Calculation of the free energy of solvation for neutral analogs of amino acid side chains. - Alessandra Villa; Alan E. Mark (J. Comput. Chem., 2002)

Sampling and convergence in free energy calculations of protein-ligand interactions: The binding of triphenoxypyridine derivatives to factor Xa and trypsin. - Alessandra Villa; Ronen Zangi; Gilles Pieffet; Alan E. Mark (J. Comput. Aided Mol. Des., 2003)

A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6. - Chris Oostenbrink; Alessandra Villa; Alan E. Mark; Wilfred F. van Gunsteren (J. Comput. Chem., 2004)

Incorporating the effect of ionic strength in free energy calculations using explicit ions. - Serena Donnini; Alan E. Mark; André H. Juffer; Alessandra Villa (J. Comput. Chem., 2005)

The free energy of locking a ring: Changing a deoxyribonucleoside to a locked nucleic acid. - You Xu; Alessandra Villa; Lennart Nilsson (J. Comput. Chem., 2017)

Sequence dependency of canonical base pair opening in the DNA double helix. - Viveca Lindahl; Alessandra Villa; Berk Hess (PLoS Comput. Biol., 2017)

Modeling pK Shift in DNA Triplexes Containing Locked Nucleic Acids. - Yossa Dwi Hartono; You Xu; Andrey Karshikoff; Lennart Nilsson; Alessandra Villa (J. Chem. Inf. Model., 2018)