List of works - Xavier Daura

-Peptides with Different Secondary-Structure Preferences: How Different Are Their Conformational Spaces?

scholarly article published November 2002 in Helvetica Chimica Acta

A Comparative Analysis of the Peptide Repertoires of HLA-DR Molecules Differentially Associated With Rheumatoid Arthritis.

scientific article

A Molecular Dynamics Simulation of the Binding Modes ofd-Glutamate andd-Glutamine to Glutamate Racemase

article

A generalized Langevin dynamics approach to model solvent dynamics effects on proteins via a solvent-accessible surface. The carboxypeptidase A inhibitor protein as a model

article

A novel approach for designing simple point charge models for liquid water with three interaction sites

scientific article published in July 2003

A strategy for analysis of (molecular) equilibrium simulations: Configuration space density estimation, clustering, and visualization

article

A structure-based strategy for epitope discovery in Burkholderia pseudomallei OppA antigen

scientific article

AGGRESCAN: a server for the prediction and evaluation of "hot spots" of aggregation in polypeptides

scientific article

Abundance of the Quorum-Sensing Factor Ax21 in Four Strains of Stenotrophomonas maltophilia Correlates with Mortality Rate in a New Zebrafish Model of Infection

scientific article

An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase

Assessing equilibration and convergence in biomolecular simulations

scientific article

Assessing the structural conservation of protein pockets to study functional and allosteric sites: implications for drug discovery

scientific article

Bestimmung von Strukturinformation aus experimentellen Messdaten für Biomoleküle

article

Biomolecular modeling: Goals, problems, perspectives

scientific article published on June 2006

Bottom-Up Instructive Quality Control in the Biofabrication of Smart Protein Materials

scientific article published on 28 October 2015

CNN-PepPred: an open-source tool to create convolutional NN models for the discovery of patterns in peptide sets—application to peptide–MHC class II binding prediction

scientific article published in 2021

Calcium binding to the purple membrane: A molecular dynamics study

scientific article published in February 2009

Calculation of NMR-relaxation parameters for flexible molecules from molecular dynamics simulations

scientific article published on 01 August 2001

Can One Derive the Conformational Preference of a β-Peptide from Its CD Spectrum?

scientific article published on 01 November 2002

Circular dichroism spectra of β-peptides: sensitivity to molecular structure and effects of motional averaging

scientific article published on 16 September 2003

Comparing geometric and kinetic cluster algorithms for molecular simulation data

scientific article

Computation of Free Energy

scholarly article by Wilfred F. van Gunsteren et al published October 2002 in Helvetica Chimica Acta

Configurational entropy elucidates the role of salt-bridge networks in protein thermostability.

scientific article

Conformational and functional variants of CD44-targeted protein nanoparticles bio-produced in bacteria

scientific article published on 14 April 2016

Crystal structure of c5321: a protective antigen present in uropathogenic Escherichia coli strains displaying an SLR fold

scientific article

Decoding the genetic and functional diversity of the DSF quorum-sensing system in Stenotrophomonas maltophilia

scientific article published on 28 July 2015

Derivation of an improved simple point charge model for liquid water: SPC/A and SPC/L

article

Deriving Structural Information from Experimentally Measured Data on Biomolecules.

scientific article

Disulfide bond formation and activation of Escherichia coli β-galactosidase under oxidizing conditions

scientific article

Draft Genome Sequence of Stenotrophomonas maltophilia Strain M30, Isolated from a Chronic Pressure Ulcer in an Elderly Patient

scientific article published on 12 June 2014

Draft Genome Sequence of Stenotrophomonas maltophilia Strain UV74 Reveals Extensive Variability within Its Genomic Group

scientific article published on 11 June 2015

Effect of Oxidative Damage on the Stability and Dimerization of Superoxide Dismutase 1.

scientific article published on April 2016

Engineering the E. coli beta-galactosidase for the screening of antiviral protease inhibitors.

scientific article published in April 2005

Enhanced Conformational Sampling in Molecular Dynamics Simulations of Solvated Peptides: Fragment-Based Local Elevation Umbrella Sampling

scientific article published in September 2010

Entropy calculations on a reversibly folding peptide: changes in solute free energy cannot explain folding behavior.

