List of works - Guido Tiana

A Combined NMR-Computational Study of the Interaction between Influenza Virus Hemagglutinin and Sialic Derivatives from Human and Avian Receptors on the Surface of Transfected Cells

scientific article published on 24 April 2018

A folding inhibitor of the HIV-1 protease.

scientific article published in March 2006

A highly compliant protein native state with a spontaneous-like mechanical unfolding pathway

scientific article published in 2012

A many-body term improves the accuracy of effective potentials based on protein coevolutionary data

scientific article

A method for partitioning the information contained in a protein sequence between its structure and function

scientific article published on 01 September 2018

An implementation of the maximum-caliber principle by replica-averaged time-resolved restrained simulations

scientific article published on 01 May 2018

Atomistic simulations of the HIV-1 protease folding inhibition

scientific article published on 28 March 2008

Beta-hairpin conformation of fibrillogenic peptides: structure and alpha-beta transition mechanism revealed by molecular dynamics simulations

scientific article

Cohesin and CTCF control the dynamics of chromosome folding

scientific article published in 2022

Corrigendum to “Kinetics of Different Processes in Human Insulin Amyloid Formation” [J. Mol. Biol. 366/1 (2007) 258-274]

scholarly article published in Journal of Molecular Biology

DamC reveals principles of chromatin folding in vivo without crosslinking and ligation

scientific article published on 27 May 2019

Denatured state is critical in determining the properties of model proteins designed on different folds.

scientific article

Deriving amino acid contact potentials from their frequencies of occurrence in proteins: a lattice model study

article

Design and folding of dimeric proteins

scientific article

Design of HIV-1-PR inhibitors that do not create resistance: blocking the folding of single monomers

scientific article published in October 2005

Design of a folding inhibitor of the HIV-1 protease

article

Design of amino acid sequences to fold into C(alpha)-model proteins

article

Designability of lattice model heteropolymers

scientific article published on 13 June 2001

Determination of Structural Ensembles of Flexible Molecules in Solution from NMR Data Undergoing Spin Diffusion

scientific article published on 05 June 2019

Dynamical Genetic Regulation

Early events in insulin fibrillization studied by time-lapse atomic force microscopy

scientific article

Early events in protein folding: Is there something more than hydrophobic burst?

scientific article

Energy profile of the space of model protein sequences

scientific article published on June 2001

Estimation of microscopic averages from metadynamics

Exploring the protein G helix free-energy surface by solute tempering metadynamics

scientific article published in June 2008

Folding and aggregation of designed proteins.

scientific article published on October 1998

Folding and misfolding of designed proteinlike chains with mutations

HIV-1 protease folding and the design of drugs which do not create resistance

scientific article published on 21 December 2007

Hierarchy of events in the folding of model proteins

article

Hierarchy of folding and unfolding events of protein G, CI2, and ACBP from explicit-solvent simulations

scientific article published in January 2011

Hydrogen Bonds in Polymer Folding

scientific article published in Physical Review Letters

Identification and characterization of folding inhibitors of hen egg lysozyme: An example of a new paradigm of drug design

scientific article published on 01 February 2009

Identification of the folding inhibitors of hen-egg lysozyme: gathering the right tools

scientific article published on 27 March 2009

Imprint of evolution on protein structures.

scientific article

Insight into the folding inhibition of the HIV-1 protease by a small peptide

scientific article

Integrating experiment, theory and simulation to determine the structure and dynamics of mammalian chromosomes

scientific article

Iterative derivation of effective potentials to sample the conformational space of proteins at atomistic scale ⬇️

scientific article published in May 2014

Kinetics of Different Processes in Human Insulin Amyloid Formation

scientific article published on 09 November 2006

Low-throughput model design of protein folding inhibitors.

scientific article

Mapping of mutation-sensitive sites in proteinlike chains

Metadynamic sampling of the free-energy landscapes of proteins coupled with a Monte Carlo algorithm

scientific article published on 6 June 2008

MicroRNA-222 Regulates Melanoma Plasticity

scientific article published on 08 August 2020

Modeling the α-helix to β-hairpin transition mechanism and the formation of oligomeric aggregates of the fibrillogenic peptide A(12–28): insights from all-atom molecular dynamics simulations

article

Modelling genome-wide topological associating domains in mouse embryonic stem cells

scientific article published on 20 January 2017

MonteGrappa: An iterative Monte Carlo program to optimize biomolecular potentials in simplified models

article published in 2015

Noncooperative interactions between transcription factors and clustered DNA binding sites enable graded transcriptional responses to environmental inputs

scientific article

Optical absorption of a green fluorescent protein variant: environment effects in a density functional study

scientific article published on 22 August 2007

Oscillations and temporal signalling in cells.

scientific article published on 18 May 2007

Predicting the tertiary structure of a lattice designed model protein from its primary structure

scientific article published on June 2001

Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription

scientific article published on May 2014

Ratcheted molecular-dynamics simulations identify efficiently the transition state of protein folding ⬇️

scientific article published on December 21, 2012

Reading the three-dimensional structure of lattice model-designed proteins from their amino acid sequence

article

Resistance proof, folding-inhibitor drugs

Role of bulk and of interface contacts in the behavior of lattice model dimeric proteins

scientific article published on 14 May 2003

Sampling the Denatured State of Polypeptides in Water, Urea, and Guanidine Chloride to Strict Equilibrium Conditions with the Help of Massively Parallel Computers

scientific article

Sequence of events in folding mechanism: beyond the Gō model

scientific article

Similar folds with different stabilization mechanisms: the cases of Prion and Doppel proteins

scientific article

Simple models of protein folding and of non-conventional drug design

article by R A Broglia et al published 30 January 2004 in Journal of Physics: Condensed Matter

Spontaneous domain formation in disordered copolymers as a mechanism for chromosome structuring

scientific article published on 01 July 2018

Stability of Designed Proteins against Mutations

scientific article published in Physical Review Letters

Statistical analysis of native contact formation in the folding of designed model proteins

article

Statistical mechanical properties of sequence space determine the efficiency of the various algorithms to predict interaction energies and native contacts from protein coevolution

scientific article published on 04 June 2019

Sustained oscillations and time delays in gene expression of protein Hes1

article

The complex folding behavior of HIV-1-protease monomer revealed by optical-tweezer single-molecule experiments and molecular dynamics simulations.

scientific article

The determinants of stability in the human prion protein: insights into folding and misfolding from the analysis of the change in the stabilization energy distribution in different conditions

scientific article published in March 2006

The dynamics of genetic control in the cell: the good and bad of being late.

scientific article published on 19 August 2013

The evolution dynamics of model proteins

article

The maturation of HIV-1 protease precursor studied by discrete molecular dynamics

scientific article published on 22 November 2013

The molecular evolution of HIV-1 protease simulated at atomic detail

scientific article published in September 2009

The network of stabilizing contacts in proteins studied by coevolutionary data

scientific article

Thermodynamic and structural effect of urea and guanidine chloride on the helical and on a hairpin fragment of GB1 from molecular simulations

scientific article published on 25 January 2017

Thermodynamic features characterizing good and bad folding sequences obtained using a simplified off-lattice protein model.

scientific article

Thermodynamics of strongly allosteric inhibition: a model study of HIV-1 protease

article

Thermodynamics of β-amyloid fibril formation

Time delay as a key to apoptosis induction in the p53 network

article by Guido Tiana et al published September 2002 in European Physical Journal B

Understanding the determinants of stability and folding of small globular proteins from their energetics

scientific article published on January 2004

Urea and guanidinium chloride denature protein L in different ways in molecular dynamics simulations

scientific article published on 13 March 2008

Use of the Metropolis algorithm to simulate the dynamics of protein chains

article

List of works by Guido Tiana

A Combined NMR-Computational Study of the Interaction between Influenza Virus Hemagglutinin and Sialic Derivatives from Human and Avian Receptors on the Surface of Transfected Cells

A folding inhibitor of the HIV-1 protease.

A highly compliant protein native state with a spontaneous-like mechanical unfolding pathway

A many-body term improves the accuracy of effective potentials based on protein coevolutionary data

A method for partitioning the information contained in a protein sequence between its structure and function

An implementation of the maximum-caliber principle by replica-averaged time-resolved restrained simulations

Atomistic simulations of the HIV-1 protease folding inhibition

Beta-hairpin conformation of fibrillogenic peptides: structure and alpha-beta transition mechanism revealed by molecular dynamics simulations

Cohesin and CTCF control the dynamics of chromosome folding

Corrigendum to “Kinetics of Different Processes in Human Insulin Amyloid Formation” [J. Mol. Biol. 366/1 (2007) 258-274]

DamC reveals principles of chromatin folding in vivo without crosslinking and ligation

Denatured state is critical in determining the properties of model proteins designed on different folds.

Deriving amino acid contact potentials from their frequencies of occurrence in proteins: a lattice model study

Design and folding of dimeric proteins

Design of HIV-1-PR inhibitors that do not create resistance: blocking the folding of single monomers

Design of a folding inhibitor of the HIV-1 protease

Design of amino acid sequences to fold into C(alpha)-model proteins

Designability of lattice model heteropolymers

Determination of Structural Ensembles of Flexible Molecules in Solution from NMR Data Undergoing Spin Diffusion

Dynamical Genetic Regulation

Early events in insulin fibrillization studied by time-lapse atomic force microscopy

Early events in protein folding: Is there something more than hydrophobic burst?

Energy profile of the space of model protein sequences

Estimation of microscopic averages from metadynamics

Exploring the protein G helix free-energy surface by solute tempering metadynamics

Folding and aggregation of designed proteins.

Folding and misfolding of designed proteinlike chains with mutations

HIV-1 protease folding and the design of drugs which do not create resistance

Hierarchy of events in the folding of model proteins

Hierarchy of folding and unfolding events of protein G, CI2, and ACBP from explicit-solvent simulations

Hydrogen Bonds in Polymer Folding

Identification and characterization of folding inhibitors of hen egg lysozyme: An example of a new paradigm of drug design

Identification of the folding inhibitors of hen-egg lysozyme: gathering the right tools

Imprint of evolution on protein structures.

Insight into the folding inhibition of the HIV-1 protease by a small peptide

Integrating experiment, theory and simulation to determine the structure and dynamics of mammalian chromosomes

Iterative derivation of effective potentials to sample the conformational space of proteins at atomistic scale ⬇️

Kinetics of Different Processes in Human Insulin Amyloid Formation

Low-throughput model design of protein folding inhibitors.

Mapping of mutation-sensitive sites in proteinlike chains

Metadynamic sampling of the free-energy landscapes of proteins coupled with a Monte Carlo algorithm

MicroRNA-222 Regulates Melanoma Plasticity

Modeling the α-helix to β-hairpin transition mechanism and the formation of oligomeric aggregates of the fibrillogenic peptide A(12–28): insights from all-atom molecular dynamics simulations

Modelling genome-wide topological associating domains in mouse embryonic stem cells

MonteGrappa: An iterative Monte Carlo program to optimize biomolecular potentials in simplified models

Noncooperative interactions between transcription factors and clustered DNA binding sites enable graded transcriptional responses to environmental inputs

Optical absorption of a green fluorescent protein variant: environment effects in a density functional study

Oscillations and temporal signalling in cells.

Predicting the tertiary structure of a lattice designed model protein from its primary structure

Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription

Ratcheted molecular-dynamics simulations identify efficiently the transition state of protein folding ⬇️

Reading the three-dimensional structure of lattice model-designed proteins from their amino acid sequence

Resistance proof, folding-inhibitor drugs

Role of bulk and of interface contacts in the behavior of lattice model dimeric proteins

Sampling the Denatured State of Polypeptides in Water, Urea, and Guanidine Chloride to Strict Equilibrium Conditions with the Help of Massively Parallel Computers

Sequence of events in folding mechanism: beyond the Gō model

Similar folds with different stabilization mechanisms: the cases of Prion and Doppel proteins

Simple models of protein folding and of non-conventional drug design

Spontaneous domain formation in disordered copolymers as a mechanism for chromosome structuring

Stability of Designed Proteins against Mutations

Statistical analysis of native contact formation in the folding of designed model proteins

Statistical mechanical properties of sequence space determine the efficiency of the various algorithms to predict interaction energies and native contacts from protein coevolution

Sustained oscillations and time delays in gene expression of protein Hes1

The complex folding behavior of HIV-1-protease monomer revealed by optical-tweezer single-molecule experiments and molecular dynamics simulations.

The determinants of stability in the human prion protein: insights into folding and misfolding from the analysis of the change in the stabilization energy distribution in different conditions

The dynamics of genetic control in the cell: the good and bad of being late.

The evolution dynamics of model proteins

The maturation of HIV-1 protease precursor studied by discrete molecular dynamics

The molecular evolution of HIV-1 protease simulated at atomic detail

The network of stabilizing contacts in proteins studied by coevolutionary data

Thermodynamic and structural effect of urea and guanidine chloride on the helical and on a hairpin fragment of GB1 from molecular simulations

Thermodynamic features characterizing good and bad folding sequences obtained using a simplified off-lattice protein model.

Thermodynamics of strongly allosteric inhibition: a model study of HIV-1 protease

Thermodynamics of β-amyloid fibril formation

Time delay as a key to apoptosis induction in the p53 network

Understanding the determinants of stability and folding of small globular proteins from their energetics

Urea and guanidinium chloride denature protein L in different ways in molecular dynamics simulations

Use of the Metropolis algorithm to simulate the dynamics of protein chains