Matteo Dal Peraro
matteo.dalperaro@epfl.ch +41 21 693 18 61 http://lbm.epfl.ch
Nationalité: Italian
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Web site: Site web: https://bioengineering.epfl.ch/
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Publications
Publications Infoscience
Journal Articles
2023
Updates on moleculARweb, the Swiss Portal for Chemistry and Structural Biology Education Using Augmented and now also Virtual Reality
Chimia. 2023-04-01. DOI : 10.2533/chimia.2023.264.2022
Article Structure and functionality of a multimeric human COQ7:COQ9 complex
Molecular Cell. 2022-11-17. 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. 2022-07-01. 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. 2022-04-04. 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. 2022-02-01. DOI : 10.2533/chimia.2022.145.2021
Prolyl endopeptidase-like is a (thio)esterase involved in mitochondrial respiratory chain function
Iscience. 2021-12-17. DOI : 10.1016/j.isci.2021.103460.BET1 variants establish impaired vesicular transport as a cause for muscular dystrophy with epilepsy
Embo Molecular Medicine. 2021-11-15. DOI : 10.15252/emmm.202013787.S-acylation controls SARS-CoV-2 membrane lipid organization and enhances infectivity
Developmental Cell. 2021-10-25. DOI : 10.1016/j.devcel.2021.09.016.Democratizing interactive, immersive experiences for science education with WebXR
Nature Computational Science. 2021-10-01. 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. 2021-09-01. DOI : 10.1128/AAC.00507-21.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. 2021-07-13. DOI : 10.1021/acs.jchemed.1c00179.Reviewing Challenges of Predicting Protein Melting Temperature Change Upon Mutation Through the Full Analysis of a Highly Detailed Dataset with High-Resolution Structures
Molecular Biotechnology. 2021-06-08. DOI : 10.1007/s12033-021-00349-0.CLoNe: automated clustering based on local density neighborhoods for application to biomolecular structural ensembles
Bioinformatics. 2021-04-01. DOI : 10.1093/bioinformatics/btaa742.Palmitoylated acyl protein thioesterase APT2 deforms membranes to extract substrate acyl chains
Nature Chemical Biology. 2021-04-01. 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. 2021-01-14. DOI : 10.1039/d0sc04394j.Assessment of transferable forcefields for protein simulations attests improved description of disordered states and secondary structure propensities, and hints at multi-protein systems as the next challenge for optimization
Computational and Structural Biotechnology Journal. 2021-04-25. DOI : 10.1016/j.csbj.2021.04.050.Extensive tissue-specific expression variation and novel regulators underlying circadian behavior
Science Advances. 2021-01-01. DOI : 10.1126/sciadv.abc3781.2020
Aerolysin nanopores decode digital information stored in tailored macromolecular analytes
Science Advances. 2020-12-09. DOI : 10.1126/sciadv.abc2661.The Human RNA Helicase DDX21 Presents a Dimerization Interface Necessary for Helicase Activity
iScience. 2020-11-18. 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. 2020-10-09. 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. 2020-09-01. 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. 2020-08-28. DOI : 10.3389/fmolb.2020.00194.Will Cryo-Electron Microscopy Shift the Current Paradigm in Protein Structure Prediction?
Journal Of Chemical Information And Modeling. 2020-05-26. 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. 2020-05-18. DOI : 10.1016/j.devcel.2020.04.015.De novo protein design enables the precise induction of RSV-neutralizing antibodies
Science. 2020-05-15. DOI : 10.1126/science.aay5051.Btk SH2-kinase interface is critical for allosteric kinase activation and its targeting inhibits B-cell neoplasms
Nature Communications. 2020-05-08. DOI : 10.1038/s41467-020-16128-5.About the need to make computational models of biological macromolecules available and discoverable
Bioinformatics. 2020-05-01. DOI : 10.1093/bioinformatics/btaa086.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.Directional Local Field Potentials in the Subthalamic Nucleus During Deep Brain Implantation of Parkinson's Disease Patients
Frontiers In Human Neuroscience. 2020-09-30. DOI : 10.3389/fnhum.2020.521282.2019
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.Conference Papers
2023
Structural characterization of Prolyl endopeptidase-like, a mitochondrial protein involved in congenital myasthenic syndrome-22
2023-07-01. p. S109-S109.Using integrative structural biology for the identification of novel aerolysin-like pore forming toxins for nanopore sensing
2023-07-01. p. S116-S116.2021
Decoding Digital Information Stored in Polymer by Nanopore
2021-02-12. p. 98A-98A. DOI : 10.1016/j.bpj.2020.11.802.2020
Structural and functional divergence of duplicated mosquito Toll and Spz compared to Drosophila
2020-05-01. Annual Meeting of the American-Association-of-Immunologists - Immunology 2020, Honolulu, HI, May 08-12, 2020.2019
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.Reviews
2022
Biological nanopores for single-molecule sensing
iScience. 2022-04-07. DOI : 10.1016/j.isci.2022.104145.2021
Computational Approaches to Explore Bacterial Toxin Entry into the Host Cell
Toxins. 2021-06-28. DOI : 10.3390/toxins13070449.State-of-the-art web services for de novo protein structure prediction
Briefings In Bioinformatics. 2021-05-01. DOI : 10.1093/bib/bbaa139.2020
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.Theses
2020
Characterization of Protein-Membrane Interfaces through a Synergistic Computational-Experimental Approach
Lausanne, EPFL, 2020. DOI : 10.5075/epfl-thesis-7278.2019
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
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.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
Structural characterization of Prolyl endopeptidase-like, a mitochondrial protein involved in congenital myasthenic syndrome-22
