Matteo Dal Peraro
Nationality: Italian
EPFL SV IBI-SV UPDALPE
AAB 0 48 (Bâtiment AAB)
Station 19
1015 Lausanne
+41 21 693 18 61
+41 21 693 21 52
Office: AAB 0 48
EPFL › SV › IBI-SV › UPDALPE
Website: https://lbm.epfl.ch/
+41 21 693 18 61
EPFL › SV › SV-SSV › SSV-ENS
Website: https://sv.epfl.ch/education
EPFL SV IBI-GE
AAB
Station 15
1015 Lausanne
+41 21 693 18 61
EPFL › SV › IBI-SV › IBI-SV-GE
Website: https://bioengineering.epfl.ch/
EPFL STI IBI-GE
AAB
Station 15
1015 Lausanne
+41 21 693 18 61
EPFL › STI › IBI-STI › IBI-STI-GE
Website: https://bioengineering.epfl.ch/
+41 21 693 18 61
EPFL › STI › STI-DEC › STI-DIR
+41 21 693 18 61
EPFL › VPA › VPA-AVP-DLE › AVP-DLE-EDOC › EDCB-GE
Website: https://go.epfl.ch/phd-edcb
+41 21 693 18 61
EPFL › SV › SV-DEC › SV-DIR
Expertise
Computational biophysics
Modeling of biological systems
Matteo Dal Peraro graduated in Physics at the University of Padua in 2000. He obtained his Ph.D. in Biophysics at the International School for Advanced Studies (SISSA, Trieste) in 2004. He then received postdoctoral training at the University of Pennsylvania (Philadelphia) under the guidance of Prof. M. L. Klein. He was nominated Tenure Track Assistant Professor at the EPFL School of Life Sciences in late 2007.
His research at the Laboratory for Biomolecular Modeling (LBM), within the Interfaculty Institute of Bioengineering (IBI), focuses on the multiscale modeling of large macromolecular systems.
Education
B.S. and M.S.
| Physics2000 – 2000 University of Padua
Ph.D.
| Biophysics2004 – 2004 International School for Advanced Studies (SISSA)
Infoscience
Journal Articles
2026
Asymmetric envelope surface disposition of secreted protein YjbI controls bimodal antibiotic susceptibilities in C. crescentus
The EMBO Journal. 2026. DOI : 10.1038/s44318-025-00668-x.ModelCIF Update: Supporting Emerging Classes of Computational Macromolecular Models
Journal of molecular biology. 2026. DOI : 10.1016/j.jmb.2026.169658.2025
Wide-field fluorescence lifetime imaging of single molecules with a gated single-photon camera
Light, science & applications. 2025. DOI : 10.1038/s41377-025-01901-2.Lumen charge governs gated ion transport in β-barrel nanopores
Nature Nanotechnology. 2025. DOI : 10.1038/s41565-025-02052-6.Cardiolipin dynamics promote membrane remodeling by mitochondrial OPA1
Nature Communications. 2025. DOI : 10.1038/s41467-025-63813-4.Structure of the Huntingtin F-actin complex reveals its role in cytoskeleton organization
Science Advances. 2025. DOI : 10.1126/sciadv.adw4124.Exploring New Nanopore Sensors from the Aerolysin Family
Small. 2025. DOI : 10.1002/smll.202501219.Analysis of Integrator-Differentiator Transimpedance Amplifiers: Speed and Gain Tradeoff Introduced by Parasitic Capacitances
IEEE Transactions on Instrumentation and Measurement. 2025. DOI : 10.1109/tim.2025.3573761.The HP1 box of KAP1 organizes HP1α for silencing of endogenous retroviral elements in embryonic stem cells
Nature Communications. 2025. DOI : 10.1038/s41467-025-60279-2.The Need to Implement Fair Principles in Biomolecular Simulations
NATURE METHODS. 2025. DOI : 10.1038/s41592-025-02635-0.MolecularWebXR: Multiuser discussions in chemistry and biology through immersive and inclusive augmented and virtual reality
Journal of molecular graphics & modelling. 2025. DOI : 10.1016/j.jmgm.2024.108932.Aerolysin Nanopore Structures Revealed at High Resolution in a Lipid Environment
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 2025. DOI : 10.1021/jacs.4c14288.BPS2025 - Identification of cyanotoxins with a biological nanopore
Biophysical Journal. 2025. DOI : 10.1016/j.bpj.2024.11.156.ACAD10 and ACAD11 enable mammalian 4-hydroxy acid lipid catabolism
Nature Structural & Molecular Biology. 2025. DOI : 10.1038/s41594-025-01596-4.2024
Virus adaptation to heparan sulfate comes with capsid stability tradeoff
eLife. 2024. DOI : 10.7554/eLife.98441.OXA β-lactamases from Acinetobacter spp. are membrane bound and secreted into outer membrane vesicles
MBIO. 2024. DOI : 10.1128/mbio.03343-24.G–PLIP: Knowledge graph neural network for structure-free protein–ligand bioactivity prediction
Computational and Structural Biotechnology Journal. 2024. DOI : 10.1016/j.csbj.2024.06.029.Missense variants in CMS22 patients reveal that PREPL has both enzymatic and nonenzymatic functions
JCI Insight. 2024. DOI : 10.1172/jci.insight.179276.A look beyond the QR code of SNARE proteins
Protein science : a publication of the Protein Society. 2024. DOI : 10.1002/pro.5158.Differential Effects of Post-translational Modifications on the Membrane Interaction of Huntingtin Protein
Acs Chemical Neuroscience. 2024. DOI : 10.1021/acschemneuro.4c00091.PeSTo-Carbs: Geometric Deep Learning for Prediction of Protein-Carbohydrate Binding Interfaces
Journal of Chemical Theory and Computation. 2024. DOI : 10.1021/acs.jctc.3c01145.A humoral stress response protects Drosophila tissues from antimicrobial peptides
Current Biology. 2024. DOI : 10.1016/j.cub.2024.02.049.2023
Deep Learning-Assisted Single-Molecule Detection of Protein Post-translational Modifications with a Biological Nanopore
Acs Nano. 2023. DOI : 10.1021/acsnano.3c08623.Bicc1 ribonucleoprotein complexes specifying organ laterality are licensed by ANKS6-induced structural remodeling of associated ANKS3
Plos Biology. 2023. DOI : 10.1371/journal.pbio.3002302.Structural mechanism of mitochondrial membrane remodelling by human OPA1
Nature. 2023. DOI : 10.1038/s41586-023-06441-6.2022
Article Structure and functionality of a multimeric human COQ7:COQ9 complex
Molecular Cell. 2022. DOI : 10.1016/j.molcel.2022.10.003.Online tools to easily build virtual molecular models for display in augmented and virtual reality on the web
Journal Of Molecular Graphics & Modelling. 2022. DOI : 10.1016/j.jmgm.2022.108164.Ultrasensitive Label-Free Detection of Protein–Membrane Interaction Exemplified by Toxin-Liposome Insertion
The Journal of Physical Chemistry Letters. 2022. DOI : 10.1021/acs.jpclett.1c04011.Visualization, Interactive Handling and Simulation of Molecules in Commodity Augmented Reality in Web Browsers Using moleculARweb's Virtual Modeling Kits
Chimia. 2022. DOI : 10.2533/chimia.2022.145.2021
Prolyl endopeptidase-like is a (thio)esterase involved in mitochondrial respiratory chain function
Iscience. 2021. DOI : 10.1016/j.isci.2021.103460.BET1 variants establish impaired vesicular transport as a cause for muscular dystrophy with epilepsy
Embo Molecular Medicine. 2021. DOI : 10.15252/emmm.202013787.S-acylation controls SARS-CoV-2 membrane lipid organization and enhances infectivity
Developmental Cell. 2021. DOI : 10.1016/j.devcel.2021.09.016.Democratizing interactive, immersive experiences for science education with WebXR
