List of works - Marco Pasi

A Protein Solvation Model Based on Residue Burial.

scientific article

Analyzing DNA curvature and its impact on the ionic environment: application to molecular dynamics simulations of minicircles

scientific article

Analyzing ion distributions around DNA.

scientific article

Analyzing ion distributions around DNA: sequence-dependence of potassium ion distributions from microsecond molecular dynamics.

scientific article

CURVES+ web server for analyzing and visualizing the helical, backbone and groove parameters of nucleic acid structures

scientific article

DNA minicircles clarify the specific role of DNA structure on retroviral integration

scientific article

Dynamic Properties of a Psychrophilic α-Amylase in Comparison with a Mesophilic Homologue

scientific article published on 01 October 2009

Expanding the repertoire of DNA shape features for genome-scale studies of transcription factor binding

scientific article published on 20 November 2017

Extra views on structure and dynamics of DNA loops on nucleosomes studied with molecular simulations.

scientific article published on 22 November 2016

Molecular determinants of enzyme cold adaptation: comparative structural and computational studies of cold- and warm-adapted enzymes

scientific article

Molecular dynamics of mesophilic-like mutants of a cold-adapted enzyme: insights into distal effects induced by the mutations

scientific article

Overview of the Nucleic-Acid Binding Properties of the HIV-1 Nucleocapsid Protein in Its Different Maturation States

scientific article published on 29 September 2020

PaLaCe: A Coarse-Grain Protein Model for Studying Mechanical Properties.

scientific article

Protein flexibility in psychrophilic and mesophilic trypsins. Evidence of evolutionary conservation of protein dynamics in trypsin-like serine-proteases.

scientific article

Structure and dynamics of DNA loops on nucleosomes studied with atomistic, microsecond-scale molecular dynamics.

scientific article

The Role of Unconventional Hydrogen Bonds in Determining BII Propensities in B-DNA.

scientific article

The static and dynamic structural heterogeneities of B-DNA: extending Calladine-Dickerson rules

scientific article published on 01 December 2019

cgDNA: a software package for the prediction of sequence-dependent coarse-grain free energies of B-form DNA

scientific article

xPyder: A PyMOL Plugin To Analyze Coupled Residues and Their Networks in Protein Structures

scientific article published on 05 July 2012

μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA

scientific article

List of works by Marco Pasi

A Protein Solvation Model Based on Residue Burial.

Analyzing DNA curvature and its impact on the ionic environment: application to molecular dynamics simulations of minicircles

Analyzing ion distributions around DNA.

Analyzing ion distributions around DNA: sequence-dependence of potassium ion distributions from microsecond molecular dynamics.

CURVES+ web server for analyzing and visualizing the helical, backbone and groove parameters of nucleic acid structures

DNA minicircles clarify the specific role of DNA structure on retroviral integration

Dynamic Properties of a Psychrophilic α-Amylase in Comparison with a Mesophilic Homologue

Expanding the repertoire of DNA shape features for genome-scale studies of transcription factor binding

Extra views on structure and dynamics of DNA loops on nucleosomes studied with molecular simulations.

Molecular determinants of enzyme cold adaptation: comparative structural and computational studies of cold- and warm-adapted enzymes

Molecular dynamics of mesophilic-like mutants of a cold-adapted enzyme: insights into distal effects induced by the mutations

Overview of the Nucleic-Acid Binding Properties of the HIV-1 Nucleocapsid Protein in Its Different Maturation States

PaLaCe: A Coarse-Grain Protein Model for Studying Mechanical Properties.

Protein flexibility in psychrophilic and mesophilic trypsins. Evidence of evolutionary conservation of protein dynamics in trypsin-like serine-proteases.

Structure and dynamics of DNA loops on nucleosomes studied with atomistic, microsecond-scale molecular dynamics.

The Role of Unconventional Hydrogen Bonds in Determining BII Propensities in B-DNA.

The static and dynamic structural heterogeneities of B-DNA: extending Calladine-Dickerson rules

cgDNA: a software package for the prediction of sequence-dependent coarse-grain free energies of B-form DNA

xPyder: A PyMOL Plugin To Analyze Coupled Residues and Their Networks in Protein Structures

μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA