Matteo Dal Peraro
matteo.dalperaro@epfl.ch +41 21 693 18 61 http://lbm.epfl.ch
Nationalité : Italian
EPFL SV IBI-SV UPDALPE
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AAB 0 48 (Bâtiment AAB)
Station 19
CH-1015 Lausanne
+41 21 693 18 61
+41 21 693 78 82
Local: AAB 0 48
EPFL > E > E-DOC > EDCB-GE
Web site: Site web: https://go.epfl.ch/phd-edcb
+41 21 693 18 61
EPFL > ENT-R > SCITAS > SCITAS-CD
Publications
Publications Infoscience
Journal Articles
2020
Salt enhances the thermostability of enteroviruses by stabilizing capsid protein interfaces
Journal of Virology. 2020-03-25. DOI : 10.1128/JVI.02176-19.Structural and DNA binding properties of mycobacterial integration host factor mIHF
Journal Of Structural Biology. 2020-03-01. DOI : 10.1016/j.jsb.2019.107434.Building blocks for commodity augmented reality-based molecular visualization and modeling in web browsers
Peerj Computer Science. 2020-02-17. DOI : 10.7717/peerj-cs.260.2019
An experiment-informed signal transduction model for the role of the Staphylococcus aureus MecR1 protein in beta-lactam resistance
Scientific Reports. 2019-12-20. DOI : 10.1038/s41598-019-55923-z.Transmembrane Prolines Mediate Signal Sensing and Decoding in Bacillus subtilis DesK Histidine Kinase
mBio. 2019-11-01. DOI : 10.1128/mBio.02564-19.Single-molecule sensing of peptides and nucleic acids by engineered aerolysin nanopores
Nature Communications. 2019-10-29. DOI : 10.1038/s41467-019-12690-9.Modelling structures in cryo-EM maps
Current Opinion In Structural Biology. 2019-10-01. DOI : 10.1016/j.sbi.2019.05.024.Editorial overview: The future after the cryo-EM resolution revolution
Current Opinion In Structural Biology. 2019-10-01. DOI : 10.1016/j.sbi.2019.07.007.A further leap of improvement in tertiary structure prediction in CASP13 prompts new routes for future assessments
Proteins-Structure Function And Bioinformatics. 2019-08-07. DOI : 10.1002/prot.25787.Active Site-Induced Evolutionary Constraints Follow Fold Polarity Principles in Soluble Globular Enzymes
Molecular Biology And Evolution. 2019-08-01. DOI : 10.1093/molbev/msz096.KAP1 is an antiparallel dimer with a functional asymmetry
Life Science Alliance. 2019-08-01. DOI : 10.26508/lsa.201900349.Molecular Profiling and Functional Analysis of Macrophage-Derived Tumor Extracellular Vesicles
Cell Reports. 2019-06-04. DOI : 10.1016/j.celrep.2019.05.008.An Isoprene Lipid-Binding Protein Promotes Eukaryotic Coenzyme Q Biosynthesis
Molecular Cell. 2019-02-21. DOI : 10.1016/j.molcel.2018.11.033.2018
Recruitment of the amyloid precursor protein by gamma-secretase at the synaptic plasma membrane
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS. 2018. DOI : 10.1016/j.bbrc.2017.10.164.Nucleo-cytosolic Shuttling of ARGONAUTE1 Prompts a Revised Model of the Plant MicroRNA Pathway
MOLECULAR CELL. 2018. DOI : 10.1016/j.molcel.2018.01.007.Mitochondrial cytochrome c oxidase biogenesis: Recent developments
SEMINARS IN CELL AND DEVELOPMENTAL BIOLOGY. 2018. DOI : 10.1016/j.semcdb.2017.08.055.Mapping the sensing spots of aerolysin for single oligonucleotides analysis
Nature Communications. 2018. DOI : 10.1038/s41467-018-05108-5.Electron transfer in an acidophilic bacterium: interaction between a diheme cytochrome and a cupredoxin
CHEMICAL SCIENCE. 2018. DOI : 10.1039/c8sc01615a.Definition and classification of evaluation units for tertiary structure prediction in CASP12 facilitated through semi-automated metrics
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS. 2018. DOI : 10.1002/prot.25403.Conserved Lipid and Small-Molecule Modulation of COQ8 Reveals Regulation of the Ancient Kinase-like UbiB Family
CELL CHEMICAL BIOLOGY. 2018. DOI : 10.1016/j.chembiol.2017.11.001.Assessment of hard target modeling in CASP12 reveals an emerging role of alignment-based contact prediction methods
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS. 2018. DOI : 10.1002/prot.25423.Assessment of data-assisted prediction by inclusion of crosslinking/mass-spectrometry and small angle X-ray scattering data in the 12(th) Critical Assessment of protein Structure Prediction experiment
