T. Malliavin

发表

Improving the prediction of organism-level toxicity through integration of chemical, protein target and cytotoxicity qHTS data† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c5tx00406c

Daniel S. Murrell, Chad H. G. Allen, R. Glen, 2016, Toxicology research.

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

R. Glen, A. Bender, S. Liggi, 2014, Future medicinal chemistry.

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

T. Malliavin, É. Laine, C. Gonçalves, 2010, Proceedings of the National Academy of Sciences.

Polypharmacology modelling using proteochemometrics (PCM): recent methodological developments, applications to target families, and future prospects

P. Prusis, A. Bender, A. IJzerman, 2015 .

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

M. Nilges, T. Malliavin, W. Vranken, 2011, Proteins.

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

T. Malliavin, L. Martínez, A. Blondel, 2011, Proteins.

Proteochemometric modeling in a Bayesian

A. Bender, T. Malliavin, E. B. Lenselink, 2014 .

Prediction of PARP Inhibition with Proteochemometric Modelling and Conformal Prediction

A. Bender, I. Cortés-Ciriano, T. Malliavin, 2015, Molecular informatics.

Ordering Protein Contact Matrices

Guillaume Bouvier, Michael Nilges, Abdel Lisser, 2018, Computational and structural biotechnology journal.

ARIA for solution and solid-state NMR.

M. Nilges, T. Malliavin, B. Bardiaux, 2012, Methods in molecular biology.

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

G. Ciccotti, T. Malliavin, L. Chiodo, 2015, PloS one.

Conformational Changes in Acetylcholine Binding Protein Investigated by Temperature Accelerated Molecular Dynamics

G. Ciccotti, T. Malliavin, L. Maragliano, 2014, PloS one.

Discrimination of agonists versus antagonists of nicotinic ligands based on docking onto AChBP structures.

Michael Nilges, Antoine Taly, Claire Colas, 2011, Journal of molecular graphics & modelling.

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

Thérèse E Malliavin, Elodie Laine, T. Malliavin, 2009, Biophysical journal.

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

T. Malliavin, Irène Pitard, 2019, Toxins.

Protein Structure Calculation using Ambiguous Restraints

M. Nilges, T. Malliavin, B. Bardiaux, 2010 .

Lobeline Docking on AChBP and Nicotinic Receptors: Discriminating Importance of the Pocket Geometry and of the Ligand Configuration

M. Nilges, T. Malliavin, D. Joseph, 2012 .

Polypharmacology modelling using proteochemometrics (PCM): recent methodological developments, applications to target families, and future prospects

Isidro Cortes-Ciriano, Gerard J. P. van Westen, Adriaan P. IJzerman, 2015 .

The conformational landscape of the ribosomal protein S15 and its influence on the protein interaction with 16S RNA.

T. Malliavin, Thomas Créty, 2007, Biophysical journal.

Systematic exploration of protein conformational space using a Distance Geometry approach

Leo Liberti, T. Malliavin, A. Mucherino, 2019, bioRxiv.

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

T. Malliavin, G. Lamothe, 2018, BMC Structural Biology.

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

G. Ciccotti, T. Malliavin, L. Maragliano, 2014, Proteins.

Comparison of Different Torsion Angle Approaches for NMR Structure Determination

M. Nilges, A. Mazur, T. Malliavin, 2006, Journal of biomolecular NMR.

Temperature Accelerated Molecular Dynamics investigation of conformational changes in acetylcholine binding protein

G. Ciccotti, T. Malliavin, L. Maragliano, 2014 .

Proteochemometrics ( PCM ) with ’ camb ’ C hemistry A ware

Daniel S. Murrell, R. Glen, A. Bender, 2015 .

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

T. Malliavin, A. Blondel, Irène Pitard, 2020, Frontiers in Molecular Biosciences.

A Structural Model of the Human (cid:11) 7 Nicotinic Receptor in an Open Conformation

G. Ciccotti, T. Malliavin, L. Chiodo, 2019 .

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

T. Malliavin, L. Chiodo, L. Maragliano, 2022, bioRxiv.

Allosteric Activation of Bordetella pertussis Adenylyl Cyclase by Calmodulin

T. Malliavin, D. Ladant, A. Chenal, 2014, The Journal of Biological Chemistry.

MUTAGENESIS STUDIES MOLECULAR DYNAMICS AND Adenylyl Cyclase by Calmodulin: Bordetella pertussis Allosteric Activation of

T. Malliavin, D. Ladant, Ana-Cristina Sotomayor-Pérez, 2014 .

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

M. Nilges, T. Malliavin, L. Martínez, 2011, BMC Structural Biology.

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

M. Nilges, T. Malliavin, B. Bardiaux, 2015, Journal of biomolecular NMR.

Low-resolution description of the conformational space for intrinsically disordered proteins

J. Idier, T. Malliavin, A. Mucherino, 2022, Scientific Reports.

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

M. Nilges, T. Malliavin, G. Bouvier, 2018, PloS one.

Analysis of peptide rotational diffusion by homonuclear NMR.