Nature Computational Science. 2021. DOI : 10.1038/s43588-021-00142-8.Specific Protein-Membrane Interactions Promote Packaging of Metallo-beta-Lactamases into Outer Membrane Vesicles
Antimicrobial Agents And Chemotherapy. 2021. DOI : 10.1128/AAC.00507-21.Investigating Crosstalk Among PTMs Provides Novel Insight Into the Structural Basis Underlying the Differential Effects of Nt17 PTMs on Mutant Httex1 Aggregation
Frontiers in Molecular Biosciences. 2021. DOI : 10.3389/fmolb.2021.686086.MoleculARweb: A Web Site for Chemistry and Structural Biology Education through Interactive Augmented Reality out of the Box in Commodity Devices
Journal Of Chemical Education. 2021. DOI : 10.1021/acs.jchemed.1c00179.CLoNe: automated clustering based on local density neighborhoods for application to biomolecular structural ensembles
Bioinformatics. 2021. DOI : 10.1093/bioinformatics/btaa742.Palmitoylated acyl protein thioesterase APT2 deforms membranes to extract substrate acyl chains
Nature Chemical Biology. 2021. DOI : 10.1038/s41589-021-00753-2.Structural basis for recognition of bacterial cell wall teichoic acid by pseudo-symmetric SH3b-like repeats of a viral peptidoglycan hydrolase
Chemical Science. 2021. DOI : 10.1039/d0sc04394j.Extensive tissue-specific expression variation and novel regulators underlying circadian behavior
Science Advances. 2021. DOI : 10.1126/sciadv.abc3781.2020
Aerolysin nanopores decode digital information stored in tailored macromolecular analytes
Science Advances. 2020. DOI : 10.1126/sciadv.abc2661.The Human RNA Helicase DDX21 Presents a Dimerization Interface Necessary for Helicase Activity
iScience. 2020. DOI : 10.1016/j.isci.2020.101811.Molecular Bases of the Membrane Association Mechanism Potentiating Antibiotic Resistance by New Delhi Metallo-beta-lactamase 1
Acs Infectious Diseases. 2020. DOI : 10.1021/acsinfecdis.0c00341.The Polyglutamine Expansion at the N-Terminal of Huntingtin Protein Modulates the Dynamic Configuration and Phosphorylation of the C-Terminal HEAT Domain
Structure. 2020. DOI : 10.1016/j.str.2020.06.008.Editorial: Multiscale Modeling From Macromolecules to Cell: Opportunities and Challenges of Biomolecular Simulations
Frontiers In Molecular Biosciences. 2020. DOI : 10.3389/fmolb.2020.00194.Will Cryo-Electron Microscopy Shift the Current Paradigm in Protein Structure Prediction?
Journal Of Chemical Information And Modeling. 2020. DOI : 10.1021/acs.jcim.0c00177.Ligand Binding to the Collagen VI Receptor Triggers a Talin-to-RhoA Switch that Regulates Receptor Endocytosis
Developmental Cell. 2020. DOI : 10.1016/j.devcel.2020.04.015.Btk SH2-kinase interface is critical for allosteric kinase activation and its targeting inhibits B-cell neoplasms
Nature Communications. 2020. DOI : 10.1038/s41467-020-16128-5.About the need to make computational models of biological macromolecules available and discoverable
Bioinformatics. 2020. DOI : 10.1093/bioinformatics/btaa086.Salt enhances the thermostability of enteroviruses by stabilizing capsid protein interfaces
Journal of Virology. 2020. DOI : 10.1128/JVI.02176-19.2019
An experiment-informed signal transduction model for the role of the Staphylococcus aureus MecR1 protein in beta-lactam resistance
Scientific Reports. 2019. DOI : 10.1038/s41598-019-55923-z.Transmembrane Prolines Mediate Signal Sensing and Decoding in Bacillus subtilis DesK Histidine Kinase
mBio. 2019. DOI : 10.1128/mBio.02564-19.Single-molecule sensing of peptides and nucleic acids by engineered aerolysin nanopores
Nature Communications. 2019. DOI : 10.1038/s41467-019-12690-9.Modelling structures in cryo-EM maps
Current Opinion In Structural Biology. 2019. DOI : 10.1016/j.sbi.2019.05.024.Editorial overview: The future after the cryo-EM resolution revolution
Current Opinion In Structural Biology. 2019. 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. DOI : 10.1002/prot.25787.Active Site-Induced Evolutionary Constraints Follow Fold Polarity Principles in Soluble Globular Enzymes
Molecular Biology And Evolution. 2019. DOI : 10.1093/molbev/msz096.KAP1 is an antiparallel dimer with a functional asymmetry
Life Science Alliance. 2019. DOI : 10.26508/lsa.201900349.An Isoprene Lipid-Binding Protein Promotes Eukaryotic Coenzyme Q Biosynthesis
Molecular Cell. 2019. DOI : 10.1016/j.molcel.2018.11.033.2017
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. DOI : 10.1093/nar/gkw128.Cryo-EM structure of aerolysin variants reveals a novel protein fold and the pore-formation process
Nature Communications. 2016. DOI : 10.1038/ncomms12062.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.Cerebellar Ataxia and Coenzyme Q Deficiency through Loss of Unorthodox Kinase Activity
Molecular Cell. 2016. DOI : 10.1016/j.molcel.2016.06.030.Olfactory receptor pseudo-pseudogenes
Nature. 2016. DOI : 10.1038/nature19824.Molecular Effects of Concentrated Solutes on Protein Hydration, Dynamics, and Electrostatics
Biophysical Journal. 2016. DOI : 10.1016/j.bpj.2016.07.011.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.Effect of the Synaptic Plasma Membrane on the Stability of the Amyloid Precursor Protein Homodimer
The Journal of Physical Chemistry Letters. 2016. DOI : 10.1021/acs.jpclett.6b01721.A rheostat mechanism governs the bifurcation of carbon flux in mycobacteria
Nature Communications. 2016. DOI : 10.1038/ncomms12527.Immobilization of the N-terminal helix stabilizes prefusion paramyxovirus fusion proteins
Proceedings Of The National Academy Of Sciences Of The United States Of America (PNAS). 2016. DOI : 10.1073/pnas.1608349113.2015
Lipid Builder: A Framework To Build Realistic Models for Biological Membranes
Journal Of Chemical Information And Modeling. 2015. DOI : 10.1021/acs.jcim.5b00501.The importance of dynamics in integrative modeling of supramolecular assemblies
Current Opinion In Structural Biology. 2015. DOI : 10.1016/j.sbi.2015.02.018.How Structural and Physicochemical Determinants Shape Sequence Constraints in a Functional Enzyme
Plos One. 2015. DOI : 10.1371/journal.pone.0118684.Assessing the potential of atomistic molecular dynamics simulations to probe reversible protein-protein recognition and binding
Scientific Reports. 2015. DOI : 10.1038/srep10549.A coiled coil switch mediates cold sensing by the thermosensory protein DesK
Molecular Microbiology. 2015. DOI : 10.1111/mmi.13118.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.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.2014
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.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 (PNAS). 2014. DOI : 10.1073/pnas.1321165111.Reaction Mechanism and Catalytic Fingerprint of Allantoin Racemase
