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List of works by Franca Fraternali

A New Crystal Form of the SARS-CoV-2 Receptor Binding Domain: CR3022 Complex-An Ideal Target for In-Crystal Fragment Screening of the ACE2 Binding Site Surface

scientific article published on 14 December 2020

A case-by-case evolutionary analysis of four imprinted retrogenes ⬇️

scientific article (publication date: May 2011)

A computational exploration of the interactions of the green tea polyphenol (-)-Epigallocatechin 3-Gallate with cardiac muscle troponin C

scientific article

A conformational study in solution of pro-somatostatin fragments by NMR and computational methods

scientific article published on 01 August 1998

A multiscale approach to the elastic moduli of biomembrane networks.

scientific article published on 17 February 2012

A refined, efficient mean solvation force model that includes the interior volume contribution

scientific article

A solvable model of the genesis of amino-acid sequences via coupled dynamics of folding and slow-genetic variation

A targeted siRNA screen identifies regulators of Cdc42 activity at the natural killer cell immunological synapse

scientific article

ALIX Regulates Tumor-Mediated Immunosuppression by Controlling EGFR Activity and PD-L1 Presentation

scientific article published on 01 July 2018

AP1S3 mutations are associated with pustular psoriasis and impaired Toll-like receptor 3 trafficking

scientific article

An Efficient Mean Solvation Force Model for Use in Molecular Dynamics Simulations of Proteins in Aqueous Solution

article

An engineered photoswitchable mammalian pyruvate kinase

scientific article

An immunoglobulin-like fold in a major plant allergen: the solution structure of Phl p 2 from timothy grass pollen

scientific article

Anatomy of protein disorder, flexibility and disease-related mutations

scientific article published on 12 August 2015

Assembly of Influenza Hemagglutinin Fusion Peptides in a Phospholipid Bilayer by Coarse-grained Computer Simulations

scientific article published on 18 November 2015

B-RAF Mutant Alleles Associated with Langerhans Cell Histiocytosis, a Granulomatous Pediatric Disease ⬇️

scientific article published on April 10, 2012

BCR-ABL residues interacting with ponatinib are critical to preserve the tumorigenic potential of the oncoprotein

scientific article published on 02 December 2013

BRepertoire: a user-friendly web server for analysing antibody repertoire data

scientific article published on 14 April 2018

Bidirectional barbed suture in laparoscopic myomectomy: clinical features.

scientific article published in December 2013

Biomechanical features of bidirectional-barbed suture: a randomized laboratory analysis.

scientific article published in March 2014

Bridging topological and functional information in protein interaction networks by short loops profiling

scientific article

Calcium regulates scallop muscle by changing myosin flexibility

scientific article published on 11 January 2006

Conformation and dynamics of a rhodamine probe attached at two sites on a protein: implications for molecular structure determination in situ

scientific article published in December 2008

Conformational analysis of dolastatin 10: an NMR and theoretical approach

scientific article published on October 1995

Conformational preferences and self-association modes of two diastereomeric statine derivatives

scientific article published on 01 November 1987

Correction: B-RAF Mutant Alleles Associated with Langerhans Cell Histiocytosis, a Granulomatous Pediatric Disease.

scientific article published on 28 June 2012

Correction: Tissue-specific shaping of the TCR repertoire and antigen specificity of iNKT cells

scientific article published on 18 March 2020

Decrypting Prion Protein Conversion into a β-Rich Conformer by Molecular Dynamics

scientific article published on 4 April 2013

Design and application of implicit solvent models in biomolecular simulations

scientific article published in April 2014

Design and solution structure of a partially rigid opioid antagonist lacking the basic center--models of antagonism

scientific article published in July 1997

Detection of allosteric signal transmission by information-theoretic analysis of protein dynamics

scientific article published on 9 November 2011

Development of new laccases by directed evolution: functional and computational analyses

scientific article

Dynamic domain threading

scientific article published in August 2006

Effects of pathological mutations on the stability of a conserved amino acid triad in retinoschisin

scientific article (publication date: 5 June 2003)

Emerging role of the ubiquitin-proteasome system as drug targets

scientific article published on January 2013

Engineering Chirally Blind Protein Pseudocapsids into Antibacterial Persisters

scientific article published on 05 December 2019

Exploring protein interiors: the role of a buried histidine in the KH module fold

scientific article

Functional cross-talk between allosteric effects of activating and inhibiting ligands underlies PKM2 regulation

scientific article published on 2 July 2019

GSATools: analysis of allosteric communication and functional local motions using a structural alphabet

scientific article published on 05 June 2013

Genetic variants and protein-protein interactions: a multidimensional network-centric view

scientific article published on 4 January 2018

Highly nonlinear pulse splitting and recombination in a two-dimensional granular network

scientific article published on 8 September 2010

Highly nonlinear solitary wave propagation in Y-shaped granular crystals with variable branch angles.