scientific article published in April 2001

EsiB, a novel pathogenic Escherichia coli secretory immunoglobulin A-binding protein impairing neutrophil activation

scientific article published on 23 July 2013

Essential dynamics of reversible peptide folding: memory-free conformational dynamics governed by internal hydrogen bonds.

scientific article

Estimating the temperature dependence of peptide folding entropies and free enthalpies from total energies in molecular dynamics simulations.

scientific article published in January 2008

Exploiting Antigenic Diversity for Vaccine Design: THE CHLAMYDIA ArtJ PARADIGM

scientific article

Exploiting protein flexibility to predict the location of allosteric sites

scientific article

Exploiting the Burkholderia pseudomallei acute phase antigen BPSL2765 for structure-based epitope discovery/design in structural vaccinology

scientific article

Factor Xa: simulation studies with an eye to inhibitor design

scientific article published on 01 August 2000

Folding-unfolding thermodynamics of a ?-heptapeptide from equilibrium simulations

scholarly article by Xavier Daura published in February 1999

Folding-unfolding thermodynamics of a beta-heptapeptide from equilibrium simulations

scientific article published on 01 February 1999

Free Energies of Transfer of Trp Analogs from Chloroform to Water: Comparison of Theory and Experiment and the Importance of Adequate Treatment of Electrostatic and Internal Interactions

scientific article published in 1996

Free energy calculations offer insights into the influence of receptor flexibility on ligand-receptor binding affinities.

scientific article published on 7 July 2011

From crystal structure to in silico epitope discovery in the Burkholderia pseudomallei flagellar hook-associated protein FlgK

scientific article

In vivo architectonic stability of fully de novo designed protein-only nanoparticles

scientific article published on 14 April 2014

Modelling of the complex between a 15-residue peptide from mSos2 and the N-terminal SH3 domain of Grb2 by molecular-dynamics simulation

scientific article

Molecular Dynamics Simulation of Peptide Folding

article

Molecular dynamics simulation study of the effect of glycerol dialkyl glycerol tetraether hydroxylation on membrane thermostability

scientific article published on 15 February 2017

Molecular dynamics simulations of a reversibly folding beta-heptapeptide in methanol: influence of the treatment of long-range electrostatic interactions.

scientific article published in March 2009

Molecular dynamics simulations of peptides containing an unnatural amino acid: dimerization, folding, and protein binding

scientific article

Molecular-Dynamics Simulations of C- and N-Terminal Peptide Derivatives of GCN4-p1 in Aqueous Solution

article

Nanoparticulate architecture of protein-based artificial viruses is supported by protein-DNA interactions

scientific article published on 9 June 2011

Oligonucleotide Analogues with a Nucleobase-Including Backbone, Part 7, Molecular Dynamics Simulation of a DNA Duplex Containing a 2′-Deoxyadenosine 8-(Hydroxymethyl)-Derived Nucleotide

scholarly article by Werngard Czechtizky et al published 11 July 2001 in Helvetica Chimica Acta

On the Entropic and Hydrophobic Properties Involved in the Inhibitory Mechanism of Carboxypeptidase A by its Natural Inhibitor from Potato

article by Baldomero Oliva et al published 1 May 1995 in Journal of Molecular Modeling

On the Relative Merits of Equilibrium and Non-Equilibrium Simulations for the Estimation of Free-Energy Differences

scientific article published on 01 December 2010

On the influence of charged side chains on the folding-unfolding equilibrium of beta-peptides: a molecular dynamics simulation study

scientific article

PARS: a web server for the prediction of Protein Allosteric and Regulatory Sites.

scientific article

Parametrization of aliphatic CHn united atoms of GROMOS96 force field

Peptide Folding: When Simulation Meets Experiment

scholarly article by Xavier Daura et al published 15 January 1999 in Angewandte Chemie

Peptide folding simulations: no solvent required?

