Timeline

Thérèse Malliavin

Group Leader

17 Sep 2022

publication

In Silico Conformational Features of Botulinum Toxins A1 and E1 According to Intraluminal Acidification.

20 Sep 2021

publication

Conformational Insights into the Control of CNF1 Toxin Activity by Peptidyl-Prolyl Isomerization: A Molecular Dynamics Perspective.

11 Sep 2021

publication

Computational and biochemical analysis of type IV pilus dynamics and stability.

26 Jan 2021

project

Multi-scale and multi-resolution bio-molecular structure determination by geometric approaches – multiBioStruct

01 Jan 2020

publication

Analyzing In Silico the Relationship Between the Activation of the Edema Factor and Its Interaction With Calmodulin.

06 Sep 2019

publication

Systematic Exploration of Protein Conformational Space Using a Distance Geometry Approach

19 Jul 2019

project

Genomic insights into the 2016-2017 cholera epidemic in Yemen

24 Jun 2019

publication

Structural Biology and Molecular Modeling to Analyze the Entry of Bacterial Toxins and Virulence Factors into Host Cells

03 Jun 2019

event

Seminar “Open-active and closed-inactive states of the human alpha7 nicotinic receptor: a molecular dynamics perspective”

01 Feb 2019

publication

Publisher Correction: Genomic insights into the 2016-2017 cholera epidemic in Yemen.

01 Jan 2019

publication

Genomic insights into the 2016-2017 cholera epidemic in Yemen.

29 Nov 2018

publication

Conformational sampling of CpxA: Connecting HAMP motions to the histidine kinase function

25 Oct 2018

publication

Closed-locked and Apo-resting State Structures of the Human α7 Nicotinic Receptor: a Computational Study

04 Sep 2018

event

Cross-linking Mass Spectrometry constraint selection and Modeling for protein structure determination

26 Apr 2018

publication

Minimal NMR distance information for rigidity of protein graphs

06 Apr 2018

event

Seminar of the Department of Structural Biology and Chemistry

03 Apr 2018

publication

re-TAMD: exploring interactions between H3 peptide and YEATS domain using enhanced sampling

16 Mar 2018

publication

Ordering Protein Contact Matrices

15 Mar 2018

event

C3BI Seminar : MixMD: Mapping Protein Surfaces to Discover Druggable Allosteric Sites

09 Mar 2018

publication

Tuning interval Branch-and-Prune for protein structure determination

25 Jan 2018

event

C3BI/Dpt.Bio.Structural Seminar – The structural basis of SMS (Short Motif Sequence), mediated communication between proteins: characterization, modeling and manipulation

04 Oct 2017

project

Conformational sampling and functional dynamics of histidine kinases

04 Oct 2017

project

Development of inhibitors targeting the allosteric activation of adenyl cyclases

30 Jun 2017

publication

A possible desensitized state conformation of the human α7 nicotinic receptor: A molecular dynamics study

26 Jun 2017

publication

Molecular Modeling of the Catalytic Domain of CyaA Deepened the Knowledge of Its Functional Dynamics

25 May 2017

event

Carlile Lavor (UNICAMP, Brazil): Distance Geometry and Conformal Clifford Algebra

16 May 2017

event

Antonio Mucherino (IRISA, University of Rennes 1): Dynamical Distance Geometry and Proteins

25 Apr 2017

event

Computational geometry for the determination of biomolecular structures

01 Oct 2016

publication

Modification in hydrophobic packing of HAMP domain induces a destabilization of the auto-phosphorylation site in the histidine kinase CpxA

12 Sep 2016

publication

Building Graphs To Describe Dynamics, Kinetics, and Energetics in the d-ALa:d-Lac Ligase VanA

12 Oct 2015

project

Computational geometry for the determination of biomolecular structures

08 Sep 2015

publication

Improved large-scale prediction of growth inhibition patterns using the NCI60 cancer cell line panel.

28 Aug 2015

publication

Chemically Aware Model Builder (camb): an R package for property and bioactivity modelling of small molecules.

24 Jul 2015

publication

A Structural Model of the Human α7 Nicotinic Receptor in an Open Conformation

23 Jul 2015

software

ARIA (Ambiguous Restraints for Iterative Assignment)

16 Jul 2015

team

Functional dynamics

07 Jul 2015

project

Bip:Bip

18 Jun 2015

publication

Comparing the Influence of Simulated Experimental Errors on 12 Machine Learning Algorithms in Bioactivity Modeling Using 12 Diverse Data Sets

03 Jun 2015

publication

Temperature Accelerated Molecular Dynamics with Soft-Ratcheting Criterion Orients Enhanced Sampling by Low-Resolution Information

15 Apr 2015

publication

Proteochemometric modelling coupled to in silico target prediction: an integrated approach for the simultaneous prediction of polypharmacology and binding affinity/potency of small molecules.

11 Apr 2015

publication

Improved reliability, accuracy and quality in automated NMR structure calculation with ARIA

21 Mar 2015

publication

Identification of binding sites and favorable ligand binding moieties by virtual screening and self-organizing map analysis

20 Mar 2015

publication

Prediction of PARP Inhibition with Proteochemometric Modelling and Conformal Prediction

28 Jan 2015

publication

An algorithm to enumerate all possible protein conformations verifying a set of distance constraints.

