Publications:


A. Villa, H. Fan, T. Wassenaar, and A. E. Mark
How Sensitive Are Nanosecond Molecular Dynamics Simulations of Proteins to Changes in the Force Field?
J. Phys. Chem. B 2007, 111, 6015 - 6025.

Á. Piñeiro, X. Banquy, S. Pérez-Casas, E. Tovar, A. García,A. Villa, A. Amigo, A. E. Mark, and M. Costas
On the Characterization of Host-Guest Complexes: Surface Tension, Calorimetry, and Molecular Dynamics of Cyclodextrins with a Non-ionic Surfactant.
J. Phys. Chem. B 2007, 111, 4383 - 4392.

A. Villa and G. Stock
What NMR Relaxation Can Tell Us about the Internal Motion of an RNA Hairpin: A Molecular Dynamics Simulation Study.
J. Chem. Theory Comput. 2006, 2, 1228 - 1236.

A. Villa, A. E. Mark, G. A. A. Saracino, U. Cosentino, D. Pitea, G. Moro, and M. Salmona
Conformational Polymorphism of the PrP106-126 Peptide in Different Environments: A Molecular Dynamics Study.
J. Phys. Chem. B 2006, 110, 1423.

Á. Piñeiro, A. Villa, T. Vagt, B. Koksch and A. E. Mark
A Molecular Dynamics Study of the Formation, Stability, and Oligomerization State of Two Designed Coiled Coils: Possibilities and Limitations.
Biophys. J. 2005, 89, 3701.

R. M. de Jong, J. J. W. Tiesinga, A. Villa, L. Tang, D. B. Janssen, and B. W. DijkstraK.
Structural Basis for the Enantioselectivity of an Epoxide Ring Opening Reaction Catalyzed by Halo Alcohol Dehalogenase HheC.
JACS, 2005, 127, 13338.

K. Pagel, K. Seeger, B. Seiwert, A. Villa, A. E. Mark, S. Berger and B. Koksch
Advanced approaches for the characterization of a de novo designed antiparallel coiled coil peptide.
OBC, 2005, 3, 1189.

S. Donnini, A. E. Mark, A. H. Juffer, A. Villa
'Incorporating the effect of ionic strength in free energy calculations using explicit ions'
J. Comput. Chem., 2005, 26, 115.

C. Oostenbrink, A. Villa, A.E. Mark, W.F. van Gunsteren
‘A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53a5 and 53a6’
J. Comput. Chem, 2004, 25, 1656.

U. Cosentino, D. Pitea, G. Moro, V. Barone, A. Villa,  R.N. Muller, F. Botteman.
‘Theoretical investigation into the influence of conformational equilibria on the water exchange process in magnetic resonance imaging contrast agents’
Theor. Chem. Acc., 2004, 111, 204.

A. Villa, R. Zangi, G. Pieffet and A.E. Mark
‘Sampling and convergence in free energy calculations of protein-ligand interactions: the binding of triphenoxypyridine derivatives to factor Xa and trypsin’
Journal of Computer-Aided Molecular Design, 2003, 17, 673.

R. Talhout, A. Villa, A.E. Mark, J.B.F.N. Engberts
‘Understanding binding affinity: a combined isothermal titration calorimetry/molecular dynamics study of the binding of a series of hydrophobically modified benzamidinium chloride inhibitors to trypsin’
JACS, 2003, 125, 10570.

U. Cosentino, A. Villa, D. Pitea, G. Moro, V. Barone, A. Maiocchi.
‘Conformational characterization of Lanthanide(III)-DOTA Complexes by ab initio investigation in vacuo and in aqueous solution’
JACS 2002, 124, 4901.

A. Villa, A.E. Mark
‘Calculation of the free energy of solvation for neutral analogues of amino Acid side chains.’
J. Comput. Chem 2002, 23, 548.

U. Cosentino, A. Villa, G. Moro, D. Pitea, V. Barone
‘Extension of computational chemistry to the study of Lanthanide(III) ions in aqueous solution: Implementation and validation of a continuum solvent approach’
J. Phys. Chem. B. 2000, 104, 8001.

A. Villa, U. Cosentino, G. Moro, D. Pitea, A. Maiocchi.
‘Force Fields parameterization of Gadolinium ion interactions with different oxygen donor atoms based on ab initio potential energy surface calculations’
J. Phys. Chem. A. 2000, 104, 3421.

U. Cosentino, G. Moro, D. Pitea, A. Villa, P.C. Fantucci, A. Maiocchi, F. Uggeri.
‘Ab initio investigations of gadolinium complexes with polyamino carboxylate ligands and force field parameterization of metal-ligand interactions’
J. Phys. Chem. A 1998, 102, 4606.

 

Thesis