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS. 2018. DOI : 10.1002/prot.25442.A Combined Computational and Experimental Study to Investigate the Role of COQ9 in Promoting COQ Biosynthesis
Biophysical Journal. 2018. DOI : 10.1016/j.bpj.2017.11.2541.2017
Evolution of Acid-Sensing Olfactory Circuits in Drosophilids
Neuron. 2017. DOI : 10.1016/j.neuron.2016.12.024.Disentangling constraints using viability evolution principles in integrative modeling of macromolecular assemblies
Scientific Reports. 2017. DOI : 10.1038/s41598-017-00266-w.2016
Cooperative motion of a key positively charged residue and metal ions for DNA replication catalyzed by human DNA Polymerase-eta
Nucleic Acids Research. 2016-03-01. DOI : 10.1093/nar/gkw128.Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server(vol 1, 242, 2016)
Bmc Bioinformatics. 2016. DOI : 10.1186/s12859-016-1315-z.Olfactory receptor pseudo-pseudogenes
Nature. 2016. DOI : 10.1038/nature19824.A rheostat mechanism governs the bifurcation of carbon flux in mycobacteria
Nature Communications. 2016. DOI : 10.1038/ncomms12527.Cerebellar Ataxia and Coenzyme Q Deficiency through Loss of Unorthodox Kinase Activity
Molecular Cell. 2016. DOI : 10.1016/j.molcel.2016.06.030.Molecular Effects of Concentrated Solutes on Protein Hydration, Dynamics, and Electrostatics
Biophysical Journal. 2016. DOI : 10.1016/j.bpj.2016.07.011.Effect of the Synaptic Plasma Membrane on the Stability of the Amyloid Precursor Protein Homodimer
Journal Of Physical Chemistry Letters. 2016. DOI : 10.1021/acs.jpclett.6b01721.Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server
Bmc Bioinformatics. 2016. DOI : 10.1186/s12859-016-1124-4.Cryo-EM structure of aerolysin variants reveals a novel protein fold and the pore-formation process
Nature Communications. 2016. DOI : 10.1038/ncomms12062.Immobilization of the N-terminal helix stabilizes prefusion paramyxovirus fusion proteins
Proceedings Of The National Academy Of Sciences Of The United States Of America. 2016. DOI : 10.1073/pnas.1608349113.X-ray structure of a lectin-bound DNA duplex containing an unnatural phenanthrenyl pair
Chemical Communications. 2016. DOI : 10.1039/c6cc00374e.2015
Lipid Builder: A Framework To Build Realistic Models for Biological Membranes
Journal Of Chemical Information And Modeling. 2015. DOI : 10.1021/acs.jcim.5b00501.Bridged bicyclic peptides as potential drug scaffolds: synthesis, structure, protein binding and stability
Chemical Science. 2015. DOI : 10.1039/c5sc01699a.A coiled coil switch mediates cold sensing by the thermosensory protein DesK
Molecular Microbiology. 2015. DOI : 10.1111/mmi.13118.GtrA Protein Rv3789 Is Required for Arabinosylation of Arabinogalactan in Mycobacterium tuberculosis
Journal Of Bacteriology. 2015. DOI : 10.1128/Jb.00628-15.Understanding and Engineering Thermostability in DNA Ligase from Thermococcus sp 1519
Biochemistry. 2015. DOI : 10.1021/bi501227b.Assessing the potential of atomistic molecular dynamics simulations to probe reversible protein-protein recognition and binding
Scientific Reports. 2015. DOI : 10.1038/srep10549.Structural insights on cholesterol endosynthesis: Binding of squalene and 2,3-oxidosqualene to supernatant protein factor
Journal Of Structural Biology. 2015. DOI : 10.1016/j.jsb.2015.05.001.The importance of dynamics in integrative modeling of supramolecular assemblies
Current Opinion In Structural Biology. 2015. DOI : 10.1016/j.sbi.2015.02.018.NAR Breakthrough Article Crystal structure of Hop2-Mnd1 and mechanistic insights into its role in meiotic recombination
Nucleic Acids Research. 2015. DOI : 10.1093/nar/gkv172.How Structural and Physicochemical Determinants Shape Sequence Constraints in a Functional Enzyme
Plos One. 2015. DOI : 10.1371/journal.pone.0118684.2014
A dimerization interface mediated by functionally critical residues creates interfacial disulfide bonds and copper sites in CueP
Journal Of Inorganic Biochemistry. 2014. DOI : 10.1016/j.jinorgbio.2014.07.022.Reaction Mechanism and Catalytic Fingerprint of Allantoin Racemase
Journal Of Physical Chemistry B. 2014. DOI : 10.1021/jp411786z.Dissecting the Effects of Concentrated Carbohydrate Solutions on Protein Diffusion, Hydration, and Internal Dynamics