The Journal of Physical Chemistry B. 2014. DOI : 10.1021/jp411786z.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.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.Dissecting the Effects of Concentrated Carbohydrate Solutions on Protein Diffusion, Hydration, and Internal Dynamics
The 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
JBIC Journal of Biological Inorganic Chemistry. 2014. DOI : 10.1007/s00775-014-1108-7.2013
Cardiolipin Models for Molecular Simulations of Bacterial and Mitochondrial Membranes
Journal of Chemical Theory and Computation. 2013. DOI : 10.1021/ct300590v.TAL Effectors Specificity Stems from Negative Discrimination
Plos One. 2013. DOI : 10.1371/journal.pone.0080261.Macromolecular Symmetric Assembly Prediction Using Swarm Intelligence Dynamic Modeling
Structure. 2013. DOI : 10.1016/j.str.2013.05.014.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.Electrostatic-Consistent Coarse-Grained Potentials for Molecular Simulations of Proteins
Journal of Chemical Theory and Computation. 2013. DOI : 10.1021/ct400137q.Molecular assembly of the aerolysin pore reveals a swirling membrane-insertion mechanism
Nature Chemical Biology. 2013. DOI : 10.1038/Nchembio.1312.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.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.In situ structural analysis of the Yersinia enterocolitica injectisome
Elife. 2013. DOI : 10.7554/eLife.00792.All-atom simulations of crowding effects on ubiquitin dynamics
Physical Biology. 2013. DOI : 10.1088/1478-3975/10/4/045006.2012
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.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.2012.15.2011
An introduction to quantum chemical methods applied to drug design
Frontiers in Bioscience. 2011. DOI : 10.2741/311.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.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.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.2010
Length control of the injectisome needle requires only one molecule of Yop secretion protein P (YscP)
Proceedings Of The National Academy Of Sciences Of The United States Of America (PNAS). 2010. DOI : 10.1073/pnas.1006985107.Understanding the Effect of Magnesium Ion Concentration on the Catalytic Activity of Ribonuclease H through Computation: Does a Third Metal Binding Site Modulate Endonuclease Catalysis?
Journal of the American Chemical Society. 2010. DOI : 10.1021/ja102933y.A nonradial coarse-grained potential for proteins produces naturally stable secondary structure elements
Journal of Chemical Theory and Computation. 2010. DOI : 10.1021/ct900457z.2009
The helical content of the YscP molecular ruler determines the length of the Yersinia injectisome
Molecular microbiology. 2009. DOI : 10.1111/j.1365-2958.2008.06556.x.Challenges and perspectives in biomolecular simulations: from atomistic picture to multiscale modeling
CHIMIA. 2009. DOI : 10.2533/chimia.2009.14.Common mechanistic features among metallo-β-lactamases: a computational study of Aeromonas hydrophila CphA enzyme
Journal of Biological Chemistry. 2009. DOI : 10.1074/jbc.M109.049502.Unraveling the Catalytic Pathway of Metalloenzyme Farnesyltransferase through QM/MM Computation
Journal of Chemical Theory and Computation. 2009. DOI : 10.1021/ct8004722.Molecular dynamics calculations suggest a conduction mechanism for the M2 proton channel from influenza A virus
Proceedings Of The National Academy Of Sciences Of The United States Of America (PNAS). 2009. DOI : 10.1073/pnas.0811720106.2008
Topologically based multipolar reconstruction of electrostatic interactions in multiscale simulations of proteins
Journal of Chemical Theory and Computation. 2008. DOI : 10.1021/ct800122x.Solution NMR structure of a designed metalloprotein and complementary molecular dynamics refinement
Structure. 2008. DOI : 10.1016/j.str.2007.11.011.Phosphodiester Cleavage in Ribonuclease H Occurs via an Associative Two-Metal-Aided Catalytic Mechanism
Journal of the American Chemical Society. 2008. DOI : 10.1021/ja8005786.2007
Role of zinc content on the catalytic efficiency of B1 metallo beta-lactamases
J Am Chem Soc. 2007. DOI : 10.1021/ja0657556.Proton shuttles and phosphatase activity in soluble epoxide hydrolase
J Am Chem Soc. 2007. DOI : 10.1021/ja066150c.The metallo-beta-lactamase GOB is a mono-Zn(II) enzyme with a novel active site
Journal of Biological Chemistry. 2007. DOI : 10.1074/jbc.M700467200.Modeling the charge distribution at metal sites in proteins for molecular dynamics simulations
J Struct Biol. 2007. DOI : 10.1016/j.jsb.2006.10.019.Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations
Current Opinion in Structural Biology. 2007. DOI : 10.1016/j.sbi.2007.03.018.2006
Polarization effects and charge transfer in the KcsA potassium channel
Biophysical Chemistry. 2006. DOI : 10.1016/j.bpc.2006.04.008.2005
Solute-solvent charge transfer in aqueous solution
ChemPhysChem. 2005. DOI : 10.1002/cphc.200500039.2004
Water-Assisted Reaction Mechanism of Monozinc b-Lactamases
Journal of the American Chemical Society. 2004. DOI : 10.1021/ja048071b.Substrate binding to mononuclear metallo-beta-lactamase from Bacillus cereus
Proteins. 2004. DOI : 10.1002/prot.10554.2003
Protonation state of Asp120 in the binuclear active site of the metallo-beta-lactamase from Bacteroides fragilis
Inorg Chem. 2003. DOI : 10.1021/ic026059j.2002
Structural determinants and hydrogen-bond network of the mononuclear zinc(II)-beta-lactamase active site
J Biol Inorg Chem. 2002. DOI : 10.1007/s00775-002-0346-2.2001
Ser133 phosphate-KIX interactions in the CREB-CBP complex: an ab initio molecular dynamics study
Eur Biophysical Journal. 2001. DOI : 10.1007/s002490000112.Conference Papers
2023
Using integrative structural biology for the identification of novel aerolysin-like pore forming toxins for nanopore sensing
2023. p. S116 - S116.Structural characterization of Prolyl endopeptidase-like, a mitochondrial protein involved in congenital myasthenic syndrome-22
2023. p. S109 - S109.2022
The role of PTM crosstalks in Httex1 structure, aggregation and membrane interaction
2022. p. 38 - 38. DOI : 10.1016/j.bpj.2021.11.2495.Bacterial nanopores open the future of data storage
2022. International Electron Devices Meeting (IEDM), San Francisco, CA, Dec 03-07, 2022. DOI : 10.1109/IEDM45625.2022.10019421.2021
Decoding Digital Information Stored in Polymer by Nanopore
2021. p. 98A - 98A. DOI : 10.1016/j.bpj.2020.11.802.2019
Overcoming the hydrophobic barrier of the membrane: The role of COQ9 in promoting coenzyme Q biosynthesis
2019. 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. 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. 256th National Meeting and Exposition of the American-Chemical-Society (ACS) - Nanoscience, Nanotechnology and Beyond, Boston, MA, Aug 19-23, 2018.2014