16 Jan 2015

publication

Prediction of the potency of mammalian cyclooxygenase inhibitors with ensemble proteochemometric modeling

01 Nov 2014

publication

Modelling ligand selectivity of serine proteases using integrative proteochemometric approaches improves model performance and allows the multi-target dependent interpretation of features

28 Jun 2014

publication

Proteochemometric modeling in a Bayesian framework

09 Jun 2014

publication

Temperature-accelerated molecular dynamics gives insights into globular conformations sampled in the free state of the AC catalytic domain

13 Feb 2014

publication

Conformational changes in acetylcholine binding protein investigated by temperature accelerated molecular dynamics

15 Jan 2014

publication

Functional motions modulating VanA ligand binding unraveled by self-organizing maps

01 Jan 2014

publication

Extending in silico mechanism-of-action analysis by annotating targets with pathways: application to cellular cytotoxicity readouts

17 Oct 2013

publication

Stabilization of the integrase-DNA complex by Mg2+ ions and prediction of key residues for binding HIV-1 integrase inhibitors

04 Jun 2013

publication

Identification of cinnamic acid derivatives as novel antagonists of the prokaryotic proton-gated ion channel GLIC

09 Jan 2012

publication

Differential role of calmodulin and calcium ions in the stabilization of the catalytic domain of adenyl cyclase CyaA from Bordetella pertussis

01 Jan 2012

publication

ARIA for solution and solid-state NMR

24 Nov 2011

publication

The redundancy of NMR restraints can be used to accelerate the unfolding behavior of an SH3 domain during molecular dynamics simulations

05 May 2011

publication

Grid computing for improving conformational sampling in NMR structure calculation

21 Mar 2011

publication

Mechanism of reactant and product dissociation from the anthrax edema factor: a locally enhanced sampling and steered molecular dynamics study

01 Mar 2011

publication

Bayesian estimation of NMR restraint potential and weight: a validation on a representative set of protein structures

01 Oct 2010

publication

Activation of the edema factor of Bacillus anthracis by calmodulin: evidence of an interplay between the EF-calmodulin interaction and calcium binding

09 Jun 2010

publication

Simultaneous use of solution, solid-state NMR and X-ray crystallography to study the conformational landscape of the Crh protein during oligomerization and crystallization

07 Jun 2010

publication

Use of allostery to identify inhibitors of calmodulin-induced activation of Bacillus anthracis edema factor

01 Dec 2009

publication

ATP conformations and ion binding modes in the active site of anthrax edema factor: a computational analysis

15 May 2009

publication

Influence of different assignment conditions on the determination of symmetric homodimeric structures with ARIA

18 Feb 2009

publication

Dynamics and energetics: a consensus analysis of the impact of calcium on EF-CaM protein complex

26 Sep 2008

publication

Structural biology by NMR: structure, dynamics, and interactions

10 Sep 2008

publication

Accurate NMR structures through minimization of an extended hybrid energy

05 Jun 2008

publication

Graphical analysis of NMR structural quality and interactive contact map of NOE assignments in ARIA

01 Jun 2008

publication

The conformational plasticity of calmodulin upon calcium complexation gives a model of its interaction with the oedema factor of Bacillus anthracis

20 Feb 2008

publication

3D structure determination of the Crh protein from highly ambiguous solid-state NMR restraints

22 Nov 2006

publication

ARIA2: automated NOE assignment and data integration in NMR structure calculation

01 Mar 2006

publication

A little guide for advanced search:

In Silico Conformational Features of Botulinum Toxins A1 and E1 According to Intraluminal Acidification.

Conformational Insights into the Control of CNF1 Toxin Activity by Peptidyl-Prolyl Isomerization: A Molecular Dynamics Perspective.

Computational and biochemical analysis of type IV pilus dynamics and stability.

Multi-scale and multi-resolution bio-molecular structure determination by geometric approaches – multiBioStruct

Analyzing In Silico the Relationship Between the Activation of the Edema Factor and Its Interaction With Calmodulin.

Systematic Exploration of Protein Conformational Space Using a Distance Geometry Approach

Genomic insights into the 2016-2017 cholera epidemic in Yemen

Structural Biology and Molecular Modeling to Analyze the Entry of Bacterial Toxins and Virulence Factors into Host Cells

Seminar “Open-active and closed-inactive states of the human alpha7 nicotinic receptor: a molecular dynamics perspective”

Publisher Correction: Genomic insights into the 2016-2017 cholera epidemic in Yemen.

Genomic insights into the 2016-2017 cholera epidemic in Yemen.