Journal Of Physical Chemistry B. 2014. DOI : 10.1021/jp4126705.Molecular dynamics simulations of apocupredoxins: insights into the formation and stabilization of copper sites under entatic control
Journal Of Biological Inorganic Chemistry. 2014. DOI : 10.1007/s00775-014-1108-7.Perturbations of the Straight Transmembrane alpha-Helical Structure of the Amyloid Precursor Protein Affect Its Processing by gamma-Secretase
Journal Of Biological Chemistry. 2014. DOI : 10.1074/jbc.M113.470781.Critical roles of isoleucine-364 and adjacent residues in a hydrophobic gate control of phospholipid transport by the mammalian P4-ATPase ATP8A2
Proceedings Of The National Academy Of Sciences Of The United States Of America. 2014. DOI : 10.1073/pnas.1321165111.ComEA Is Essential for the Transfer of External DNA into the Periplasm in Naturally Transformable Vibrio cholerae Cells
PLoS Genetics. 2014. DOI : 10.1371/journal.pgen.1004066.2013
In situ structural analysis of the Yersinia enterocolitica injectisome
Elife. 2013. DOI : 10.7554/eLife.00792.TAL Effectors Specificity Stems from Negative Discrimination
Plos One. 2013. DOI : 10.1371/journal.pone.0080261.Molecular assembly of the aerolysin pore reveals a swirling membrane-insertion mechanism
Nature Chemical Biology. 2013. DOI : 10.1038/Nchembio.1312.Macromolecular Symmetric Assembly Prediction Using Swarm Intelligence Dynamic Modeling
Structure. 2013. DOI : 10.1016/j.str.2013.05.014.All-atom simulations of crowding effects on ubiquitin dynamics
Physical Biology. 2013. DOI : 10.1088/1478-3975/10/4/045006.Electrostatic-Consistent Coarse-Grained Potentials for Molecular Simulations of Proteins
Journal Of Chemical Theory And Computation. 2013. DOI : 10.1021/ct400137q.Arranged Sevenfold: Structural Insights into the C-Terminal Oligomerization Domain of Human C4b-Binding Protein
Journal Of Molecular Biology. 2013. DOI : 10.1016/j.jmb.2012.12.017.In-depth analysis of hyaline fibromatosis syndrome frameshift mutations at the same site reveal the necessity of personalized therapy
Human mutation. 2013. DOI : 10.1002/humu.22324.Cardiolipin Models for Molecular Simulations of Bacterial and Mitochondrial Membranes
Journal Of Chemical Theory And Computation. 2013. DOI : 10.1021/ct300590v.Assembly of the Transmembrane Domain of E. coli PhoQ Histidine Kinase: Implications for Signal Transduction from Molecular Simulations
Plos Computational Biology. 2013. DOI : 10.1371/journal.pcbi.1002878.Molecular Simulations Highlight the Role of Metals in Catalysis and Inhibition of Type II Topoisomerase
Journal Of Chemical Theory And Computation. 2013. DOI : 10.1021/ct300691u.2012
On the active site of mononuclear B1 metallo beta-lactamases: a computational study
Journal Of Computer-Aided Molecular Design. 2012. DOI : 10.1007/s10822-012-9571-0.Palmitoylated calnexin is a key component of the ribosome-translocon complex
Embo Journal. 2012. DOI : 10.1038/emboj.2012.15.The Lipopolysaccharide from Capnocytophaga canimorsus Reveals an Unexpected Role of the Core-Oligosaccharide in MD-2 Binding
PLoS Pathogens. 2012. DOI : 10.1371/journal.ppat.1002667.2011
Atypical DNA recognition mechanism used by the EspR virulence regulator of Mycobacterium tuberculosis
Molecular Microbiology. 2011. DOI : 10.1111/j.1365-2958.2011.07813.x.Dual Chaperone Role of the C-Terminal Propeptide in Folding and Oligomerization of the Pore-Forming Toxin Aerolysin
PLoS Pathogens. 2011. DOI : 10.1371/journal.ppat.1002135.An introduction to quantum chemical methods applied to drug design
Frontiers in Bioscience. 2011. DOI : 10.2741/311.Computational study of drug binding to the membrane-bound tetrameric M2 peptide bundle from influenza A virus
Biochimica et Biophysica Acta (BBA) - Biomembranes. 2011. DOI : 10.1016/j.bbamem.2010.03.025.Conference Papers
2019
Overcoming the hydrophobic barrier of the membrane: The role of COQ9 in promoting coenzyme Q biosynthesis
2019-03-31. National Meeting of the American-Chemical-Society (ACS), Orlando, FL, Mar 31-Apr 04, 2019.Molecular Simulations Give Insights into the NDM-1/Membrane Interaction that Causes Rise of a Super-Bacterium