2023-07-01. p. S109-S109.Using integrative structural biology for the identification of novel aerolysin-like pore forming toxins for nanopore sensing
2023-07-01. p. S116-S116.Updates on moleculARweb, the Swiss Portal for Chemistry and Structural Biology Education Using Augmented and now also Virtual Reality
Chimia. 2023-04-01. DOI : 10.2533/chimia.2023.264.Article Structure and functionality of a multimeric human COQ7:COQ9 complex
Molecular Cell. 2022-11-17. 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. 2022-07-01. DOI : 10.1016/j.jmgm.2022.108164.Biological nanopores for single-molecule sensing
iScience. 2022-04-07. DOI : 10.1016/j.isci.2022.104145.Ultrasensitive Label-Free Detection of Protein–Membrane Interaction Exemplified by Toxin-Liposome Insertion
The Journal of Physical Chemistry Letters. 2022-04-04. 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. 2022-02-01. DOI : 10.2533/chimia.2022.145.Prolyl endopeptidase-like is a (thio)esterase involved in mitochondrial respiratory chain function
Iscience. 2021-12-17. DOI : 10.1016/j.isci.2021.103460.BET1 variants establish impaired vesicular transport as a cause for muscular dystrophy with epilepsy
Embo Molecular Medicine. 2021-11-15. DOI : 10.15252/emmm.202013787.S-acylation controls SARS-CoV-2 membrane lipid organization and enhances infectivity
Developmental Cell. 2021-10-25. DOI : 10.1016/j.devcel.2021.09.016.Democratizing interactive, immersive experiences for science education with WebXR
Nature Computational Science. 2021-10-01. 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. 2021-09-01. DOI : 10.1128/AAC.00507-21.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. 2021-07-13. DOI : 10.1021/acs.jchemed.1c00179.Computational Approaches to Explore Bacterial Toxin Entry into the Host Cell
Toxins. 2021-06-28. DOI : 10.3390/toxins13070449.Reviewing Challenges of Predicting Protein Melting Temperature Change Upon Mutation Through the Full Analysis of a Highly Detailed Dataset with High-Resolution Structures
Molecular Biotechnology. 2021-06-08. DOI : 10.1007/s12033-021-00349-0.State-of-the-art web services for de novo protein structure prediction
Briefings In Bioinformatics. 2021-05-01. DOI : 10.1093/bib/bbaa139.CLoNe: automated clustering based on local density neighborhoods for application to biomolecular structural ensembles
Bioinformatics. 2021-04-01. DOI : 10.1093/bioinformatics/btaa742.Palmitoylated acyl protein thioesterase APT2 deforms membranes to extract substrate acyl chains
Nature Chemical Biology. 2021-04-01. DOI : 10.1038/s41589-021-00753-2.Decoding Digital Information Stored in Polymer by Nanopore
2021-02-12. p. 98A-98A. DOI : 10.1016/j.bpj.2020.11.802.Structural basis for recognition of bacterial cell wall teichoic acid by pseudo-symmetric SH3b-like repeats of a viral peptidoglycan hydrolase
Chemical Science. 2021-01-14. DOI : 10.1039/d0sc04394j.Assessment of transferable forcefields for protein simulations attests improved description of disordered states and secondary structure propensities, and hints at multi-protein systems as the next challenge for optimization
Computational and Structural Biotechnology Journal. 2021-04-25. DOI : 10.1016/j.csbj.2021.04.050.Extensive tissue-specific expression variation and novel regulators underlying circadian behavior
Science Advances. 2021-01-01. DOI : 10.1126/sciadv.abc3781.Aerolysin nanopores decode digital information stored in tailored macromolecular analytes
Science Advances. 2020-12-09. DOI : 10.1126/sciadv.abc2661.The Human RNA Helicase DDX21 Presents a Dimerization Interface Necessary for Helicase Activity
iScience. 2020-11-18. 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. 2020-10-09. 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. 2020-09-01. 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. 2020-08-28. DOI : 10.3389/fmolb.2020.00194.Will Cryo-Electron Microscopy Shift the Current Paradigm in Protein Structure Prediction?
Journal Of Chemical Information And Modeling. 2020-05-26. 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. 2020-05-18. DOI : 10.1016/j.devcel.2020.04.015.De novo protein design enables the precise induction of RSV-neutralizing antibodies
Science. 2020-05-15. DOI : 10.1126/science.aay5051.Btk SH2-kinase interface is critical for allosteric kinase activation and its targeting inhibits B-cell neoplasms
Nature Communications. 2020-05-08. DOI : 10.1038/s41467-020-16128-5.About the need to make computational models of biological macromolecules available and discoverable
Bioinformatics. 2020-05-01. DOI : 10.1093/bioinformatics/btaa086.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.Structural and functional divergence of duplicated mosquito Toll and Spz compared to Drosophila
2020-05-01. Annual Meeting of the American-Association-of-Immunologists - Immunology 2020, Honolulu, HI, May 08-12, 2020.Single-molecule studies of amyloid proteins: from biophysical properties to diagnostic perspectives
Quarterly Reviews Of Biophysics. 2020-01-01. DOI : 10.1017/S0033583520000086.Directional Local Field Potentials in the Subthalamic Nucleus During Deep Brain Implantation of Parkinson's Disease Patients
Frontiers In Human Neuroscience. 2020-09-30. DOI : 10.3389/fnhum.2020.521282.Characterization of Protein-Membrane Interfaces through a Synergistic Computational-Experimental Approach
Lausanne, EPFL, 2020. DOI : 10.5075/epfl-thesis-7278.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.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.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
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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
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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.Enseignement & Phd
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