Conformational sampling of CpxA: Connecting HAMP motions to the histidine kinase function

Closed-locked and Apo-resting State Structures of the Human α7 Nicotinic Receptor: a Computational Study

Cross-linking Mass Spectrometry constraint selection and Modeling for protein structure determination

Minimal NMR distance information for rigidity of protein graphs

Seminar of the Department of Structural Biology and Chemistry

re-TAMD: exploring interactions between H3 peptide and YEATS domain using enhanced sampling

Ordering Protein Contact Matrices

C3BI Seminar : MixMD: Mapping Protein Surfaces to Discover Druggable Allosteric Sites

Tuning interval Branch-and-Prune for protein structure determination

C3BI/Dpt.Bio.Structural Seminar – The structural basis of SMS (Short Motif Sequence), mediated communication between proteins: characterization, modeling and manipulation

Conformational sampling and functional dynamics of histidine kinases

Development of inhibitors targeting the allosteric activation of adenyl cyclases

A possible desensitized state conformation of the human α7 nicotinic receptor: A molecular dynamics study

Molecular Modeling of the Catalytic Domain of CyaA Deepened the Knowledge of Its Functional Dynamics

Carlile Lavor (UNICAMP, Brazil): Distance Geometry and Conformal Clifford Algebra

Antonio Mucherino (IRISA, University of Rennes 1): Dynamical Distance Geometry and Proteins

Computational geometry for the determination of biomolecular structures

Modification in hydrophobic packing of HAMP domain induces a destabilization of the auto-phosphorylation site in the histidine kinase CpxA

Building Graphs To Describe Dynamics, Kinetics, and Energetics in the d-ALa:d-Lac Ligase VanA

Computational geometry for the determination of biomolecular structures

Improved large-scale prediction of growth inhibition patterns using the NCI60 cancer cell line panel.

Chemically Aware Model Builder (camb): an R package for property and bioactivity modelling of small molecules.

A Structural Model of the Human α7 Nicotinic Receptor in an Open Conformation

ARIA (Ambiguous Restraints for Iterative Assignment)

Functional dynamics

Bip:Bip

Comparing the Influence of Simulated Experimental Errors on 12 Machine Learning Algorithms in Bioactivity Modeling Using 12 Diverse Data Sets

Temperature Accelerated Molecular Dynamics with Soft-Ratcheting Criterion Orients Enhanced Sampling by Low-Resolution Information

Proteochemometric modelling coupled to in silico target prediction: an integrated approach for the simultaneous prediction of polypharmacology and binding affinity/potency of small molecules.

Improved reliability, accuracy and quality in automated NMR structure calculation with ARIA

Identification of binding sites and favorable ligand binding moieties by virtual screening and self-organizing map analysis

Prediction of PARP Inhibition with Proteochemometric Modelling and Conformal Prediction

An algorithm to enumerate all possible protein conformations verifying a set of distance constraints.

Prediction of the potency of mammalian cyclooxygenase inhibitors with ensemble proteochemometric modeling

Modelling ligand selectivity of serine proteases using integrative proteochemometric approaches improves model performance and allows the multi-target dependent interpretation of features

Proteochemometric modeling in a Bayesian framework

Temperature-accelerated molecular dynamics gives insights into globular conformations sampled in the free state of the AC catalytic domain

Conformational changes in acetylcholine binding protein investigated by temperature accelerated molecular dynamics

Functional motions modulating VanA ligand binding unraveled by self-organizing maps

Extending in silico mechanism-of-action analysis by annotating targets with pathways: application to cellular cytotoxicity readouts

Stabilization of the integrase-DNA complex by Mg2+ ions and prediction of key residues for binding HIV-1 integrase inhibitors

Identification of cinnamic acid derivatives as novel antagonists of the prokaryotic proton-gated ion channel GLIC

Differential role of calmodulin and calcium ions in the stabilization of the catalytic domain of adenyl cyclase CyaA from Bordetella pertussis

ARIA for solution and solid-state NMR

The redundancy of NMR restraints can be used to accelerate the unfolding behavior of an SH3 domain during molecular dynamics simulations

Grid computing for improving conformational sampling in NMR structure calculation

Mechanism of reactant and product dissociation from the anthrax edema factor: a locally enhanced sampling and steered molecular dynamics study

Bayesian estimation of NMR restraint potential and weight: a validation on a representative set of protein structures

Activation of the edema factor of Bacillus anthracis by calmodulin: evidence of an interplay between the EF-calmodulin interaction and calcium binding

Simultaneous use of solution, solid-state NMR and X-ray crystallography to study the conformational landscape of the Crh protein during oligomerization and crystallization

Use of allostery to identify inhibitors of calmodulin-induced activation of Bacillus anthracis edema factor

ATP conformations and ion binding modes in the active site of anthrax edema factor: a computational analysis

Influence of different assignment conditions on the determination of symmetric homodimeric structures with ARIA

Dynamics and energetics: a consensus analysis of the impact of calcium on EF-CaM protein complex

Structural biology by NMR: structure, dynamics, and interactions

Accurate NMR structures through minimization of an extended hybrid energy

Graphical analysis of NMR structural quality and interactive contact map of NOE assignments in ARIA

The conformational plasticity of calmodulin upon calcium complexation gives a model of its interaction with the oedema factor of Bacillus anthracis

3D structure determination of the Crh protein from highly ambiguous solid-state NMR restraints

ARIA2: automated NOE assignment and data integration in NMR structure calculation

Comparison of different torsion angle approaches for NMR structure determination