2019-02-15. 63rd Annual Meeting of the Biophysical-Society, Baltimore, MD, Mar 02-06, 2019. p. 205A-205A. DOI : 10.1016/j.bpj.2018.11.1132.2018
Exploiting the role of membrane anchoring on the peculiar biological behaviour of multi-drug resistant enzyme New Delhi metallo-beta-lactamase 1
2018-08-19. 256th National Meeting and Exposition of the American-Chemical-Society (ACS) - Nanoscience, Nanotechnology and Beyond, Boston, MA, Aug 19-23, 2018.2014
A Computational Study of Ligand Binding in Chemosensory Ionotropic Glutamate Receptors
2014. 58th Annual Meeting of the Biophysical-Society, San Francisco, CA, FEB 15-19, 2014. p. 152A-152A.The Amyloid Precursor Protein Maintains an Ideal&Alpha-Helical Conformation in the Lipid Bilayer
2014. 58th Annual Meeting of the Biophysical-Society, San Francisco, CA, FEB 15-19, 2014. p. 53A-53A.2013
Dynamics of catalytic metals during DNA cleavage in type II topoisomerase
2013. 245th National Meeting of the American-Chemical-Society (ACS), New Orleans, LA, APR 07-11, 2013.The Molecular Assembly of the Aerolysin Pore Reveals a Unique Swirling Membrane-Insertion Mechanism
2013. 57th Annual Meeting of the Biophysical-Society. p. 395A-395A.Intrinsic Transmembrane Flexibility of the Amyloid Precursor Protein Explored by Molecular Simulations
2013. 57th Annual Meeting of the Biophysical-Society, Philadelphia, PA, FEB 02-06, 2013. p. 226A-226A.2011
Development of a chemical-detailed coarse-grained force field for proteins
2011. 242nd National Meeting of the American-Chemical-Society (ACS), Denver, CO, Aug 28-Sep 01, 2011. p. 28-COMP.2010
Effect of magnesium ion concentration on the catalytic activity of ribonuclease H: Does a third metal bound at the active site modulate endonuclease catalysis?
2010. p. 394-PHYS.Shedding a new light on photolyases: Accurate molecular modeling as a tool for undestanding DNA repairing enzymes
2010. p. 20-PHYS.Common catalytic features among cofactor independent racemases and epimerases: A computational perspective
2010. p. 88-COMP.Conformational coupling between LOV and kinase domains in phototropins: A computational perspective
2010. p. 436-COMP.Assembly and function of large Gram-negative bacterial machines studied by molecular simulation integrated with experimental data
2010. p. 425-COMP.Coarse-graining electrostatics in multiscale molecular simulations
2010. p. 391-COMP.Reviews
2020
Single-molecule studies of amyloid proteins: from biophysical properties to diagnostic perspectives
Quarterly Reviews Of Biophysics. 2020-01-01. DOI : 10.1017/S0033583520000086.2016
Pore-forming toxins: ancient, but never really out of fashion
Nature Reviews Microbiology. 2016. DOI : 10.1038/nrmicro.2015.3.2015
Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop
Structure. 2015. DOI : 10.1016/j.str.2015.05.013.Catalytic Metal Ions and Enzymatic Processing of DNA and RNA
Accounts Of Chemical Research. 2015. DOI : 10.1021/ar500314j.2014
HCV E2 core structures and mAbs: something is still missing
Drug Discovery Today. 2014. DOI : 10.1016/j.drudis.2014.08.011.2013
Peptide-Based Vaccinology: Experimental and Computational Approaches to Target Hypervariable Viruses through the Fine Characterization of Protective Epitopes Recognized by Monoclonal Antibodies and the Identification of T-Cell-Activating Peptides
Clinical & Developmental Immunology. 2013. DOI : 10.1155/2013/521231.Theses
2018
Constrained optimization applied to multiscale integrative modeling
EPFL, 2018. DOI : 10.5075/epfl-thesis-8630.2017
Studying membrane-protein interplay by modeling realistic conditions
Lausanne, EPFL, 2017. DOI : 10.5075/epfl-thesis-7934.2015
Modeling and Engineering Proteins Thermostability
Lausanne, EPFL, 2015. DOI : 10.5075/epfl-thesis-6637.2014
New models and techniques to simulate realistic biological membranes
Lausanne, EPFL, 2014. DOI : 10.5075/epfl-thesis-6310.2013
Multiscale simulations of protein dynamics
Lausanne, EPFL, 2013. DOI : 10.5075/epfl-thesis-5841.Molecular Modeling of Membrane Embedded Proteins
Lausanne, EPFL, 2013. DOI : 10.5075/epfl-thesis-5695.2012