Peptides of Aminoxy Acids: A Molecular Dynamics Simulation Study of Conformational Equilibria under Various Conditions

article

Polypeptide folding on a conformational-space network: dependence of network topology on the structural discretization procedure.

scientific article published in July 2010

Prediction of Antigenic B and T Cell Epitopes via Energy Decomposition Analysis: Description of the Web-Based Prediction Tool BEPPE.

scientific article published in January 2015

PrionW: a server to identify proteins containing glutamine/asparagine rich prion-like domains and their amyloid cores

scientific article published on 14 May 2015

Procarboxypeptidase A from the insect pest Helicoverpa armigera and its derived enzyme. Two forms with new functional properties.

scientific article

Protein nanodisk assembling and intracellular trafficking powered by an arginine-rich (R9) peptide

scientific article published in February 2010

Proteomic analysis of outer membrane proteins and vesicles of a clinical isolate and a collection strain of Stenotrophomonas maltophilia

scientific article published on 9 May 2016

RGD-based cell ligands for cell-targeted drug delivery act as potent trophic factors

scientific article published on 25 July 2012

Redefining the PF06864 Pfam Family Based on Burkholderia pseudomallei PilO2Bp S-SAD Crystal Structure

scientific article

Reply

scholarly article by Wilfred F. Van Gunsteren et al published 17 December 2001 in Angewandte Chemie International Edition

Reversible peptide folding in solution by molecular dynamics simulation

scientific article published in July 1998

Sequence- and Structure-Based Immunoreactive Epitope Discovery for Burkholderia pseudomallei Flagellin

scientific article published on 29 July 2015

Sheltering DNA in self-organizing, protein-only nano-shells as artificial viruses for gene delivery.

scientific article published on 21 November 2013

Stability of SIV gp32 Fusion-Peptide Single-Layer Protofibrils as Monitored by Molecular-Dynamics Simulations

scientific article published on 01 February 2005

Stenotrophomonas maltophilia responds to exogenous AHL signals through the LuxR solo SmoR (Smlt1839).

scientific article

Structural and biochemical characterization of NarE, an iron-containing ADP-ribosyltransferase from Neisseria meningitidis

scientific article

Structure and Conformation ofβ-Oligopeptide Derivatives with Simple Proteinogenic Side Chains: Circular Dichroism and Molecular Dynamics Investigations

scholarly article by Dieter Seebach et al published 19 January 2000 in Helvetica Chimica Acta

Structure and atomic fluctuation patterns of potato carboxypeptidase a inhibitor protein

article by B. Oliva et al published June 1995 in European Biophysics Journal

Structure-based design of a B cell antigen from B. pseudomallei

scientific article

Studying the Stability of a Helical β-Heptapeptide by Molecular Dynamics Simulations

article

The Key to Solving the Protein-Folding Problem Lies in an Accurate Description of the Denatured State

scholarly article by Wilfred F. van Gunsteren et al published 19 January 2001 in Angewandte Chemie

The Key to Solving the Protein-Folding Problem Lies in an Accurate Description of the Denatured State Financial support from the Schweizerischer Nationalfonds (Project no. 21-50929.97) is gratefully acknowledged

scientific article published on 01 January 2001

The beta-peptide hairpin in solution: conformational study of a beta-hexapeptide in methanol by NMR spectroscopy and MD simulation

scientific article published in March 2001

The effect of motional averaging on the calculation of NMR-derived structural properties

scientific article published on 01 September 1999

The phylogenetic landscape and nosocomial spread of the multidrug-resistant opportunist Stenotrophomonas maltophilia

scientific article published on 27 April 2020

The rheumatoid arthritis-associated allele HLA-DR10 (DRB11001) shares part of its repertoire with HLA-DR1 (DRB10101) and HLA-DR4 (DRB*0401).

scientific article

The role of hydration in protein stability: comparison of the cold and heat unfolded states of Yfh1.

scientific article

Thyroglobulin peptides associate in vivo to HLA-DR in autoimmune thyroid glands

scientific article published in July 2008

Two different rpf clusters distributed among a population of Stenotrophomonas maltophilia clinical strains display differential diffusible signal factor production and virulence regulation

scientific article

Understanding the molecular determinants driving the immunological specificity of the protective pilus 2a backbone protein of group B streptococcus

scientific article

Validation of molecular simulation by comparison with experiment: Rotational reorientation of tryptophan in water

Validation of the GROMOS force-field parameter set 45Alpha3 against nuclear magnetic resonance data of hen egg lysozyme.

scientific article

Why is a protective antigen protective?

scientific article published on December 2009

antibacTR: dynamic antibacterial-drug-target ranking integrating comparative genomics, structural analysis and experimental annotation

scientific article published on 17 January 2014

beta-hairpin folding and stability: molecular dynamics simulations of designed peptides in aqueous solution.

scientific article

List of works by Xavier Daura

-Peptides with Different Secondary-Structure Preferences: How Different Are Their Conformational Spaces?