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. DOI : 10.1016/j.bpj.2013.11.377.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. DOI : 10.1016/j.bpj.2013.11.872.2013
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.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. DOI : 10.1016/j.bpj.2012.11.1278.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. DOI : 10.1016/j.bpj.2012.11.2205.2011
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
A four-helix bundle model for E-coli PhoO transmembrane domain
2010. 35th Congress of the Federation-of-European-Biochemical-Societies, Gothenburg, SWEDEN, Jun 26-Jul 01, 2010. p. 193 - 194.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.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.Shedding a new light on photolyases: Accurate molecular modeling as a tool for undestanding DNA repairing enzymes
2010. p. 20 - PHYS.Coarse-graining electrostatics in multiscale molecular simulations
2010. p. 391 - COMP.A model for the assembly and activation process of the pore-forming toxin Aerolysin
2010. 35th Congress of the Federation-of-European-Biochemical-Societies, Gothenburg, SWEDEN, Jun 26-Jul 01, 2010. p. 194 - 194.Assembly and function of large Gram-negative bacterial machines studied by molecular simulation integrated with experimental data
2010. p. 425 - COMP.2008
Unraveling the enzymatic mechanism of the protein farnesyltransferase: A QM/MM study
2008. 236th National Meeting of the American-Chemical-Society, Philadelphia, PA, Aug 17-21, 2008. p. 258 - COMP.Topologically-based multipolar reconstruction of electrostatic interactions in multiscale simulations of proteins
2008. 236th National Meeting of the American-Chemical-Society, Philadelphia, PA, Aug 17-21, 2008. p. 57 - COMP.Reviews
2022
Biological nanopores for single-molecule sensing
iScience. 2022. DOI : 10.1016/j.isci.2022.104145.2021
State-of-the-art web services for de novo protein structure prediction
Briefings In Bioinformatics. 2021. DOI : 10.1093/bib/bbaa139.2016
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
2024
Study of disease-associated proteins using integrative structural biology: the case of GOLPH3 and PREPL
Lausanne, EPFL, 2024. DOI : 10.5075/epfl-thesis-10807.Exploring ion and analyte transport in beta-barrel forming biological nanopores
Lausanne, EPFL, 2024. DOI : 10.5075/epfl-thesis-10672.Label-Efficient Deep Learning Methods for Event Detection, Object Segmentation and Cell Tracking in Biological Microscopy Images
Lausanne, EPFL, 2024. DOI : 10.5075/epfl-thesis-11163.Investigating the intra-molecular and inter-molecular effects of post-translational modifications on intrinsically disordered protein regions and structured protein regions
Lausanne, EPFL, 2024. DOI : 10.5075/epfl-thesis-10530.2023
A Geometric Transformer for Structural Biology: Development and Applications of the Protein Structure Transformer
Lausanne, EPFL, 2023. DOI : 10.5075/epfl-thesis-10309.2021
New Methods for the Integrative Dynamic Modeling of Biomolecular Structures
Lausanne, EPFL, 2021. DOI : 10.5075/epfl-thesis-8284.2020
Characterization of Protein-Membrane Interfaces through a Synergistic Computational-Experimental Approach
Lausanne, EPFL, 2020. DOI : 10.5075/epfl-thesis-7278.Beneficial axis of the renin-angiotensin system: from applications to drug discovery
Lausanne, EPFL, 2020. DOI : 10.5075/epfl-thesis-10223.2019
Structural and functional characterisation of the KRAB-domain associated protein 1
Lausanne, EPFL, 2019. DOI : 10.5075/epfl-thesis-7154.Characterization of Coenzyme Q Biosynthesis Proteins through Integrative Modeling at the Protein-Membrane Interface
Lausanne, EPFL, 2019. DOI : 10.5075/epfl-thesis-9641.Exploring on Protein-DNA interactions
Lausanne, EPFL, 2019. DOI : 10.5075/epfl-thesis-9426.2018
Structural and functional analysis of host attachment proteins from contractile injection systems
Lausanne, EPFL, 2018. DOI : 10.5075/epfl-thesis-8267.2017
Evaluation of oxidation-sensitive polymersomes as vaccine nanocarriers to enhance humoral responses against arenavirus envelope glycoproteins
Lausanne, EPFL, 2017. DOI : 10.5075/epfl-thesis-8193.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.Working Papers
2025
MolecularWeb Democratizes Web-Based, Immersive, Multiuser Molecular Graphics And Modeling
2025Sub-Nanomolar Detection and Discrimination of Microcystin Congeners Using Aerolysin Nanopores
2025Practical outcomes from CASP16 for users in need of biomolecular structure prediction
2025Posters
2022
Identification of single amino acid with engineered aerolysin nanopores
Single-Molecule Protein Sequencing 3 (SMPS3), Delft, The Netherlands, October 31-November 3, 2022.Talks
2022
Bacterial proteolytic enzymes as biological scissors in the fate of enteroviruses in natural ecosystems
Swiss Society for Microbiology Annual Meeting - SMM 2022, Lausanne, Switzerland, August 30 - September 1, 2022.Mechanisms of inactivation of non-enveloped viruses in natural ecosystems: bacterial proteolytic enzymes as biological scissors in the fate of enteroviruses
7th International Society for Food and Environmental Virology Conference - ISFEV2020, Santiago de Compostela, Spain, May 16-20, 2022.2018
Structural characterization of thermoresistant enteroviruses
ISFEV 2018 - 6th Food and Environmental Virology Conference, Tempe, Arizona, USA, October 7-10, 2018.Patents
2025
Uses of aerolysin nanopores
WO2025003492 . 2025.2024
Mutant aerolysin and uses thereof
EP4362028 . 2024.2022
Mutant aerolysin and uses thereof
US11845779 ; US2022127310 . 2022.Systems and methods for digital information decoding and data storage in hybrid macromolecules
US2023377649 ; EP4222742 ; WO2022069022 . 2022.2024
Dissecting the membrane association mechanism of aerolysin pore at femtomolar concentrations using water as a probe
2024.Journal Articles
2026
Asymmetric envelope surface disposition of secreted protein YjbI controls bimodal antibiotic susceptibilities in C. crescentus
The EMBO Journal. 2026. DOI : 10.1038/s44318-025-00668-x.ModelCIF Update: Supporting Emerging Classes of Computational Macromolecular Models
Journal of molecular biology. 2026. DOI : 10.1016/j.jmb.2026.169658.2025
Wide-field fluorescence lifetime imaging of single molecules with a gated single-photon camera
Light, science & applications. 2025. DOI : 10.1038/s41377-025-01901-2.Lumen charge governs gated ion transport in β-barrel nanopores
Nature Nanotechnology. 2025. DOI : 10.1038/s41565-025-02052-6.Cardiolipin dynamics promote membrane remodeling by mitochondrial OPA1