T. Malliavin, E. Giudice, 2002, Biopolymers.

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

T. Malliavin, 2017, Toxins.

Tuning interval Branch-and-Prune for protein structure determination

M. Nilges, T. Malliavin, L. Liberti, 2018, Journal of Global Optimization.

Frontiers in Characterising Structure and Dynamics by NMR

M. Habeck, M. Nilges, P. Markwick, 2007 .

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

Isidro Cortes-Ciriano, Gerard J. P. van Westen, Guillaume Bouvier, 2015, Bioinform..

Blind testing of routine, fully automated determination of protein structures from NMR data.

Harald Schwalbe, Bin Wu, David Baker, 2012, Structure.

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

Isidro Cortes-Ciriano, Gerard J. P. van Westen, Therese E. Malliavin, 2015, Journal of Cheminformatics.

Structural Biology by NMR: Structure, Dynamics, and Interactions

Michael Nilges, Therese E. Malliavin, Phineus R. Markwick, 2008, PLoS Comput. Biol..

Gifa V. 4: A complete package for NMR data set processing

T. Malliavin, J. Pons, M. Delsuc, 1996, Journal of biomolecular NMR.

Accurate NMR structures through minimization of an extended hybrid energy.

Michael Nilges, Michael Habeck, Wolfgang Rieping, 2008, Structure.

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

Isidro Cortes-Ciriano, Gerard J. P. van Westen, Therese E. Malliavin, 2015, Journal of Cheminformatics.

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

A. Azman, F. Weill, N. Thomson, 2019, Nature.

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

Michael Nilges, Therese E. Malliavin, Michael Habeck, 2007, Bioinform..

Refined solution structure and backbone dynamics of 15N-labeled C12A-p8MTCP studied by NMR relaxation

J. Lefèvre, T. Malliavin, M. Stern, 1999, Journal of biomolecular NMR.

Systematic exploration of protein conformational space using a Distance Geometry approach

Leo Liberti, Antonio Mucherino, Carlile Lavor, 2019, bioRxiv.

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

T. Malliavin, P. Corringer, C. Van Renterghem, 2013, Journal of medicinal chemistry.

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

Isidro Cortes-Ciriano, Guillaume Bouvier, Michael Nilges, 2015, Journal of chemical theory and computation.

Molecular Motions as a Drug Target: Mechanistic Simulations of Anthrax Toxin Edema Factor Function Led to the Discovery of Novel Allosteric Inhibitors

T. Malliavin, L. Martínez, É. Laine, 2012, Toxins.

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

Leo Liberti, Guillaume Bouvier, Michael Nilges, 2015, BMC Bioinformatics.

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

Michael Nilges, Michael Habeck, Wolfgang Rieping, 2009, Proteins.

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

Thérèse E Malliavin, Leandro Martínez, Elodie Laine, 2010, Biophysical journal.

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

Elodie Laine, T. Malliavin, É. Laine, 2008, Proteins.

Tuning interval Branch-and-Prune for protein structure determination

Leo Liberti, Michael Nilges, Therese E. Malliavin, 2018, Journal of Global Optimization.

Functional Motions Modulating VanA Ligand Binding Unraveled by Self-Organizing Maps

Guillaume Bouvier, Michael Nilges, Therese E. Malliavin, 2014, J. Chem. Inf. Model..

Maximum Entropy Processing of DOSY NMR Spectra

T. Malliavin, M. Delsuc, 1998 .

Molecular dynamics simulations of HPr under hydrostatic pressure

T. Malliavin, M. Canalia, 2004, Biopolymers.

Stability of the I-motif structure is related to the interactions between phosphodiester backbones.

T. Malliavin, J. Leroy, K. Snoussi, 2003, Biophysical journal.

Computational and biochemical analysis of type IV Pilus dynamics and stability

M. Nilges, T. Malliavin, Yasaman Karami, 2021, bioRxiv.

Proteochemometric modeling in a Bayesian framework

Isidro Cortes-Ciriano, Gerard J. P. van Westen, Therese E. Malliavin, 2014, Journal of Cheminformatics.