Molecular Modeling of Bacterial Nanomachineries
Lausanne, EPFL, 2012. DOI : 10.5075/epfl-thesis-5404.Book Chapters
2014
New Strategies for Integrative Dynamic Modeling of Macromolecular Assembly
Biomolecular Modelling And Simulations; San Diego: Elsevier Academic Press Inc, 2014. p. 77-111.Infoscience
Salt enhances the thermostability of enteroviruses by stabilizing capsid protein interfaces
Journal of Virology. 2020-03-25. DOI : 10.1128/JVI.02176-19.Structural and DNA binding properties of mycobacterial integration host factor mIHF
Journal Of Structural Biology. 2020-03-01. DOI : 10.1016/j.jsb.2019.107434.Building blocks for commodity augmented reality-based molecular visualization and modeling in web browsers
Peerj Computer Science. 2020-02-17. DOI : 10.7717/peerj-cs.260.Single-molecule studies of amyloid proteins: from biophysical properties to diagnostic perspectives
Quarterly Reviews Of Biophysics. 2020-01-01. DOI : 10.1017/S0033583520000086.An experiment-informed signal transduction model for the role of the Staphylococcus aureus MecR1 protein in beta-lactam resistance
Scientific Reports. 2019-12-20. DOI : 10.1038/s41598-019-55923-z.Transmembrane Prolines Mediate Signal Sensing and Decoding in Bacillus subtilis DesK Histidine Kinase
mBio. 2019-11-01. DOI : 10.1128/mBio.02564-19.Single-molecule sensing of peptides and nucleic acids by engineered aerolysin nanopores
Nature Communications. 2019-10-29. DOI : 10.1038/s41467-019-12690-9.Modelling structures in cryo-EM maps
Current Opinion In Structural Biology. 2019-10-01. DOI : 10.1016/j.sbi.2019.05.024.Editorial overview: The future after the cryo-EM resolution revolution
Current Opinion In Structural Biology. 2019-10-01. DOI : 10.1016/j.sbi.2019.07.007.A further leap of improvement in tertiary structure prediction in CASP13 prompts new routes for future assessments
Proteins-Structure Function And Bioinformatics. 2019-08-07. DOI : 10.1002/prot.25787.Active Site-Induced Evolutionary Constraints Follow Fold Polarity Principles in Soluble Globular Enzymes
Molecular Biology And Evolution. 2019-08-01. DOI : 10.1093/molbev/msz096.KAP1 is an antiparallel dimer with a functional asymmetry
Life Science Alliance. 2019-08-01. DOI : 10.26508/lsa.201900349.Molecular Profiling and Functional Analysis of Macrophage-Derived Tumor Extracellular Vesicles
Cell Reports. 2019-06-04. DOI : 10.1016/j.celrep.2019.05.008.Overcoming the hydrophobic barrier of the membrane: The role of COQ9 in promoting coenzyme Q biosynthesis
2019-03-31. National Meeting of the American-Chemical-Society (ACS), Orlando, FL, Mar 31-Apr 04, 2019.An Isoprene Lipid-Binding Protein Promotes Eukaryotic Coenzyme Q Biosynthesis
Molecular Cell. 2019-02-21. DOI : 10.1016/j.molcel.2018.11.033.Molecular Simulations Give Insights into the NDM-1/Membrane Interaction that Causes Rise of a Super-Bacterium
2019-02-15. 63rd Annual Meeting of the Biophysical-Society, Baltimore, MD, Mar 02-06, 2019. p. 205A-205A. DOI : 10.1016/j.bpj.2018.11.1132.Exploiting the role of membrane anchoring on the peculiar biological behaviour of multi-drug resistant enzyme New Delhi metallo-beta-lactamase 1
2018-08-19. 256th National Meeting and Exposition of the American-Chemical-Society (ACS) - Nanoscience, Nanotechnology and Beyond, Boston, MA, Aug 19-23, 2018.Recruitment of the amyloid precursor protein by gamma-secretase at the synaptic plasma membrane
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS. 2018. DOI : 10.1016/j.bbrc.2017.10.164.Nucleo-cytosolic Shuttling of ARGONAUTE1 Prompts a Revised Model of the Plant MicroRNA Pathway
MOLECULAR CELL. 2018. DOI : 10.1016/j.molcel.2018.01.007.Mitochondrial cytochrome c oxidase biogenesis: Recent developments
SEMINARS IN CELL AND DEVELOPMENTAL BIOLOGY. 2018. DOI : 10.1016/j.semcdb.2017.08.055.Mapping the sensing spots of aerolysin for single oligonucleotides analysis
Nature Communications. 2018. DOI : 10.1038/s41467-018-05108-5.Electron transfer in an acidophilic bacterium: interaction between a diheme cytochrome and a cupredoxin
CHEMICAL SCIENCE. 2018. DOI : 10.1039/c8sc01615a.Definition and classification of evaluation units for tertiary structure prediction in CASP12 facilitated through semi-automated metrics