Nature Communications. 2025. DOI : 10.1038/s41467-025-63813-4.Structure of the Huntingtin F-actin complex reveals its role in cytoskeleton organization
Science Advances. 2025. DOI : 10.1126/sciadv.adw4124.Exploring New Nanopore Sensors from the Aerolysin Family
Small. 2025. DOI : 10.1002/smll.202501219.Analysis of Integrator-Differentiator Transimpedance Amplifiers: Speed and Gain Tradeoff Introduced by Parasitic Capacitances
IEEE Transactions on Instrumentation and Measurement. 2025. DOI : 10.1109/tim.2025.3573761.The HP1 box of KAP1 organizes HP1α for silencing of endogenous retroviral elements in embryonic stem cells
Nature Communications. 2025. DOI : 10.1038/s41467-025-60279-2.The Need to Implement Fair Principles in Biomolecular Simulations
NATURE METHODS. 2025. DOI : 10.1038/s41592-025-02635-0.MolecularWebXR: Multiuser discussions in chemistry and biology through immersive and inclusive augmented and virtual reality
Journal of molecular graphics & modelling. 2025. DOI : 10.1016/j.jmgm.2024.108932.Aerolysin Nanopore Structures Revealed at High Resolution in a Lipid Environment
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 2025. DOI : 10.1021/jacs.4c14288.BPS2025 - Identification of cyanotoxins with a biological nanopore
Biophysical Journal. 2025. DOI : 10.1016/j.bpj.2024.11.156.ACAD10 and ACAD11 enable mammalian 4-hydroxy acid lipid catabolism
Nature Structural & Molecular Biology. 2025. DOI : 10.1038/s41594-025-01596-4.2024
Virus adaptation to heparan sulfate comes with capsid stability tradeoff
eLife. 2024. DOI : 10.7554/eLife.98441.OXA β-lactamases from Acinetobacter spp. are membrane bound and secreted into outer membrane vesicles
MBIO. 2024. DOI : 10.1128/mbio.03343-24.G–PLIP: Knowledge graph neural network for structure-free protein–ligand bioactivity prediction
Computational and Structural Biotechnology Journal. 2024. DOI : 10.1016/j.csbj.2024.06.029.Missense variants in CMS22 patients reveal that PREPL has both enzymatic and nonenzymatic functions
JCI Insight. 2024. DOI : 10.1172/jci.insight.179276.A look beyond the QR code of SNARE proteins
Protein science : a publication of the Protein Society. 2024. DOI : 10.1002/pro.5158.Differential Effects of Post-translational Modifications on the Membrane Interaction of Huntingtin Protein
Acs Chemical Neuroscience. 2024. DOI : 10.1021/acschemneuro.4c00091.PeSTo-Carbs: Geometric Deep Learning for Prediction of Protein-Carbohydrate Binding Interfaces
Journal of Chemical Theory and Computation. 2024. DOI : 10.1021/acs.jctc.3c01145.A humoral stress response protects Drosophila tissues from antimicrobial peptides
Current Biology. 2024. DOI : 10.1016/j.cub.2024.02.049.2023
Deep Learning-Assisted Single-Molecule Detection of Protein Post-translational Modifications with a Biological Nanopore
Acs Nano. 2023. DOI : 10.1021/acsnano.3c08623.Bicc1 ribonucleoprotein complexes specifying organ laterality are licensed by ANKS6-induced structural remodeling of associated ANKS3
Plos Biology. 2023. DOI : 10.1371/journal.pbio.3002302.Structural mechanism of mitochondrial membrane remodelling by human OPA1
Nature. 2023. DOI : 10.1038/s41586-023-06441-6.2022
Article Structure and functionality of a multimeric human COQ7:COQ9 complex
Molecular Cell. 2022. DOI : 10.1016/j.molcel.2022.10.003.Online tools to easily build virtual molecular models for display in augmented and virtual reality on the web
Journal Of Molecular Graphics & Modelling. 2022. DOI : 10.1016/j.jmgm.2022.108164.Ultrasensitive Label-Free Detection of Protein–Membrane Interaction Exemplified by Toxin-Liposome Insertion
The Journal of Physical Chemistry Letters. 2022. DOI : 10.1021/acs.jpclett.1c04011.Visualization, Interactive Handling and Simulation of Molecules in Commodity Augmented Reality in Web Browsers Using moleculARweb's Virtual Modeling Kits
Chimia. 2022. DOI : 10.2533/chimia.2022.145.2021
Prolyl endopeptidase-like is a (thio)esterase involved in mitochondrial respiratory chain function
Iscience. 2021. DOI : 10.1016/j.isci.2021.103460.BET1 variants establish impaired vesicular transport as a cause for muscular dystrophy with epilepsy
Embo Molecular Medicine. 2021. DOI : 10.15252/emmm.202013787.S-acylation controls SARS-CoV-2 membrane lipid organization and enhances infectivity
Developmental Cell. 2021. DOI : 10.1016/j.devcel.2021.09.016.Democratizing interactive, immersive experiences for science education with WebXR
Nature Computational Science. 2021. DOI : 10.1038/s43588-021-00142-8.Specific Protein-Membrane Interactions Promote Packaging of Metallo-beta-Lactamases into Outer Membrane Vesicles
Antimicrobial Agents And Chemotherapy. 2021. DOI : 10.1128/AAC.00507-21.Investigating Crosstalk Among PTMs Provides Novel Insight Into the Structural Basis Underlying the Differential Effects of Nt17 PTMs on Mutant Httex1 Aggregation
Frontiers in Molecular Biosciences. 2021. DOI : 10.3389/fmolb.2021.686086.MoleculARweb: A Web Site for Chemistry and Structural Biology Education through Interactive Augmented Reality out of the Box in Commodity Devices
Journal Of Chemical Education. 2021. DOI : 10.1021/acs.jchemed.1c00179.Palmitoylated acyl protein thioesterase APT2 deforms membranes to extract substrate acyl chains
Nature Chemical Biology. 2021. DOI : 10.1038/s41589-021-00753-2.CLoNe: automated clustering based on local density neighborhoods for application to biomolecular structural ensembles
Bioinformatics. 2021. DOI : 10.1093/bioinformatics/btaa742.Structural basis for recognition of bacterial cell wall teichoic acid by pseudo-symmetric SH3b-like repeats of a viral peptidoglycan hydrolase
Chemical Science. 2021. DOI : 10.1039/d0sc04394j.Extensive tissue-specific expression variation and novel regulators underlying circadian behavior
Science Advances. 2021. DOI : 10.1126/sciadv.abc3781.2020
Aerolysin nanopores decode digital information stored in tailored macromolecular analytes
Science Advances. 2020. DOI : 10.1126/sciadv.abc2661.The Human RNA Helicase DDX21 Presents a Dimerization Interface Necessary for Helicase Activity
iScience. 2020. DOI : 10.1016/j.isci.2020.101811.Molecular Bases of the Membrane Association Mechanism Potentiating Antibiotic Resistance by New Delhi Metallo-beta-lactamase 1
Acs Infectious Diseases. 2020. DOI : 10.1021/acsinfecdis.0c00341.The Polyglutamine Expansion at the N-Terminal of Huntingtin Protein Modulates the Dynamic Configuration and Phosphorylation of the C-Terminal HEAT Domain
Structure. 2020. DOI : 10.1016/j.str.2020.06.008.Editorial: Multiscale Modeling From Macromolecules to Cell: Opportunities and Challenges of Biomolecular Simulations
Frontiers In Molecular Biosciences. 2020. DOI : 10.3389/fmolb.2020.00194.Will Cryo-Electron Microscopy Shift the Current Paradigm in Protein Structure Prediction?
