esteban, I. Donati, S. Pantano, M. Villegas, J. Benegas and S. Paoletti Dissecting the conformational determinants of chitosan and chitlac oligomers‐REVISED. Biopolymers (2018), e23221
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E.N. Frigini, J.J. López Cascales, R.D. Porasso Molecular dynamics simulations of glyphosate in a DPPC lipid bilayer. Chemistry and Physics of Lipids (2018), 213, 111-117.
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J.M. Alonso, A. Arroyuelo, P.G. Garay, O.A. Martin and J.A. Vila Finite Dimension: A Mathematical Tool To Analise Glycans. Scientific Reports (2018), 8, 4426-4436.
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P.G. Garay, J.A. Vila, O.A. Martin CheSweet: An application to predict glycan’s chemicals shifts. Journal of Open Source Software. 2018. 3(21), 488.
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Y.N. Vorobjev, H.A. Scheraga, J.A. Vila Coupled molecular dynamics and continuum electrostatic method to compute the ionization pKa’s of proteins as a function of pH. Test on a large set of proteins. Journal of Biomolecular Structure and Dynamics (2018) 36(3) 561-574.
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__________________________________________________________________ 2017 __________________________________________________________________
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Y.N. Vorobjev, H.A. Scheraga, J.A. Vila. A comprehensive Analysis of the Computed Tautomer Fractions of the Imidazole Ring of Histidines in Loligo vulgaris. Journal of Biomolecular Structure and Dynamics. 2017
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E.E. Barrera, E.N.Frigini, R.D. Porasso, S. Pantano Modeling DMPC lipid membranes with SIRAH force-field Journal of Molecular Modeling. 2017
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J.A. Vila, H.A. Scheraga Limiting values of the one-bond C-H spin-spin coupling constants of the imidazole ring of histidine at high-pH Journal of Molecular Structure. 2017.
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G. Baldi, M. Texeira, O.A. Martin, H.R. Grau, E.G. Jobbágy Opportunities drive the global distribution of protected areas. PeerJ. 2017.
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__________________________________________________________________ 2015 __________________________________________________________________
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R.D. Porasso, N.M. Ale, F. Ciocco Aloia, D. Masone, M.G. Del Popolo, A. Ben Altabef, A. Gomez-Zavaglia, S.B. Diaz, J.A. Vila Interaction of glycine, lysine, proline and histidine with dipalmitoylphosphatidylcholine lipid bilayers: a theoretical and experimental study. The Royal Society of Chemistry. 2015
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__________________________________________________________________ 2014 __________________________________________________________________
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P. Garay, O.A. Martin, H.A. Scheraga, J.A. Vila Factors affecting the computation of the 13C shielding in disaccharides Journal of Computational Chemistry; 2014, p. 1 - 6.
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K. Kachlishvili, G. Maisuradze, O.A. Martin, A. Liwo, J.A. Vila, H.A. Scheraga Accounting for a mirror-image conformation as a subtle effect in protein folding Proceedings of the National Academy of Sciences of the United States of America; 2014, vol. 111 p. 8458 - 8463.
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K. Baler, O.A. Martin, M.A. Carignano, G.A. Ameer, J.A. Vila, I. Szleifer Electrostatic Unfolding and Interactions of Albumin Driven by pH Changes: A Molecular Dynamics Study Journal of Physical Chemistry B; 2014 vol. 118 921-930.
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J.A. Vila, Y.A. Arnautova, O.A. Martin, H.A. Scheraga Are accurate computations of the 13C' shielding feasible at the DFT level of theory? Journal of Computational Chemistry; 2014 vol. 35 309-312.
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__________________________________________________________________ 2012 __________________________________________________________________
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J.A Vila, S. Sue, J.S. Fraser, H.A. Scheraga, H.J. Dyson CheShift-2 resolves a local inconsistency between two X-ray crystal structures Journal of Biomolecular NMR; 2012, vol. 54 193-198.
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J.A. Vila Limiting values of the 15N chemical shift of the imidazole ring of histidine at high pH
Journal of Physical Chemistry B; 2012. vol 116 6665–6669.
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O.A. Martin, J.A. Vila, H.A. Scheraga. CheShift-2: graphic validation of protein structures Bioinformatics; 2012 vol. 28 1538-1539.
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M.J. Figueras, O.A. Martin, P.C. Echeverria, N. De Miguel, A. Naguleswaran, W.J. Sullivan, M.M. Corvi, S.O. Angel. Toxoplasma gondii Sis1-like J-domain protein is a cytosolic chaperone associated to HSP90/HSP70 complex International Journal of Biological Macromolecules; 2012 vol. 50 725-33.
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__________________________________________________________________ 2011 __________________________________________________________________
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J.A. Vila, Y.A. Arnautova, Y.N. Vorobjev, H.A. Scheraga Assessing the fractions of tautomeric forms of the imidazole ring of histidine in proteins as a function of pH Proceedings of the National Academy of Sciences of the United States of America; 2011 vol. 108 p. 5602 - 5607.
J.J. Cascales, S.D. Oliveira Costa, R.D. Porasso Thermodynamic study of benzocaine insertion into different lipid bilayers Journal of Chemical Physics; 2011 vol. 135 p. 1351031 - 1351037.
