Alessandra Villa

发表

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, 2003, J. Comput. Aided Mol. Des..

A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force‐field parameter sets 53A5 and 53A6

Chris Oostenbrink, Wilfred F. van Gunsteren, Alessandra Villa, 2004, J. Comput. Chem..

Modeling pK Shift in DNA Triplexes Containing Locked Nucleic Acids

Lennart Nilsson, Alessandra Villa, Yossa Dwi Hartono, 2018, J. Chem. Inf. Model..

Calculation of the free energy of solvation for neutral analogs of amino acid side chains

Alessandra Villa, Alan E. Mark, A. Mark, 2002, J. Comput. Chem..

The free energy of locking a ring: Changing a deoxyribonucleoside to a locked nucleic acid

You Xu, Lennart Nilsson, Alessandra Villa, 2017, J. Comput. Chem..

Sequence dependency of canonical base pair opening in the DNA double helix

Berk Hess, Alessandra Villa, Viveca Lindahl, 2017, PLoS Comput. Biol..

Modeling and Simulation of Oligonucleotide Hybrids: Outlining a Strategy.

Lennart Nilsson, Alessandra Villa, L. Nilsson, 2019, Methods in molecular biology.

Incorporating the effect of ionic strength in free energy calculations using explicit ions

Alessandra Villa, Alan E. Mark, André H. Juffer, 2005, J. Comput. Chem..

Molecular basis of egg coat cross-linking sheds light on ZP1-associated female infertility

Alessandra Villa, A. Villa, L. Jovine, 2019, Nature Communications.

Driving forces for adsorption of amphiphilic peptides to the air-water interface.

Berk Hess, Alessandra Villa, Mehmet Sayar, 2010, The journal of physical chemistry. B.

Self-assembling dipeptides: conformational sampling in solvent-free coarse-grained simulation.

Alessandra Villa, Christine Peter, Nico F A van der Vegt, 2009, Physical chemistry chemical physics : PCCP.

On the characterization of host-guest complexes: surface tension, calorimetry, and molecular dynamics of cyclodextrins with a non-ionic surfactant.

Miguel Costas, Alessandra Villa, Alan E Mark, 2007, The journal of physical chemistry. B.

New strategy for the extension of the serum half-life of antibody fragments.

Alessandra Villa, Dario Neri, Christoph E. Dumelin, 2009, Bioconjugate chemistry.

How sensitive are nanosecond molecular dynamics simulations of proteins to changes in the force field?

Alessandra Villa, Alan E Mark, Tsjerk Wassenaar, 2007, The journal of physical chemistry. B.

A molecular dynamics study of the formation, stability, and oligomerization state of two designed coiled coils: possibilities and limitations.

Alessandra Villa, Alan E Mark, Beate Koksch, 2005, Biophysical journal.

Loop–loop interaction in an adenine-sensing riboswitch: A molecular dynamics study

Lennart Nilsson, Alessandra Villa, L. Nilsson, 2013, RNA.

Molecular dynamics simulation study of the binding of purine bases to the aptamer domain of the guanine sensing riboswitch

Gerhard Stock, Alessandra Villa, Jens Wöhnert, 2009, Nucleic acids research.

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.

Reinskje Talhout, Alessandra Villa, Alan E Mark, 2003, Journal of the American Chemical Society.

Transferability of Nonbonded Interaction Potentials for Coarse-Grained Simulations: Benzene in Water.

Alessandra Villa, Christine Peter, Nico F A van der Vegt, 2010, Journal of chemical theory and computation.

Force Field Parametrization for Gadolinium Complexes Based on ab Initio Potential Energy Surface Calculations

Alessandra Villa, Ugo Cosentino, Demetrio Pitea, 2000 .

Inclusion of ionization states of ligands in affinity calculations

Gerrit Groenhof, Alessandra Villa, Alan E Mark, 2009, Proteins.

Self-assembling dipeptides: including solvent degrees of freedom in a coarse-grained model.

Alessandra Villa, Christine Peter, Nico F A van der Vegt, 2009, Physical chemistry chemical physics : PCCP.

A Challenge for Peptide Coarse Graining: Transferability of Fragment-Based Models

Alessandra Villa, Christine Peter, Mehmet Sayar, 2011 .

Magnesium Ion-Water Coordination and Exchange in Biomolecular Simulations.

Lennart Nilsson, Alessandra Villa, L. Nilsson, 2012, Journal of chemical theory and computation.