Journal Of Chemical Information And Modeling. 2020. DOI : 10.1021/acs.jcim.0c00177.Ligand Binding to the Collagen VI Receptor Triggers a Talin-to-RhoA Switch that Regulates Receptor Endocytosis
Developmental Cell. 2020. DOI : 10.1016/j.devcel.2020.04.015.Btk SH2-kinase interface is critical for allosteric kinase activation and its targeting inhibits B-cell neoplasms
Nature Communications. 2020. DOI : 10.1038/s41467-020-16128-5.About the need to make computational models of biological macromolecules available and discoverable
Bioinformatics. 2020. DOI : 10.1093/bioinformatics/btaa086.Salt enhances the thermostability of enteroviruses by stabilizing capsid protein interfaces
Journal of Virology. 2020. DOI : 10.1128/JVI.02176-19.2019
An experiment-informed signal transduction model for the role of the Staphylococcus aureus MecR1 protein in beta-lactam resistance
Scientific Reports. 2019. DOI : 10.1038/s41598-019-55923-z.Transmembrane Prolines Mediate Signal Sensing and Decoding in Bacillus subtilis DesK Histidine Kinase
mBio. 2019. DOI : 10.1128/mBio.02564-19.Single-molecule sensing of peptides and nucleic acids by engineered aerolysin nanopores
Nature Communications. 2019. DOI : 10.1038/s41467-019-12690-9.Editorial overview: The future after the cryo-EM resolution revolution
Current Opinion In Structural Biology. 2019. DOI : 10.1016/j.sbi.2019.07.007.Modelling structures in cryo-EM maps
Current Opinion In Structural Biology. 2019. DOI : 10.1016/j.sbi.2019.05.024.A further leap of improvement in tertiary structure prediction in CASP13 prompts new routes for future assessments
Proteins-Structure Function And Bioinformatics. 2019. DOI : 10.1002/prot.25787.Active Site-Induced Evolutionary Constraints Follow Fold Polarity Principles in Soluble Globular Enzymes
Molecular Biology And Evolution. 2019. DOI : 10.1093/molbev/msz096.KAP1 is an antiparallel dimer with a functional asymmetry
Life Science Alliance. 2019. DOI : 10.26508/lsa.201900349.An Isoprene Lipid-Binding Protein Promotes Eukaryotic Coenzyme Q Biosynthesis
Molecular Cell. 2019. DOI : 10.1016/j.molcel.2018.11.033.2017
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. DOI : 10.1093/nar/gkw128.A rheostat mechanism governs the bifurcation of carbon flux in mycobacteria
Nature Communications. 2016. DOI : 10.1038/ncomms12527.Effect of the Synaptic Plasma Membrane on the Stability of the Amyloid Precursor Protein Homodimer
The 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(vol 1, 242, 2016)
Bmc Bioinformatics. 2016. DOI : 10.1186/s12859-016-1315-z.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.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.Immobilization of the N-terminal helix stabilizes prefusion paramyxovirus fusion proteins
Proceedings Of The National Academy Of Sciences Of The United States Of America (PNAS). 2016. DOI : 10.1073/pnas.1608349113.Cryo-EM structure of aerolysin variants reveals a novel protein fold and the pore-formation process
Nature Communications. 2016. DOI : 10.1038/ncomms12062.Olfactory receptor pseudo-pseudogenes
Nature. 2016. DOI : 10.1038/nature19824.2015
Lipid Builder: A Framework To Build Realistic Models for Biological Membranes
Journal Of Chemical Information And Modeling. 2015. DOI : 10.1021/acs.jcim.5b00501.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.How Structural and Physicochemical Determinants Shape Sequence Constraints in a Functional Enzyme
Plos One. 2015. DOI : 10.1371/journal.pone.0118684.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.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/gkv172.2014
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.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.Dissecting the Effects of Concentrated Carbohydrate Solutions on Protein Diffusion, Hydration, and Internal Dynamics
The Journal of Physical Chemistry B. 2014. DOI : 10.1021/jp4126705.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
The Journal of Physical Chemistry B. 2014. DOI : 10.1021/jp411786z.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 (PNAS). 2014. DOI : 10.1073/pnas.1321165111.Molecular dynamics simulations of apocupredoxins: insights into the formation and stabilization of copper sites under entatic control
JBIC Journal of Biological Inorganic Chemistry. 2014. DOI : 10.1007/s00775-014-1108-7.2013
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.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.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.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.Macromolecular Symmetric Assembly Prediction Using Swarm Intelligence Dynamic Modeling
Structure. 2013. DOI : 10.1016/j.str.2013.05.014.In situ structural analysis of the Yersinia enterocolitica injectisome
Elife. 2013. DOI : 10.7554/eLife.00792.Molecular assembly of the aerolysin pore reveals a swirling membrane-insertion mechanism
Nature Chemical Biology. 2013. DOI : 10.1038/Nchembio.1312.Electrostatic-Consistent Coarse-Grained Potentials for Molecular Simulations of Proteins
Journal of Chemical Theory and Computation. 2013. DOI : 10.1021/ct400137q.Cardiolipin Models for Molecular Simulations of Bacterial and Mitochondrial Membranes
Journal of Chemical Theory and Computation. 2013. DOI : 10.1021/ct300590v.All-atom simulations of crowding effects on ubiquitin dynamics
Physical Biology. 2013. DOI : 10.1088/1478-3975/10/4/045006.TAL Effectors Specificity Stems from Negative Discrimination
Plos One. 2013. DOI : 10.1371/journal.pone.0080261.2012
Palmitoylated calnexin is a key component of the ribosome-translocon complex
Embo Journal. 2012. DOI : 10.1038/emboj.2012.15.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.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
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.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.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.An introduction to quantum chemical methods applied to drug design
Frontiers in Bioscience. 2011. DOI : 10.2741/311.2010
A nonradial coarse-grained potential for proteins produces naturally stable secondary structure elements
Journal of Chemical Theory and Computation. 2010. DOI : 10.1021/ct900457z.Understanding the Effect of Magnesium Ion Concentration on the Catalytic Activity of Ribonuclease H through Computation: Does a Third Metal Binding Site Modulate Endonuclease Catalysis?
