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. 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.

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

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

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.

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.

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.

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.

J.A. Vila , P. Serrano, K. Wuthrich, H.A. Scheraga
Sequential nearest-neighbor effects on computed ¹³C^α 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 ¹³C^α and ¹³C^β Chemical Shifts of Cysteine and Cystine Residues in Proteins: A Quantum Chemical Approach
Journal of Biomolecular NMR; 2010 vol. 46 p. 217 - 225.

J.A. Vila, H.A. Baldoni, H.A. Scheraga
Performance of Density Functional Models to Reproduce Observed ¹³C^α 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 ¹³C^α 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 ¹³C^α 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 ¹³C^α 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).

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 ¹³C^α 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 ¹³C^α 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 ¹³C^α 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.

J.A. Vila, M.E. Villegas, H.A. Baldoni, H.A. Scheraga
Predicting ¹³C^α 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 ¹³C^α 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