-
2024Structure and Dynamics of Type 4a Pili and Type 2 Secretion System Endopili, In: Macromolecular Protein Complexes V, vol 104. Chapter 21. p549-563.
-
2024Protein interaction explorer (PIE): a comprehensive platform for navigating protein-protein interactions and ligand binding pockets., Bioinformatics 2024 Jul; 40(7): .
-
2024A comprehensive dataset of protein-protein interactions and ligand binding pockets for advancing drug discovery, Scientific Data , 2024, 11 (1), pp.402. ⟨10.1038/s41597-024-03233-z⟩.
-
2024Insights from structure-activity relationships and the binding mode of peptidic α-ketoamide inhibitors of the malaria drug target subtilisin-like SUB1., Eur J Med Chem 2024 Apr; 269(): 116308.
-
2024Mechanism of action of phthalazinone derivatives against rabies virus., Antiviral Res 2024 Apr; 224(): 105838.
-
2023Membrane platform protein PulF of the Klebsiella type II secretion system forms a trimeric ion channel essential for endopilus assembly and protein secretion., mBio 2023 Dec; (): e0142323.
-
2023The Mla system of diderm Firmicute Veillonella parvula reveals an ancestral transenvelope bridge for phospholipid trafficking., Nat Commun 2023 Nov; 14(1): 7642.
-
2023SARS‐CoV‐2‐related bat virus behavior in human‐relevant models sheds light on the origin of COVID‐19, EMBO Reports, 2023, 24 (4), pp.e56055. ⟨10.15252/embr.202256055⟩.
-
2023Structure and dynamic association of an assembly platform subcomplex of the bacterial type II secretion system., Structure 2023 Feb; 31(2): 152-165.e7.
-
2022A Robust and Sensitive Spectrophotometric Assay for the Enzymatic Activity of Bacterial Adenylate Cyclase Toxins., Toxins (Basel) 2022 Oct; 14(10): .
-
2022In Silico Conformational Features of Botulinum Toxins A1 and E1 According to Intraluminal Acidification., Toxins (Basel) 2022 Sep; 14(9): .
-
2022Building Protein Atomic Models from Cryo-EM Density Maps and Residue Co-Evolution., Biomolecules 2022 Sep; 12(9): .
-
2022Mechanism of threonine ADP-ribosylation of F-actin by a Tc toxin., Nat Commun 2022 Jul; 13(1): 4202.
-
2022A highly sensitive cell-based luciferase assay for high-throughput automated screening of SARS-CoV-2 nsp5/3CLpro inhibitors., Antiviral Res 2022 May; 201(): 105272.
-
2022Secondary structure and 1H, 15 N & 13C resonance assignments of the periplasmic domain of OutG, major pseudopilin from Dickeya dadantii type II secretion system., Biomol NMR Assign 2022 Apr; (): .
-
2022Structural and molecular determinants for the interaction of ExbB from Serratia marcescens and HasB, a TonB paralog, Commun Biol . 2022 Apr 13;5(1):355. .
-
2022Discovery of bat coronaviruses close to SARS-CoV-2 and infectious for human cells., Nautre 604 (2022) 330.
-
2022Characterization of the Interaction Domains between the Phosphoprotein and the Nucleoprotein of Human Metapneumovirus., J Virol 2022 01; 96(2): e0090921.
-
2022Deciphering the Molecular Interaction Between the Adhesion G Protein-Coupled Receptor ADGRV1 and its PDZ-Containing Regulator PDZD7., Front Mol Biosci 2022 ; 9(): 923740.
-
2021InDeep: 3D fully convolutional neural networks to assist in silico drug design on protein-protein interactions., Bioinformatics 2022 Feb; 38(5): 1261-1268.
-
2021Characterization of the interaction domains between the phosphoprotein and the nucleoprotein of human Metapneumovirus., J Virol 2021 Nov; (): JVI0090921.
-
20211 H, 15 N and 13 C resonance assignments of the C-terminal domain of PulL, a component of the Klebsiella oxytoca type II secretion system, Biomol NMR Assign . 2021 Oct;15(2):455-459. .
-
2021Conformational Insights into the Control of CNF1 Toxin Activity by Peptidyl-Prolyl Isomerization: A Molecular Dynamics Perspective., Int J Mol Sci 2021 Sep; 22(18): .