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS. 2018. DOI : 10.1002/prot.25403.Conserved Lipid and Small-Molecule Modulation of COQ8 Reveals Regulation of the Ancient Kinase-like UbiB Family
CELL CHEMICAL BIOLOGY. 2018. DOI : 10.1016/j.chembiol.2017.11.001.Assessment of hard target modeling in CASP12 reveals an emerging role of alignment-based contact prediction methods
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS. 2018. DOI : 10.1002/prot.25423.Assessment of data-assisted prediction by inclusion of crosslinking/mass-spectrometry and small angle X-ray scattering data in the 12(th) Critical Assessment of protein Structure Prediction experiment
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS. 2018. DOI : 10.1002/prot.25442.A Combined Computational and Experimental Study to Investigate the Role of COQ9 in Promoting COQ Biosynthesis
Biophysical Journal. 2018. DOI : 10.1016/j.bpj.2017.11.2541.Constrained optimization applied to multiscale integrative modeling
EPFL, 2018. DOI : 10.5075/epfl-thesis-8630.Studying membrane-protein interplay by modeling realistic conditions
Lausanne, EPFL, 2017. DOI : 10.5075/epfl-thesis-7934.Evolution of Acid-Sensing Olfactory Circuits in Drosophilids
Neuron. 2017. DOI : 10.1016/j.neuron.2016.12.024.Disentangling constraints using viability evolution principles in integrative modeling of macromolecular assemblies
Scientific Reports. 2017. DOI : 10.1038/s41598-017-00266-w.Cooperative motion of a key positively charged residue and metal ions for DNA replication catalyzed by human DNA Polymerase-eta
Nucleic Acids Research. 2016-03-01. DOI : 10.1093/nar/gkw128.Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server(vol 1, 242, 2016)
Bmc Bioinformatics. 2016. DOI : 10.1186/s12859-016-1315-z.Olfactory receptor pseudo-pseudogenes
Nature. 2016. DOI : 10.1038/nature19824.A rheostat mechanism governs the bifurcation of carbon flux in mycobacteria
Nature Communications. 2016. DOI : 10.1038/ncomms12527.Cerebellar Ataxia and Coenzyme Q Deficiency through Loss of Unorthodox Kinase Activity
Molecular Cell. 2016. DOI : 10.1016/j.molcel.2016.06.030.Molecular Effects of Concentrated Solutes on Protein Hydration, Dynamics, and Electrostatics
Biophysical Journal. 2016. DOI : 10.1016/j.bpj.2016.07.011.Effect of the Synaptic Plasma Membrane on the Stability of the Amyloid Precursor Protein Homodimer
Journal Of Physical Chemistry Letters. 2016. DOI : 10.1021/acs.jpclett.6b01721.Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server
Bmc Bioinformatics. 2016. DOI : 10.1186/s12859-016-1124-4.Cryo-EM structure of aerolysin variants reveals a novel protein fold and the pore-formation process
Nature Communications. 2016. DOI : 10.1038/ncomms12062.Immobilization of the N-terminal helix stabilizes prefusion paramyxovirus fusion proteins
Proceedings Of The National Academy Of Sciences Of The United States Of America. 2016. DOI : 10.1073/pnas.1608349113.X-ray structure of a lectin-bound DNA duplex containing an unnatural phenanthrenyl pair
Chemical Communications. 2016. DOI : 10.1039/c6cc00374e.Pore-forming toxins: ancient, but never really out of fashion
Nature Reviews Microbiology. 2016. DOI : 10.1038/nrmicro.2015.3.Lipid Builder: A Framework To Build Realistic Models for Biological Membranes
Journal Of Chemical Information And Modeling. 2015. DOI : 10.1021/acs.jcim.5b00501.Bridged bicyclic peptides as potential drug scaffolds: synthesis, structure, protein binding and stability
Chemical Science. 2015. DOI : 10.1039/c5sc01699a.A coiled coil switch mediates cold sensing by the thermosensory protein DesK
Molecular Microbiology. 2015. DOI : 10.1111/mmi.13118.GtrA Protein Rv3789 Is Required for Arabinosylation of Arabinogalactan in Mycobacterium tuberculosis
Journal Of Bacteriology. 2015. DOI : 10.1128/Jb.00628-15.Understanding and Engineering Thermostability in DNA Ligase from Thermococcus sp 1519
Biochemistry. 2015. DOI : 10.1021/bi501227b.Assessing the potential of atomistic molecular dynamics simulations to probe reversible protein-protein recognition and binding