Journal of the American Chemical Society. 2010. DOI : 10.1021/ja102933y.Length control of the injectisome needle requires only one molecule of Yop secretion protein P (YscP)
Proceedings Of The National Academy Of Sciences Of The United States Of America (PNAS). 2010. DOI : 10.1073/pnas.1006985107.2009
Molecular dynamics calculations suggest a conduction mechanism for the M2 proton channel from influenza A virus
Proceedings Of The National Academy Of Sciences Of The United States Of America (PNAS). 2009. DOI : 10.1073/pnas.0811720106.Unraveling the Catalytic Pathway of Metalloenzyme Farnesyltransferase through QM/MM Computation
Journal of Chemical Theory and Computation. 2009. DOI : 10.1021/ct8004722.Common mechanistic features among metallo-β-lactamases: a computational study of Aeromonas hydrophila CphA enzyme
Journal of Biological Chemistry. 2009. DOI : 10.1074/jbc.M109.049502.The helical content of the YscP molecular ruler determines the length of the Yersinia injectisome
Molecular microbiology. 2009. DOI : 10.1111/j.1365-2958.2008.06556.x.Challenges and perspectives in biomolecular simulations: from atomistic picture to multiscale modeling
CHIMIA. 2009. DOI : 10.2533/chimia.2009.14.2008
Solution NMR structure of a designed metalloprotein and complementary molecular dynamics refinement
Structure. 2008. DOI : 10.1016/j.str.2007.11.011.Phosphodiester Cleavage in Ribonuclease H Occurs via an Associative Two-Metal-Aided Catalytic Mechanism
Journal of the American Chemical Society. 2008. DOI : 10.1021/ja8005786.Topologically based multipolar reconstruction of electrostatic interactions in multiscale simulations of proteins
Journal of Chemical Theory and Computation. 2008. DOI : 10.1021/ct800122x.2007
The metallo-beta-lactamase GOB is a mono-Zn(II) enzyme with a novel active site
Journal of Biological Chemistry. 2007. DOI : 10.1074/jbc.M700467200.Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations
Current Opinion in Structural Biology. 2007. DOI : 10.1016/j.sbi.2007.03.018.Proton shuttles and phosphatase activity in soluble epoxide hydrolase
J Am Chem Soc. 2007. DOI : 10.1021/ja066150c.Modeling the charge distribution at metal sites in proteins for molecular dynamics simulations
J Struct Biol. 2007. DOI : 10.1016/j.jsb.2006.10.019.Role of zinc content on the catalytic efficiency of B1 metallo beta-lactamases
J Am Chem Soc. 2007. DOI : 10.1021/ja0657556.2006
Polarization effects and charge transfer in the KcsA potassium channel
Biophysical Chemistry. 2006. DOI : 10.1016/j.bpc.2006.04.008.2005
Solute-solvent charge transfer in aqueous solution
ChemPhysChem. 2005. DOI : 10.1002/cphc.200500039.2004
Substrate binding to mononuclear metallo-beta-lactamase from Bacillus cereus
Proteins. 2004. DOI : 10.1002/prot.10554.Water-Assisted Reaction Mechanism of Monozinc b-Lactamases
Journal of the American Chemical Society. 2004. DOI : 10.1021/ja048071b.2003
Protonation state of Asp120 in the binuclear active site of the metallo-beta-lactamase from Bacteroides fragilis
Inorg Chem. 2003. DOI : 10.1021/ic026059j.2002
Structural determinants and hydrogen-bond network of the mononuclear zinc(II)-beta-lactamase active site
J Biol Inorg Chem. 2002. DOI : 10.1007/s00775-002-0346-2.2001
Ser133 phosphate-KIX interactions in the CREB-CBP complex: an ab initio molecular dynamics study
Eur Biophysical Journal. 2001. DOI : 10.1007/s002490000112.Conference Papers
2023
Structural characterization of Prolyl endopeptidase-like, a mitochondrial protein involved in congenital myasthenic syndrome-22
2023. p. S109 - S109.Using integrative structural biology for the identification of novel aerolysin-like pore forming toxins for nanopore sensing
2023. p. S116 - S116.2022
The role of PTM crosstalks in Httex1 structure, aggregation and membrane interaction
2022. p. 38 - 38. DOI : 10.1016/j.bpj.2021.11.2495.Bacterial nanopores open the future of data storage
2022. International Electron Devices Meeting (IEDM), San Francisco, CA, Dec 03-07, 2022. DOI : 10.1109/IEDM45625.2022.10019421.2021
Decoding Digital Information Stored in Polymer by Nanopore
2021. p. 98A - 98A. DOI : 10.1016/j.bpj.2020.11.802.2019
Overcoming the hydrophobic barrier of the membrane: The role of COQ9 in promoting coenzyme Q biosynthesis
2019. 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. 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. 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. DOI : 10.1016/j.bpj.2013.11.872.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. DOI : 10.1016/j.bpj.2013.11.377.2013
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. DOI : 10.1016/j.bpj.2012.11.1278.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. DOI : 10.1016/j.bpj.2012.11.2205.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, 2013.2011
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
Coarse-graining electrostatics in multiscale molecular simulations
2010. p. 391 - COMP.A model for the assembly and activation process of the pore-forming toxin Aerolysin
2010. 35th Congress of the Federation-of-European-Biochemical-Societies, Gothenburg, SWEDEN, Jun 26-Jul 01, 2010. p. 194 - 194.Assembly and function of large Gram-negative bacterial machines studied by molecular simulation integrated with experimental data
2010. p. 425 - COMP.Conformational coupling between LOV and kinase domains in phototropins: A computational perspective
2010. p. 436 - COMP.A four-helix bundle model for E-coli PhoO transmembrane domain
2010. 35th Congress of the Federation-of-European-Biochemical-Societies, Gothenburg, SWEDEN, Jun 26-Jul 01, 2010. p. 193 - 194.Common catalytic features among cofactor independent racemases and epimerases: A computational perspective
2010. p. 88 - COMP.Shedding a new light on photolyases: Accurate molecular modeling as a tool for undestanding DNA repairing enzymes
2010. p. 20 - PHYS.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.2008
Unraveling the enzymatic mechanism of the protein farnesyltransferase: A QM/MM study
2008. 236th National Meeting of the American-Chemical-Society, Philadelphia, PA, Aug 17-21, 2008. p. 258 - COMP.Topologically-based multipolar reconstruction of electrostatic interactions in multiscale simulations of proteins
2008. 236th National Meeting of the American-Chemical-Society, Philadelphia, PA, Aug 17-21, 2008. p. 57 - COMP.Reviews
2022