A Comparative Analysis of the Peptide Repertoires of HLA-DR Molecules Differentially Associated With Rheumatoid Arthritis.

A Molecular Dynamics Simulation of the Binding Modes ofd-Glutamate andd-Glutamine to Glutamate Racemase

A generalized Langevin dynamics approach to model solvent dynamics effects on proteins via a solvent-accessible surface. The carboxypeptidase A inhibitor protein as a model

A novel approach for designing simple point charge models for liquid water with three interaction sites

A strategy for analysis of (molecular) equilibrium simulations: Configuration space density estimation, clustering, and visualization

A structure-based strategy for epitope discovery in Burkholderia pseudomallei OppA antigen

AGGRESCAN: a server for the prediction and evaluation of "hot spots" of aggregation in polypeptides

Abundance of the Quorum-Sensing Factor Ax21 in Four Strains of Stenotrophomonas maltophilia Correlates with Mortality Rate in a New Zebrafish Model of Infection

An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase

Assessing equilibration and convergence in biomolecular simulations

Assessing the structural conservation of protein pockets to study functional and allosteric sites: implications for drug discovery

Bestimmung von Strukturinformation aus experimentellen Messdaten für Biomoleküle

Biomolecular modeling: Goals, problems, perspectives

Bottom-Up Instructive Quality Control in the Biofabrication of Smart Protein Materials

CNN-PepPred: an open-source tool to create convolutional NN models for the discovery of patterns in peptide sets—application to peptide–MHC class II binding prediction

Calcium binding to the purple membrane: A molecular dynamics study

Calculation of NMR-relaxation parameters for flexible molecules from molecular dynamics simulations

Can One Derive the Conformational Preference of a β-Peptide from Its CD Spectrum?

Circular dichroism spectra of β-peptides: sensitivity to molecular structure and effects of motional averaging

Comparing geometric and kinetic cluster algorithms for molecular simulation data

Computation of Free Energy

Configurational entropy elucidates the role of salt-bridge networks in protein thermostability.

Conformational and functional variants of CD44-targeted protein nanoparticles bio-produced in bacteria

Crystal structure of c5321: a protective antigen present in uropathogenic Escherichia coli strains displaying an SLR fold

Decoding the genetic and functional diversity of the DSF quorum-sensing system in Stenotrophomonas maltophilia

Derivation of an improved simple point charge model for liquid water: SPC/A and SPC/L

Deriving Structural Information from Experimentally Measured Data on Biomolecules.

Disulfide bond formation and activation of Escherichia coli β-galactosidase under oxidizing conditions

Draft Genome Sequence of Stenotrophomonas maltophilia Strain M30, Isolated from a Chronic Pressure Ulcer in an Elderly Patient

Draft Genome Sequence of Stenotrophomonas maltophilia Strain UV74 Reveals Extensive Variability within Its Genomic Group

Effect of Oxidative Damage on the Stability and Dimerization of Superoxide Dismutase 1.

Engineering the E. coli beta-galactosidase for the screening of antiviral protease inhibitors.

Enhanced Conformational Sampling in Molecular Dynamics Simulations of Solvated Peptides: Fragment-Based Local Elevation Umbrella Sampling

Entropy calculations on a reversibly folding peptide: changes in solute free energy cannot explain folding behavior.

EsiB, a novel pathogenic Escherichia coli secretory immunoglobulin A-binding protein impairing neutrophil activation

Essential dynamics of reversible peptide folding: memory-free conformational dynamics governed by internal hydrogen bonds.

Estimating the temperature dependence of peptide folding entropies and free enthalpies from total energies in molecular dynamics simulations.