scientific article published on 6 March 2012

Homology-Based Modeling of Universal Stress Protein from Listeria innocua Up-Regulated under Acid Stress Conditions

scientific article published on 20 December 2016

How Förster resonance energy transfer imaging improves the understanding of protein interaction networks in cancer biology

scientific article published on 15 February 2011

Hydrogen-bonding propensities of sphingomyelin in solution and in a bilayer assembly: a molecular dynamics study

scientific article

Identifying Extrinsic versus Intrinsic Drivers of Variation in Cell Behavior in Human iPSC Lines from Healthy Donors

Implicit Solvation Parameters Derived from Explicit Water Forces in Large-Scale Molecular Dynamics Simulations

scientific article

In silico identification of rescue sites by double force scanning

scientific article published on 14 August 2017

In silico phosphorylation of the autoinhibited form of p47(phox): insights into the mechanism of activation

scientific article

Inhibitor-induced HER2-HER3 heterodimerisation promotes proliferation through a novel dimer interface

scientific article published in May 2018

Interaction of malaria parasite-inhibitory antibodies with the merozoite surface protein MSP1(19) by computational docking

scientific article published on February 2007

Interactions of the C2 domain of human factor V with a model membrane

scientific article

Investigating Ebola virus pathogenicity using molecular dynamics

scientific article published on 11 August 2017

Josephin domain of ataxin-3 contains two distinct ubiquitin-binding sites

scientific article published in December 2009

Large-scale modelling of the divergent spectrin repeats in nesprins: giant modular proteins

scientific article

Lipid Head Group Parameterization for GROMOS 54A8: A Consistent Approach with Protein Force Field Description

scientific article published on 09 September 2019

Mapping disease-related missense mutations in the immunoglobulin-like fold domain of lamin A/C reveals novel genotype-phenotype associations for laminopathies

scientific article published on 26 December 2013

Mapping the active site of factor Xa by selective inhibitors: An NMR and MD study ⬇️

scientific article published on February 15, 1998

MinSet: a general approach to derive maximally representative database subsets by using fragment dictionaries and its application to the SCOP database

scientific article published on 3 January 2007

Mode of binding of camptothecins to double helix oligonucleotides

scientific article

Modeling and in situ identification of material parameters for layered structures based on carbon nanotube arrays

article

Modularity and homology: modelling of the titin type I modules and their interfaces

article

Modularity and homology: modelling of the type II module family from titin

article

Molecular determinants of peculiar properties of a Pleurotus ostreatus laccase: Analysis by site-directed mutagenesis

article

Molecular interactions of ASPP1 and ASPP2 with the p53 protein family and the apoptotic promoters PUMA and Bax.

scientific article published on 2 August 2008

Mutants of the tumour suppressor p53 L1 loop as second-site suppressors for restoring DNA binding to oncogenic p53 mutations: structural and biochemical insights

article

Mutation of the RAD51C gene in a Fanconi anemia-like disorder

scientific article published on 18 April 2010

Neurologically active plant compounds and peptide hormones: a chirality connection

article

Novel RNA-binding motif: the KH module

scientific article

On the estimation of the curvatures and bending rigidity of membrane networks via a local maximum-entropy approach

POPS: A fast algorithm for solvent accessible surface areas at atomic and residue level

scientific article

POPSCOMP: an automated interaction analysis of biomolecular complexes

scientific article

Pan-cancer transcriptomic analysis dissects immune and proliferative functions of APOBEC3 cytidine deaminases

scientific article published on 01 February 2019

Parameter optimized surfaces (POPS): analysis of key interactions and conformational changes in the ribosome

scientific article

PinSnps: structural and functional analysis of SNPs in the context of protein interaction networks

scientific article

Plasticity and conformational equilibria of influenza fusion peptides in model lipid bilayers

scientific article published on 15 January 2014

Plasticity of influenza haemagglutinin fusion peptides and their interaction with lipid bilayers

scientific article

Pooled sequencing of 531 genes in inflammatory bowel disease identifies an associated rare variant in BTNL2 and implicates other immune related genes

scientific article

Probing the early stages of prion protein (PrP) aggregation with atomistic molecular dynamics simulations

scholarly article by Francesca Collu et al published 2018 in Chemical Communications