Biological nanopores for single-molecule sensing
iScience. 2022. DOI : 10.1016/j.isci.2022.104145.2021
State-of-the-art web services for de novo protein structure prediction
Briefings In Bioinformatics. 2021. DOI : 10.1093/bib/bbaa139.2016
Pore-forming toxins: ancient, but never really out of fashion
Nature Reviews Microbiology. 2016. DOI : 10.1038/nrmicro.2015.3.2015
Catalytic Metal Ions and Enzymatic Processing of DNA and RNA
Accounts Of Chemical Research. 2015. DOI : 10.1021/ar500314j.Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop
Structure. 2015. DOI : 10.1016/j.str.2015.05.013.2014
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
2024
Label-Efficient Deep Learning Methods for Event Detection, Object Segmentation and Cell Tracking in Biological Microscopy Images
Lausanne, EPFL, 2024. DOI : 10.5075/epfl-thesis-11163.Exploring ion and analyte transport in beta-barrel forming biological nanopores
Lausanne, EPFL, 2024. DOI : 10.5075/epfl-thesis-10672.Investigating the intra-molecular and inter-molecular effects of post-translational modifications on intrinsically disordered protein regions and structured protein regions
Lausanne, EPFL, 2024. DOI : 10.5075/epfl-thesis-10530.Study of disease-associated proteins using integrative structural biology: the case of GOLPH3 and PREPL
Lausanne, EPFL, 2024. DOI : 10.5075/epfl-thesis-10807.2023
A Geometric Transformer for Structural Biology: Development and Applications of the Protein Structure Transformer
Lausanne, EPFL, 2023. DOI : 10.5075/epfl-thesis-10309.2021
New Methods for the Integrative Dynamic Modeling of Biomolecular Structures
Lausanne, EPFL, 2021. DOI : 10.5075/epfl-thesis-8284.2020
Beneficial axis of the renin-angiotensin system: from applications to drug discovery
Lausanne, EPFL, 2020. DOI : 10.5075/epfl-thesis-10223.Characterization of Protein-Membrane Interfaces through a Synergistic Computational-Experimental Approach
Lausanne, EPFL, 2020. DOI : 10.5075/epfl-thesis-7278.2019
Characterization of Coenzyme Q Biosynthesis Proteins through Integrative Modeling at the Protein-Membrane Interface
Lausanne, EPFL, 2019. DOI : 10.5075/epfl-thesis-9641.Exploring on Protein-DNA interactions
Lausanne, EPFL, 2019. DOI : 10.5075/epfl-thesis-9426.Structural and functional characterisation of the KRAB-domain associated protein 1
Lausanne, EPFL, 2019. DOI : 10.5075/epfl-thesis-7154.2018
Structural and functional analysis of host attachment proteins from contractile injection systems
Lausanne, EPFL, 2018. DOI : 10.5075/epfl-thesis-8267.2017
Studying membrane-protein interplay by modeling realistic conditions
Lausanne, EPFL, 2017. DOI : 10.5075/epfl-thesis-7934.Evaluation of oxidation-sensitive polymersomes as vaccine nanocarriers to enhance humoral responses against arenavirus envelope glycoproteins
Lausanne, EPFL, 2017. DOI : 10.5075/epfl-thesis-8193.2015
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
Molecular Modeling of Membrane Embedded Proteins
Lausanne, EPFL, 2013. DOI : 10.5075/epfl-thesis-5695.Multiscale simulations of protein dynamics
Lausanne, EPFL, 2013. DOI : 10.5075/epfl-thesis-5841.2012
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.Working Papers
2025
MolecularWeb Democratizes Web-Based, Immersive, Multiuser Molecular Graphics And Modeling
2025Sub-Nanomolar Detection and Discrimination of Microcystin Congeners Using Aerolysin Nanopores
2025Practical outcomes from CASP16 for users in need of biomolecular structure prediction
2025Posters
2022
Identification of single amino acid with engineered aerolysin nanopores
Single-Molecule Protein Sequencing 3 (SMPS3), Delft, The Netherlands, October 31-November 3, 2022.Talks
2022
Bacterial proteolytic enzymes as biological scissors in the fate of enteroviruses in natural ecosystems
Swiss Society for Microbiology Annual Meeting - SMM 2022, Lausanne, Switzerland, August 30 - September 1, 2022.Mechanisms of inactivation of non-enveloped viruses in natural ecosystems: bacterial proteolytic enzymes as biological scissors in the fate of enteroviruses
7th International Society for Food and Environmental Virology Conference - ISFEV2020, Santiago de Compostela, Spain, May 16-20, 2022.2018
Structural characterization of thermoresistant enteroviruses
ISFEV 2018 - 6th Food and Environmental Virology Conference, Tempe, Arizona, USA, October 7-10, 2018.Patents
2025
Uses of aerolysin nanopores
WO2025003492 . 2025.2024
Mutant aerolysin and uses thereof
EP4362028 . 2024.2022
Systems and methods for digital information decoding and data storage in hybrid macromolecules
US2023377649 ; EP4222742 ; WO2022069022 . 2022.Mutant aerolysin and uses thereof
US11845779 ; US2022127310 . 2022.2024
Dissecting the membrane association mechanism of aerolysin pore at femtomolar concentrations using water as a probe
2024.Teaching & PhD
PhD Students
Verena Rukes, Parth Bibekar, Arthur Samurkas, Fernando Augusto Teixeira Pinto Meireles, Benedikt Singer, Artemiy Burov, Ekaterina Pyatova, Edoardo Cavani, Alissa Agerova, Marianna Mitsioni, Jana Susanne Anton, Roxana Ghasemi
Past EPFL PhD Students
Matteo Thomas Degiacomi, Thomas Lemmin, Enrico Spiga, Christophe Bovigny, Hasan Pezeshgi Modarres, Martina Audagnotto, Giorgio Elikem Tamo, Alexandra Styliani Kalantzi, Deniz Aydin, Giulia Fonti, Alessio Prunotto, Sylvain Träger, Lucien Fabrice Krapp, Zhidian Zhang, Simon Finn Mayer, Anastasia Theodoropoulou, Benjamin Gallusser
Past EPFL PhD Students as codirector
Michel Plattner, Maiia Bragina
Courses
Biological chemistry I
BIO-212
Biochemistry is a key discipline for the Life Sciences. Biological Chemistry I and II are two tightly interconnected courses that aim to describe and understand in molecular terms the processes that make life possible.
Scientific literature analysis in computational molecular biology
BIO-468
The goal of this course is to learn to analyze a scientific paper critically, asking whether the data presented support the conclusions that are drawn. The analysis is presented in the form of a summary presentation and critical, constructive assessments of the paper.
Structural biology
BIO-315
The main focus of this course is on the molecular interactions defining the structure, dynamics and function of biological systems. The principal experimental and computational techniques used in structural biology, as well as molecular modeling and design will be introduced and practiced.