Scientific Reports. 2015. DOI : 10.1038/srep10549.Structural insights on cholesterol endosynthesis: Binding of squalene and 2,3-oxidosqualene to supernatant protein factor
Journal Of Structural Biology. 2015. DOI : 10.1016/j.jsb.2015.05.001.The importance of dynamics in integrative modeling of supramolecular assemblies
Current Opinion In Structural Biology. 2015. DOI : 10.1016/j.sbi.2015.02.018.NAR Breakthrough Article Crystal structure of Hop2-Mnd1 and mechanistic insights into its role in meiotic recombination
Nucleic Acids Research. 2015. DOI : 10.1093/nar/gkv172.Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop
Structure. 2015. DOI : 10.1016/j.str.2015.05.013.Modeling and Engineering Proteins Thermostability
Lausanne, EPFL, 2015. DOI : 10.5075/epfl-thesis-6637.How Structural and Physicochemical Determinants Shape Sequence Constraints in a Functional Enzyme
Plos One. 2015. DOI : 10.1371/journal.pone.0118684.Catalytic Metal Ions and Enzymatic Processing of DNA and RNA
Accounts Of Chemical Research. 2015. DOI : 10.1021/ar500314j.HCV E2 core structures and mAbs: something is still missing
Drug Discovery Today. 2014. DOI : 10.1016/j.drudis.2014.08.011.New Strategies for Integrative Dynamic Modeling of Macromolecular Assembly
Biomolecular Modelling And Simulations; San Diego: Elsevier Academic Press Inc, 2014. p. 77-111.A dimerization interface mediated by functionally critical residues creates interfacial disulfide bonds and copper sites in CueP
Journal Of Inorganic Biochemistry. 2014. DOI : 10.1016/j.jinorgbio.2014.07.022.New models and techniques to simulate realistic biological membranes
Lausanne, EPFL, 2014. DOI : 10.5075/epfl-thesis-6310.Reaction Mechanism and Catalytic Fingerprint of Allantoin Racemase
Journal Of Physical Chemistry B. 2014. DOI : 10.1021/jp411786z.A Computational Study of Ligand Binding in Chemosensory Ionotropic Glutamate Receptors
2014. 58th Annual Meeting of the Biophysical-Society, San Francisco, CA, FEB 15-19, 2014. p. 152A-152A.The Amyloid Precursor Protein Maintains an Ideal&Alpha-Helical Conformation in the Lipid Bilayer
2014. 58th Annual Meeting of the Biophysical-Society, San Francisco, CA, FEB 15-19, 2014. p. 53A-53A.Dissecting the Effects of Concentrated Carbohydrate Solutions on Protein Diffusion, Hydration, and Internal Dynamics
Journal Of Physical Chemistry B. 2014. DOI : 10.1021/jp4126705.Molecular dynamics simulations of apocupredoxins: insights into the formation and stabilization of copper sites under entatic control
Journal Of Biological Inorganic Chemistry. 2014. DOI : 10.1007/s00775-014-1108-7.Perturbations of the Straight Transmembrane alpha-Helical Structure of the Amyloid Precursor Protein Affect Its Processing by gamma-Secretase
Journal Of Biological Chemistry. 2014. DOI : 10.1074/jbc.M113.470781.Critical roles of isoleucine-364 and adjacent residues in a hydrophobic gate control of phospholipid transport by the mammalian P4-ATPase ATP8A2
Proceedings Of The National Academy Of Sciences Of The United States Of America. 2014. DOI : 10.1073/pnas.1321165111.ComEA Is Essential for the Transfer of External DNA into the Periplasm in Naturally Transformable Vibrio cholerae Cells
PLoS Genetics. 2014. DOI : 10.1371/journal.pgen.1004066.In situ structural analysis of the Yersinia enterocolitica injectisome
Elife. 2013. DOI : 10.7554/eLife.00792.TAL Effectors Specificity Stems from Negative Discrimination
Plos One. 2013. DOI : 10.1371/journal.pone.0080261.Dynamics of catalytic metals during DNA cleavage in type II topoisomerase
2013. 245th National Meeting of the American-Chemical-Society (ACS), New Orleans, LA, APR 07-11, 2013.Multiscale simulations of protein dynamics
Lausanne, EPFL, 2013. DOI : 10.5075/epfl-thesis-5841.Molecular assembly of the aerolysin pore reveals a swirling membrane-insertion mechanism
Nature Chemical Biology. 2013. DOI : 10.1038/Nchembio.1312.Peptide-Based Vaccinology: Experimental and Computational Approaches to Target Hypervariable Viruses through the Fine Characterization of Protective Epitopes Recognized by Monoclonal Antibodies and the Identification of T-Cell-Activating Peptides