O.A Martin, H.A. Garro, M.B. Kurina Sanz, CR Pungitore, CE, Tonn In silico study of the inhibition of DNA polymerase by a novel catalpol derivative Journal of molecular modeling; 2011 vol. 17 2717-2723.
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__________________________________________________________________ 2009 __________________________________________________________________
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J.A. Vila, H.A. Baldoni, H.A. Scheraga Performance of Density Functional Models to Reproduce Observed 13Cα Chemical Shifts of Proteins in Solution Journal of Computational Chemistry; 2009 vol. 30 p. 884 - 892.
Y.A. Arnautova, J.A. Vila, O.A Martin, H.A. Scheraga What can we learn by computing 13Cα chemical shifts for X-ray protein models? Acta Crystallographica Section D-Biological Crystallography; 2009 vol. D65 p. 697 - 703.
Y.A. Arnautova, Y.N. Vorobjev, J.A. Vila, H.A. Scheraga Identifying native-like protein structures with scoring functions based on all-atom ECEPP force fields, implicit solvent models and structure relaxation Proteins; Structure, Function and Genetics 2009 vol. 77 p. 38 - 51.
J.A. Vila, Y.A. Arnautova, O.A Martin, H.A. Scheraga Quantum-Mechanics-Derived 13Cα Chemical Shift Server (CheShift) for Protein Structure Validation Proceedings of the National Academy of Sciences of United States of America; 2009 vol. 106 p. 16972 - 16977.
J.A. Vila, H.A. Scheraga Assessing the Accuracy of Protein Structures by Quantum Mechanical Computations of 13Cα Chemical Shifts Accounts of Chemical Research; 2009 vol. 42 p. 1445 - 1553.
R.D. Porasso, J.J. López Cascales Study of the effect of Na+ and Ca2+ ion concentration on the structure of an asymmetric DPPC/DPPC+DPPS lipid bilayer by Molecular Dynamics Simulation Colloids and Surfaces B-Biointerfaces; 2009 vol. 73 p. 42 - 50.
R.D. Porasso, W.F. Bennett, S.D. Oliveira Costa, J.J. López Cascales Study of the benzocaine transfer from aqueous solution to the interior of a biological membrane Journal of Physical Chemistry B; 2009 vol. 113 p. 9988 - 9994.
O.A. Martin, M. E. Villegas, C.F. Aguilar Three-dimensional studies of pathogenic peptides from the c-terminal of Trypanosoma cruzi ribosomal P proteins and their interaction with a monoclonal antibody structural model PMC biophysics; 2009 2 (1).
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__________________________________________________________________ 2008 __________________________________________________________________
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J.A.Vila, J.M. Aramini, P. Rossi, A. Kuzin, M. Su, J. Seetharaman, R. Xiao, L. Tong, G. T. Montelione, H. A. Scheraga Quantum Chemical 13Cα Chemical Shift Calculations for Protein NMR Structure Determination, Refinement, and Validation Proceedings of the National Academy of Sciences of the United States of America; 2008 vol. 105 p. 14389 - 14394.
J.A. Vila, Y.A. Arnautova, H.A. Scheraga Use of 13Cα chemical shifts for accurate determination of beta-Sheet structures in solution Proceedings of the National Academy of Sciences of the United States of America; 2008 vol. 105 p. 1891 - 1896.
J.A. Vila, H.A. Scheraga Factors Affecting the Use of 13Cα Chemical Shifts to Determine, Refine and Validate Protein Structures Proteins: Structure, Function and Genetics; 2008 vol. 71 p. 641 - 654.
Y.A. Vorobjev, J.A. Vila, H.A. Scheraga FAMBE-pH: a Fast and Accurate Method to Compute the Total Solvation Free Energies of Proteins Journal of Physical Chemistry B; 2008 vol. 112 p. 11122 - 11136.
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__________________________________________________________________ 2007 __________________________________________________________________
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J.A. Vila, M.E. Villegas, H.A. Baldoni, H.A. Scheraga Predicting 13Cα chemical shifts for validation of protein structures Journal of Biomolecular NMR; 2007 vol. 38 p. 221 - 235
J.A. Vila, D.R. Ripoll, H.A. Scheraga Use of 13Cα chemical-shifts in protein structure determination Journal of Physical Chemistry B; 2007 vol. 111 p. 6577 - 6585.
J. Makowska, S. Rodziewics-Motowidło, K. Bagińska, M. Makowski, J.A. Vila, A. Liwo, L. Chmurzynski, H.A. Scheraga Further evidence for the absence of persistent polyproline II conformation in the XAO peptide Biophysical Journal; 2007 vol. 92 p. 2904 - 2917.
M.E. Villegas, J.A. Vila, H.A. Scheraga Effects of Side-Chain Orientation on the 13C Chemical Shifts of Antiparallel beta-sheet Model Peptides Journal of Biomolecular NMR; 2007 vol. 37 p. 137 - 146.
M.Y. Niv, D.R. Ripoll, J.A. Vila, A. Liwo, E.S. Vanamee, A.K. Aggarwal, H. Winstein, H.A. Scheraga Topology of Type II REases revisited; structural classes and the common conserved core Nucleic Acids Research; 2007 vol. 35 p. 2227 – 2237
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