Promiscuous antibodies characterised by their physico-chemical properties: From sequence to structure and back

scientific article published on 14 September 2016

Protein networks reveal detection bias and species consistency when analysed by information-theoretic methods

scientific article

Protein-protein interaction networks studies and importance of 3D structure knowledge

scientific article published on December 2013

Protein-water interactions in MD simulations: POPS/POPSCOMP solvent accessibility analysis, solvation forces and hydration sites

scientific article published in January 2012

RNA-dependent oligomerization of APOBEC3G is required for restriction of HIV-1

scientific article

Rationalisation of the differences between APOBEC3G structures from crystallography and NMR studies by molecular dynamics simulations

scientific article

Reorganization in apo- and holo-beta-lactoglobulin upon protonation of Glu89: molecular dynamics and pKa calculations

scientific article published on March 2004

Restrained and unrestrained molecular dynamics simulations in the NVT ensemble of alamethicin

article

RhoBTB1 interacts with ROCKs and inhibits invasion

scientific article published on 13 September 2019

SARS-CoV-2 spike protein predicted to form stable complexes with host receptor protein orthologues from mammals

scientific article published on 02 May 2020

Short loop functional commonality identified in leukaemia proteome highlights crucial protein sub-networks

scientific article published on 01 March 2021

Significant Differences in Physicochemical Properties of Human Immunoglobulin Kappa and Lambda CDR3 Regions

scientific article

Single-Cell Transcriptomic Analyses Define Distinct Peripheral B Cell Subsets and Discrete Development Pathways

scientific article published on 18 March 2021

Specialized Dynamical Properties of Promiscuous Residues Revealed by Simulated Conformational Ensembles

scientific article published on 27 September 2013

Stability and Cations Coordination of DNA and RNA 14-Mer G-Quadruplexes: A Multiscale Computational Approach

Structural Properties of Green Tea Catechins

scientific article published on 14 September 2015

Structural features of the regulatory ACT domain of phenylalanine hydroxylase

scientific article published on 14 November 2013

Structural insight into the h TERT intron 6 sequence d(GGGGTGAAAGGGG) from 1H-NMR study

scholarly article by Ada Virno et al published 26 November 2007 in Nucleosides, Nucleotides & Nucleic Acids

Structural versatility of peptides containing C alpha, alpha-dialkylated glycines. An X-ray diffraction study of six 1-aminocyclopropane-1-carboxylic acid rich peptides

scientific article published in December 1989

Structural versatility of peptides containing Cα,α-dialkylated glycines: conformational energy computations, i.r. absorption and 1H n.m.r. analysis of 1-aminocyclopropane-1-carboxylic acid homopeptides

article

Structure and Dynamics of Nanoconfined Water Between Surfactant Monolayers

scientific article published on 26 December 2019

Structure and stability insights into tumour suppressor p53 evolutionary related proteins

scientific article

Surface Accessibility and Dynamics of Macromolecular Assemblies Probed by Covalent Labeling Mass Spectrometry and Integrative Modeling

scientific article (publication date: 7 February 2017)

Symmetry-breaking transitions in the early steps of protein self-assembly

scientific article published on 02 March 2020

TITINdb-a computational tool to assess titin's role as a disease gene

scientific article published in November 2017

Tailored graph ensembles as proxies or null models for real networks I: tools for quantifying structure

scientific article

The oligomerization properties of prion protein are restricted to the H2H3 domain

The p73 DNA binding domain displays enhanced stability relative to its homologue, the tumor suppressor p53, and exhibits cooperative DNA binding.

scientific article published on 9 February 2008

The solution structure of the first KH domain of FMR1, the protein responsible for the fragile X syndrome

scientific article

Thermal unfolding simulations of apo-calmodulin using leap-dynamics

scientific article published in March 2003

Tissue-specific shaping of the TCR repertoire and antigen specificity of iNKT cells

scientific article published on 16 December 2019

Toward the understanding of MNEI sweetness from hydration map surfaces

scientific article

Towards the identification of the allosteric Phe-binding site in phenylalanine hydroxylase

scientific article published on 19 October 2015

Transitional B Cells in Early Human B Cell Development - Time to Revisit the Paradigm?

scientific article published on 02 December 2016

Understanding the structural details of APOBEC3-DNA interactions using graph-based representations

scientific article published on 12 August 2020

Urea–Water Solvation Forces on Prion Structures ⬇️

scientific article published on August 14, 2012

Water molecules as structural determinants among prions of low sequence identity

scientific article

When a module is not a domain: the case of the REJ module and the redefinition of the architecture of polycystin-1.

scientific article published on May 2011

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