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The Molecular Modelling Group
2012
O. Allnér, L. Nilsson, and A. Villa
Magnesium ion-water coordination and exchange in biomolecular simulations
J. Chem. Theory Comput. 2012, 8, 1493-1502.
2011
O. Engin, A. Villa, C. Peter and M. Sayar
A Challenge for Peptide Coarse Graining: Transferability of Fragment-Based Models,
Macromol. Theory Simul. 2011 20, 451-465.
2010
O. Engin, A. Villa, M. Sayar and B. Hess.
Driving forces for adsorption of amphiphilic peptides to the air-water interface,
J. Phys. Chem. B 2010 114, 11093-11101.
A. Villa, C. Peter, and N. F. A. van der Vegt.
Transferability of nonbonded interaction potentials for coarse-qrained simulations: Benzene in water,
J. Chem. Theory Comput. 2010, 6, 2434-2444.
2009
A. Villa, J. Wöhnert, and Gerhard Stock.
Molecular dynamics simulation study of the binding of purine bases to the aptamer domain of the guanine sensing riboswitch,
Nucleic Acids Research 2009, 37, 4774-4786.
A. Villa, B. Hess, and H. Saint-Martin.
Dynamics and Structure of Ln(III)-aquo ions: A comparative molecular dynamics study using ab initio based flexible and polarizable model potentials,
J. Phys. Chem. B 2009, 113, 7270-7281.
U. Cosentino, D. Pitea, G. Moro, G. A. A. Saracino, and A. Villa.
Conformational behaviour determines the low-relaxivity state of a conditional MRI contrast agent,
Phys. Chem. Chem. Phys. 2009, 11, 3943-3950.
A. Villa, C. Peter, and N. F. A. van der Vegt.
Self-assembling dipeptides: conformational sampling in solvent-free coarse-grained simulation,
Phys. Chem. Chem. Phys. 2009, 11, 2068-2076.
A. Villa, N. F. A. van der Vegt, and C. Peter.
Self-assembling dipeptides: including solvent degrees of freedom in a coarse-grained model.
Phys. Chem. Chem. Phys. 2009, 11, 2077-2086.
S. Donnini, A. Villa, G. Groenhof, A. E. Mark, R. K. Wierenga, and A. Juffer.
Inclusion of ionization states of ligand in affinity calculations.
PROTEINS: Structure, Function, and Bioinformatics 2009 , 76, 138 - 150.
G. A. A. Saracino, A. Villa, G. Moro, U. Cosentino, and M. Salmona.
Spontaneous beta-helical fold in prion protein. The case of PrP(82-146)
PROTEINS: Structure, Function, and Bioinformatics 2009, 75, 964-976.
2008
J Ferner, A. Villa, E. Duchardt, E. Widjajakusuma, J. Wöhnert, G. Stock, and H. Schwalbe
NMR and MD studies of the temperature-dependent dynamics of RNA YNMG-tetraloops
Nucleic Acids Research 2008, 36, 1928-1940
A. Villa, E. Widjajakusuma, and G. Stock
Molecular Dynamics Simulation of the Structure, Dynamics, and Thermostability of the RNA Hairpins uCACGg and cUUCGg
J. Phys. Chem. B 2008, 112, 134-142
2007
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. Garcí a,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.
2006
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.
2005
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. Dijkstra.
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.
2004
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.
2003
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.
2002
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 analogs of amino acid side chains.
J. Comput. Chem 2002, 23, 548.
2000
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 Field parameterization of Gadolinium complexes based on ab initio potential energy surface calculations
J. Phys. Chem. A. 2000, 104, 3421.
1998
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