-
2021Computational and biochemical analysis of type IV pilus dynamics and stability., Structure 2021 Dec; 29(12): 1397-1409.e6.
-
2021Rational design of ASCT2 inhibitors using an integrated experimental-computational approach, Proc. Natl. Acad. Sci. USA 118 (2021) e21040931188.
-
2021Multi-replica biased sampling for photoisomerization processes in conjugated polymers, J. Chem. Phys. 154, 174108 (2021).
-
20211H, 15 N and 13C resonance assignments of the C-terminal domain of PulL, a component of the Klebsiella oxytoca type II secretion system., Biomol NMR Assign 2021 Oct; 15(2): 455-459.
-
2021A Structural and Dynamic Analysis of the Partially Disordered Polymerase-Binding Domain in RSV Phosphoprotein., Biomolecules 2021 Aug; 11(8): .
-
2021Host-Pathogen Adhesion as the Basis of Innovative Diagnostics for Emerging Pathogens., Diagnostics (Basel) 2021 Jul; 11(7): .
-
2021Phylogenetic analysis of Harmonin homology domains., BMC Bioinformatics 2021 Apr; 22(1): 190.
-
2021Advanced In Vivo Cross-Linking Mass Spectrometry Platform to Characterize Proteome-Wide Protein Interactions., Anal Chem 2021 Feb; (): .
-
2021New machine learning and physics-based scoring functions for drug discovery., Sci Rep 2021 Feb; 11(1): 3198.
-
2021The iPPI-DB initiative: a community-centered database of protein-protein interaction modulators., Bioinformatics 2021 Apr; 37(1): 89-96.
-
2021Structural determination of Streptococcus pyogenes M1 protein interactions with human immunoglobulin G using integrative structural biology., PLoS Comput Biol 2021 Jan; 17(1): e1008169.
-
2021Structural and molecular basis of cross-seeding barriers in amyloids., Proc Natl Acad Sci U S A 2021 Jan; 118(1): .
-
2021Automatic Bayesian Weighting for SAXS Data., Front Mol Biosci 2021 ; 8(): 671011.
-
2021Structures of Pathological and Functional Amyloids and Prions, a Solid-State NMR Perspective., Front Mol Neurosci 2021 ; 14(): 670513.
-
2020Predicting substitutions to modulate disorder and stability in coiled-coils., BMC Bioinformatics 2020 Dec; 21(Suppl 19): 573.
-
2020Deciphering the Unexpected Binding Capacity of the Third PDZ Domain of Whirlin to Various Cochlear Hair Cell Partners., J Mol Biol 2020 11; 432(22): 5920-5937.
-
2020Hidden kinetic traps in multidomain folding highlight the presence of a misfolded but functionally competent intermediate., Proc Natl Acad Sci U S A 2020 08; 117(33): 19963-19969.
-
2020Aβ(1-42) tetramer and octamer structures reveal edge conductivity pores as a mechanism for membrane damage., Nat Commun 2020 Jun; 11(1): 3014.
-
2020ARIAweb: a server for automated NMR structure calculation., Nucleic Acids Res. 2020 May; (): .
-
2020Fr-PPIChem: An academic compound library dedicated to protein-protein interactions, ACS Chem. Biol. 2020 Apr;.
-
2020Analyzing In Silico the Relationship Between the Activation of the Edema Factor and Its Interaction With Calmodulin., Front Mol Biosci 2020 ; 7(): 586544.
-
2019Structure and function of minor pilins of type IV pili., Med Microbiol Immunol 2020 Jun; 209(3): 301-308.
-
2019Quantitative Structural Interpretation of Protein Crosslinks, Structure 2019 Nov;.
-
2019Systematic Exploration of Protein Conformational Space Using a Distance Geometry Approach, J Chem Inf Model 2019 Sep;.
-
2019GEMME: a simple and fast global epistatic model predicting mutational effects, Mol. Biol. Evol. 2019 Aug;.
-
2019Structural Biology and Molecular Modeling to Analyze the Entry of Bacterial Toxins and Virulence Factors into Host Cells, Toxins (Basel) 2019 Jun;11(6).
-
2019Dynamics of a type 2 secretion system pseudopilus unraveled by complementary approaches, J. Biomol. NMR 2019 Jul;73(6-7):293-303.