Exploiting Antigenic Diversity for Vaccine Design: THE CHLAMYDIA ArtJ PARADIGM

Exploiting protein flexibility to predict the location of allosteric sites

Exploiting the Burkholderia pseudomallei acute phase antigen BPSL2765 for structure-based epitope discovery/design in structural vaccinology

Factor Xa: simulation studies with an eye to inhibitor design

Folding-unfolding thermodynamics of a ?-heptapeptide from equilibrium simulations

Folding-unfolding thermodynamics of a beta-heptapeptide from equilibrium simulations

Free Energies of Transfer of Trp Analogs from Chloroform to Water: Comparison of Theory and Experiment and the Importance of Adequate Treatment of Electrostatic and Internal Interactions

Free energy calculations offer insights into the influence of receptor flexibility on ligand-receptor binding affinities.

From crystal structure to in silico epitope discovery in the Burkholderia pseudomallei flagellar hook-associated protein FlgK

In vivo architectonic stability of fully de novo designed protein-only nanoparticles

Modelling of the complex between a 15-residue peptide from mSos2 and the N-terminal SH3 domain of Grb2 by molecular-dynamics simulation

Molecular Dynamics Simulation of Peptide Folding

Molecular dynamics simulation study of the effect of glycerol dialkyl glycerol tetraether hydroxylation on membrane thermostability

Molecular dynamics simulations of a reversibly folding beta-heptapeptide in methanol: influence of the treatment of long-range electrostatic interactions.

Molecular dynamics simulations of peptides containing an unnatural amino acid: dimerization, folding, and protein binding

Molecular-Dynamics Simulations of C- and N-Terminal Peptide Derivatives of GCN4-p1 in Aqueous Solution

Nanoparticulate architecture of protein-based artificial viruses is supported by protein-DNA interactions

Oligonucleotide Analogues with a Nucleobase-Including Backbone, Part 7, Molecular Dynamics Simulation of a DNA Duplex Containing a 2′-Deoxyadenosine 8-(Hydroxymethyl)-Derived Nucleotide

On the Entropic and Hydrophobic Properties Involved in the Inhibitory Mechanism of Carboxypeptidase A by its Natural Inhibitor from Potato

On the Relative Merits of Equilibrium and Non-Equilibrium Simulations for the Estimation of Free-Energy Differences

On the influence of charged side chains on the folding-unfolding equilibrium of beta-peptides: a molecular dynamics simulation study

PARS: a web server for the prediction of Protein Allosteric and Regulatory Sites.

Parametrization of aliphatic CHn united atoms of GROMOS96 force field

Peptide Folding: When Simulation Meets Experiment

Peptide folding simulations: no solvent required?

Peptides of Aminoxy Acids: A Molecular Dynamics Simulation Study of Conformational Equilibria under Various Conditions

Polypeptide folding on a conformational-space network: dependence of network topology on the structural discretization procedure.

Prediction of Antigenic B and T Cell Epitopes via Energy Decomposition Analysis: Description of the Web-Based Prediction Tool BEPPE.

PrionW: a server to identify proteins containing glutamine/asparagine rich prion-like domains and their amyloid cores

Procarboxypeptidase A from the insect pest Helicoverpa armigera and its derived enzyme. Two forms with new functional properties.

Protein nanodisk assembling and intracellular trafficking powered by an arginine-rich (R9) peptide

Proteomic analysis of outer membrane proteins and vesicles of a clinical isolate and a collection strain of Stenotrophomonas maltophilia

RGD-based cell ligands for cell-targeted drug delivery act as potent trophic factors

Redefining the PF06864 Pfam Family Based on Burkholderia pseudomallei PilO2Bp S-SAD Crystal Structure

Reply

Reversible peptide folding in solution by molecular dynamics simulation

Sequence- and Structure-Based Immunoreactive Epitope Discovery for Burkholderia pseudomallei Flagellin

Sheltering DNA in self-organizing, protein-only nano-shells as artificial viruses for gene delivery.

Stability of SIV gp32 Fusion-Peptide Single-Layer Protofibrils as Monitored by Molecular-Dynamics Simulations

Stenotrophomonas maltophilia responds to exogenous AHL signals through the LuxR solo SmoR (Smlt1839).

Structural and biochemical characterization of NarE, an iron-containing ADP-ribosyltransferase from Neisseria meningitidis

The rheumatoid arthritis-associated allele HLA-DR10 (DRB11001) shares part of its repertoire with HLA-DR1 (DRB10101) and HLA-DR4 (DRB*0401).