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List of works by Alessandra Villa

Advanced approaches for the characterization of a de novo designed antiparallel coiled coil peptide

scientific article published on 24 February 2005

Axons Embedded in a Tissue CAN Withstand Larger Deformations Than Isolated Axons Before Mechanoporation Occurs

scientific article published on 01 September 2019

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

scientific article

Computational Study of Uracil Tautomeric Forms in the Ribosome: The Case of Uracil and 5-Oxyacetic Acid Uracil in the First Anticodon Position of tRNA.

scientific article published on 20 December 2017

Conformational behaviour determines the low-relaxivity state of a conditional MRI contrast agent

scientific article

Conformational characterization of lanthanide(III)-DOTA complexes by ab initio investigation in vacuo and in aqueous solution.

scientific article

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

scientific article published on September 2010

Dynamics and Structure of Ln(III)−Aqua Ions: A Comparative Molecular Dynamics Study Using ab Initio Based Flexible and Polarizable Model Potentials

scientific article published on 21 May 2009

Effect of mutations on internal dynamics of an RNA hairpin from hepatitis B virus.

scientific article published on 18 August 2016

Elucidating the Relation between Internal Motions and Dihedral Angles in an RNA Hairpin Using Molecular Dynamics

scientific article published on August 2014

How Sensitive Are Nanosecond Molecular Dynamics Simulations of Proteins to Changes in the Force Field?

scientific article published in May 2007

Inclusion of ionization states of ligands in affinity calculations

scientific article

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

scientific article published on 30 January 2005

LNA effects on DNA binding and conformation: from single strand to duplex and triplex structures

scientific article published on 8 September 2017

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

scientific article published on 28 May 2013

Magnesium Ion-Water Coordination and Exchange in Biomolecular Simulations

scientific article published on 22 March 2012

Modeling and Simulation of Oligonucleotide Hybrids: Outlining a Strategy

scientific article published on 01 January 2019

Modeling pK Shift in DNA Triplexes Containing Locked Nucleic Acids

scientific article published on 23 March 2018

Molecular Dynamics Simulation of the Structure, Dynamics, and Thermostability of the RNA Hairpins uCACGg and cUUCGg

scientific article published in January 2008

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

scientific article published on 12 July 2019

NMR and MD studies of the temperature-dependent dynamics of RNA YNMG-tetraloops.

scientific article published on 13 February 2008

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

scientific article

Role of Pseudoisocytidine Tautomerization in Triplex-Forming Oligonucleotides: In Silico and in Vitro Studies.

scientific article published on 17 May 2017

Role of lipid composition on the structural and mechanical features of axonal membranes: a molecular simulation study.

scientific article published on 29 May 2019

Sampling and convergence in free energy calculations of protein-ligand interactions: the binding of triphenoxypyridine derivatives to factor Xa and trypsin

scientific article published in October 2003

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

scientific article published on 2 February 2009

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

scientific article published on 2 February 2009

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

scientific article

Spontaneous β-helical fold in prion protein: The case of PrP(82-146)

scientific article published in June 2009

Structural Basis of Egg Coat-Sperm Recognition at Fertilization.

scientific article

Structural basis for the enantioselectivity of an epoxide ring opening reaction catalyzed by halo alcohol dehalogenase HheC.

scientific article published in September 2005

The ability of locked nucleic acid oligonucleotides to pre-structure the double helix: A molecular simulation and binding study

scientific article published on 12 February 2019

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

scientific article published on 19 January 2017

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

scientific article published on 21 July 2010

Triple helical DNA in a duplex context and base pair opening

scientific article

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

scientific article published in September 2003

What NMR Relaxation Can Tell Us about the Internal Motion of an RNA Hairpin:  A Molecular Dynamics Simulation Study

scientific article published on 22 August 2006

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