Clinical & Developmental Immunology. 2013. DOI : 10.1155/2013/521231.Macromolecular Symmetric Assembly Prediction Using Swarm Intelligence Dynamic Modeling
Structure. 2013. DOI : 10.1016/j.str.2013.05.014.All-atom simulations of crowding effects on ubiquitin dynamics
Physical Biology. 2013. DOI : 10.1088/1478-3975/10/4/045006.Electrostatic-Consistent Coarse-Grained Potentials for Molecular Simulations of Proteins
Journal Of Chemical Theory And Computation. 2013. DOI : 10.1021/ct400137q.Arranged Sevenfold: Structural Insights into the C-Terminal Oligomerization Domain of Human C4b-Binding Protein
Journal Of Molecular Biology. 2013. DOI : 10.1016/j.jmb.2012.12.017.In-depth analysis of hyaline fibromatosis syndrome frameshift mutations at the same site reveal the necessity of personalized therapy
Human mutation. 2013. DOI : 10.1002/humu.22324.Molecular Modeling of Membrane Embedded Proteins
Lausanne, EPFL, 2013. DOI : 10.5075/epfl-thesis-5695.The Molecular Assembly of the Aerolysin Pore Reveals a Unique Swirling Membrane-Insertion Mechanism
2013. 57th Annual Meeting of the Biophysical-Society. p. 395A-395A.Intrinsic Transmembrane Flexibility of the Amyloid Precursor Protein Explored by Molecular Simulations
2013. 57th Annual Meeting of the Biophysical-Society, Philadelphia, PA, FEB 02-06, 2013. p. 226A-226A.Cardiolipin Models for Molecular Simulations of Bacterial and Mitochondrial Membranes
Journal Of Chemical Theory And Computation. 2013. DOI : 10.1021/ct300590v.Assembly of the Transmembrane Domain of E. coli PhoQ Histidine Kinase: Implications for Signal Transduction from Molecular Simulations
Plos Computational Biology. 2013. DOI : 10.1371/journal.pcbi.1002878.Molecular Simulations Highlight the Role of Metals in Catalysis and Inhibition of Type II Topoisomerase
Journal Of Chemical Theory And Computation. 2013. DOI : 10.1021/ct300691u.Molecular Modeling of Bacterial Nanomachineries
Lausanne, EPFL, 2012. DOI : 10.5075/epfl-thesis-5404.On the active site of mononuclear B1 metallo beta-lactamases: a computational study
Journal Of Computer-Aided Molecular Design. 2012. DOI : 10.1007/s10822-012-9571-0.Palmitoylated calnexin is a key component of the ribosome-translocon complex
Embo Journal. 2012. DOI : 10.1038/emboj.2012.15.The Lipopolysaccharide from Capnocytophaga canimorsus Reveals an Unexpected Role of the Core-Oligosaccharide in MD-2 Binding
PLoS Pathogens. 2012. DOI : 10.1371/journal.ppat.1002667.Development of a chemical-detailed coarse-grained force field for proteins
2011. 242nd National Meeting of the American-Chemical-Society (ACS), Denver, CO, Aug 28-Sep 01, 2011. p. 28-COMP.Atypical DNA recognition mechanism used by the EspR virulence regulator of Mycobacterium tuberculosis
Molecular Microbiology. 2011. DOI : 10.1111/j.1365-2958.2011.07813.x.Dual Chaperone Role of the C-Terminal Propeptide in Folding and Oligomerization of the Pore-Forming Toxin Aerolysin
PLoS Pathogens. 2011. DOI : 10.1371/journal.ppat.1002135.An introduction to quantum chemical methods applied to drug design
Frontiers in Bioscience. 2011. DOI : 10.2741/311.Computational study of drug binding to the membrane-bound tetrameric M2 peptide bundle from influenza A virus
Biochimica et Biophysica Acta (BBA) - Biomembranes. 2011. DOI : 10.1016/j.bbamem.2010.03.025.Effect of magnesium ion concentration on the catalytic activity of ribonuclease H: Does a third metal bound at the active site modulate endonuclease catalysis?
2010. p. 394-PHYS.Shedding a new light on photolyases: Accurate molecular modeling as a tool for undestanding DNA repairing enzymes
2010. p. 20-PHYS.Common catalytic features among cofactor independent racemases and epimerases: A computational perspective
2010. p. 88-COMP.Conformational coupling between LOV and kinase domains in phototropins: A computational perspective
2010. p. 436-COMP.Assembly and function of large Gram-negative bacterial machines studied by molecular simulation integrated with experimental data
2010. p. 425-COMP.Coarse-graining electrostatics in multiscale molecular simulations
2010. p. 391-COMP.Enseignement & Phd
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