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

Isidro Cortes-Ciriano, Therese E. Malliavin, Shardul Paricharak, 2015, Journal of Cheminformatics.

Genomic insights into the 2016-2017 Yemeni cholera epidemic

A. Azman, F. Weill, N. Thomson, 2018, Nature.

Closed-Locked and Apo-Resting State Structures of the Human α7 Nicotinic Receptor: A Computational Study

Thérèse E Malliavin, Grazia Cottone, Letizia Chiodo, 2018, J. Chem. Inf. Model..

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

Guillaume Bouvier, Michael Nilges, Thérèse E Malliavin, 2014, Proteins.

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

Isidro Cortes-Ciriano, Therese E. Malliavin, Andreas Bender, 2015, J. Chem. Inf. Model..

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

M. Nilges, T. Malliavin, B. Bardiaux, 2008, Journal of the American Chemical Society.

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

Isidro Cortes-Ciriano, Guillaume Bouvier, Michael Nilges, 2015, BMC Bioinformatics.

Applications of proteochemometrics - from species extrapolation to cell line sensitivity modelling

Daniel S. Murrell, A. Bender, I. Cortés-Ciriano, 2015, BMC Bioinformatics.

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

T. Malliavin, L. Chiodo, L. Maragliano, 2017, Biophysical chemistry.

Minimal NMR distance information for rigidity of protein graphs

Bruce Randall Donald, Leo Liberti, Michael Nilges, 2019, Discret. Appl. Math..

Use of the Cadzow procedure in 2D NMR for the reduction of t1 noise

T. Malliavin, M. Delsuc, C. Brissac, 1995, Journal of biomolecular NMR.

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

T. Malliavin, E. Lemichez, Eléa Paillarès, 2021, International journal of molecular sciences.

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

M. Nilges, T. Malliavin, P. Alzari, 2016, Biopolymers.

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

Andreas Bender, Gerard J P van Westen, Oscar Méndez-Lucio, 2014, Integrative biology : quantitative biosciences from nano to macro.

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

M. Nilges, T. Malliavin, L. Martínez, 2009, Proteins.

Genomic insights into the 2016-2017 Yemeni cholera epidemic

A. Azman, F. Weill, N. Thomson, 2018, Nature.

New Crystal Form of Human Neuropilin-1 b1 Fragment with Six Electrostatic Mutations Complexed with KDKPPR Peptide Ligand

T. Malliavin, M. Barberi-Heyob, C. Didierjean, 2023, Molecules.

NMRb: a web-site repository for raw NMR datasets

Therese E. Malliavin, Jean-Luc Pons, Marc-André Delsuc, 2004, Bioinform..

Advances and Applications in Bioinformatics and Chemistry Dovepress Simultaneous Use of Solution, Solid-state Nmr and X-ray Crystallography to Study the Conformational Landscape of the Crh Protein during Oligomerization and Crystallization

M. Nilges, T. Malliavin, B. Bardiaux, 2022 .

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

R. Glen, A. Bender, Alexios Koutsoukas, 2014, Future medicinal chemistry.

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

M. Nilges, T. Malliavin, B. Bardiaux, 2008, Journal of the American Chemical Society.

Tandem domain structure determination based on a systematic enumeration of conformations

T. Malliavin, 2021, Scientific Reports.

Secondary structure assignment of proteins in the absence of sequence information

T. Malliavin, L. Liberti, Sammy Khalife, 2021, Bioinformatics advances.

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

M. Nilges, T. Malliavin, W. Vranken, 2011, Proteins.

Computation of relaxation matrix elements from incomplete NOESY data sets

Thérèse E. Malliavin, T. Malliavin, J. Lallemand, 1992 .

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

M. Habeck, M. Nilges, T. Malliavin, 2007, Bioinform..

Blind testing of routine, fully automated determination of protein structures from NMR data.

Oliver F. Lange, Gaohua Liu, G. Montelione, 2012, Structure.

Distance Geometry in Structural Biology: New Perspectives

Antonio Mucherino, Michael Nilges, Thérèse E. Malliavin, 2013, Distance Geometry.

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

M. Habeck, M. Nilges, T. Malliavin, 2022 .

From NMR chemical shifts to amino acid types: Investigation of the predictive power carried by nuclei

Thérèse E Malliavin, Marc-André Delsuc, Pierre Nicolas, 2004, Journal of biomolecular NMR.