__________________________________________________________________ 2020__________________________________________________________________

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

__________________________________________________________________ 2019 __________________________________________________________________

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.


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.


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.


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.


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.


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


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.

__________________________________________________________________ 2018 __________________________________________________________________

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

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

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.

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.

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.

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.

__________________________________________________________________ 2017 __________________________________________________________________

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

E.E. Barrera, E.N.Frigini, R.D. Porasso, S. Pantano
Modeling DMPC lipid membranes with SIRAH force-field
Journal of Molecular Modeling. 2017

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.

G. Baldi​, M. Texeira, O.A. Martin, H.R. Grau, E.G. Jobbágy
Opportunities drive the global distribution of protected areas. PeerJ. 2017.

__________________________________________________________________ 2016 __________________________________________________________________

A. Arroyuelo, J.A. Vila, O.A. Martin
Azahar: a PyMOL plugin for construction, visualization and analysis of glycan molecules
Journal of Computer-Aided Molecular Design. 2016.

P.G. Garay, O.A. Martin, H.A. Scheraga, J.A. Vila
Detection of methylation, acetylation and glycosylation of protein residues by monitoring 13C chemical-shift changes: A quantum-chemical study
PeerJ. 2016

__________________________________________________________________ 2015 __________________________________________________________________

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

__________________________________________________________________ 2014 __________________________________________________________________

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.

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.

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.

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.

__________________________________________________________________ 2013 __________________________________________________________________

O.A. Martin, Y.A. Arnautova, A.A. Icazatti, H.A. Scheraga, and J.A. Vila
Physics-based method to validate and repair flaws in protein structures
Proceedings of the National Academy of Sciences of the United States of America. 2013, vol. 110 16826-16831.

__________________________________________________________________ 2012 __________________________________________________________________

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.

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.

O.A. Martin, J.A. Vila, H.A. Scheraga.
CheShift-2: graphic validation of protein structures
Bioinformatics; 2012 vol. 28 1538-1539.

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.

__________________________________________________________________ 2011 __________________________________________________________________

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.

__________________________________________________________________ 2010 __________________________________________________________________

J.A. Vila , P. Serrano, K. Wuthrich, H.A. Scheraga
Sequential nearest-neighbor effects on computed 13Cα chemical shifts
Journal of Biomolecular NMR; 2010 vol. 48 p. 23 - 30.

O.A Martin, M.E. Villegas, J.A. Vila, H.A. Scheraga
Analysis of 13Cα and 13Cβ Chemical Shifts of Cysteine and Cystine Residues in Proteins: A Quantum Chemical Approach
Journal of Biomolecular NMR; 2010 vol. 46 p. 217 - 225.

__________________________________________________________________ 2009 __________________________________________________________________

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).


__________________________________________________________________ 2008 __________________________________________________________________

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.


__________________________________________________________________ 2007 __________________________________________________________________

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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