-
2019DaReUS-Loop: a web server to model multiple loops in homology models, Nucleic Acids Res. 2019 May;.
-
2019Structure and Assembly of the Enterohemorrhagic Escherichia coli Type 4 Pilus., Structure. 2019 Apr 9. doi: 10.1016/j.str.2019.03.021..
-
2019Single-site phosphorylation within the His-tag sequence attached to a recombinant protein, Anal. Biochem. 2019 Feb;.
-
2019Publisher Correction: Genomic insights into the 2016-2017 cholera epidemic in Yemen., Nature 2019 02; 566(7745): E14.
-
2019Bayesian Weighing of Electron Cryo-Microscopy Data for Integrative Structural Modeling, Structure 27 (2019) 175-188.
-
2019Genomic insights into the 2016-2017 cholera epidemic in Yemen., Nature 2019 01; 565(7738): 230-233.
-
2018Target engagement and binding mode of an anti-tuberculosis drug to its bacterial target deciphered in whole living cells by NMR., Biochemistry. 2019 Feb 12;58(6):526-533. doi: 10.1021/acs.biochem.8b00975. .
-
2018Conformational sampling of CpxA: Connecting HAMP motions to the histidine kinase function, PLoS ONE 2018;13(11):e0207899.
-
2018Determination of Structural Ensembles of Proteins: Restraining vs Reweighting, J. Chem. Theory Comput. 2018, 14, 6632−6641.
-
2018A Versatile Computational Strategy To Characterize the Free-Energy Landscape of Excited States in Oligofluorenes, J Chem Theory Comput 2018 Nov;14(11):5441-5445.
-
2018“Infostery” analysis of short molecular dynamics simulations identifies highly sensitive residues and predicts deleterious mutations, Sci Rep 2018 Oct;8(1):16126.
-
2018Closed-locked and Apo-resting State Structures of the Human α7 Nicotinic Receptor: a Computational Study, J Chem Inf Model 2018 Oct;.
-
2018Biogenesis and structure of a type VI secretion baseplate, Nat Microbiol 2018 Oct;.
-
2018Structure and dynamics of Helicobacter pylori nickel-chaperone HypA: an integrated approach using NMR spectroscopy, functional assays and computational tools, J. Biol. Inorg. Chem. 2018 Sep;.
-
2018DaReUS-Loop: accurate loop modeling using fragments from remote or unrelated proteins, Sci Rep 2018 Sep;8(1):13673.
-
2018Biasing Smarter, Not Harder, by Partitioning Collective Variables into Families in Parallel Bias Metadynamics, J Chem Theory Comput 2018 Oct;14(10):4985-4990.
-
2018Structural plasticity of the HHD2 domain of whirlin., FEBS J 2018 Oct; 285(20): 3738-3752.
-
2018Probing Structural Changes during Self-assembly of Surface-Active Hydrophobin Proteins that Form Functional Amyloids in Fungi., J Mol Biol 2018 10; 430(20): 3784-3801.
-
2018Reversible inhibition of the ClpP protease via an N-terminal conformational switch, Proc. Natl. Acad. Sci. U.S.A. 2018 07;115(28):E6447-E6456.
-
2018Calcium sequestration by fungal melanin inhibits calcium-calmodulin signalling to prevent LC3-associated phagocytosis, Nat Microbiol 2018 May;.
-
2018The protofilament architecture of a de novo designed coiled coil-based amyloidogenic peptide, J. Struct. Biol. 2018 May;.
-
2018Minimal NMR distance information for rigidity of protein graphs, Discrete Appl Math 2019 Mar;256:91-104.
-
2018Simultaneous Determination of Protein Structure and Dynamics Using Cryo-Electron Microscopy, Biophys. J. 2018 Apr;114(7):1604-1613.
-
20183D Structure Determination of Amyloid Fibrils using Solid-State NMR Spectroscopy, Methods 2018 Apr;.
-
2018re-TAMD: exploring interactions between H3 peptide and YEATS domain using enhanced sampling, BMC Struct. Biol. 2018 04;18(1):4.
-
2018Structural Ensemble Modulation upon Small-Molecule Binding to Disordered Proteins, J. Mol. Biol. 430 (2018) 2288.
-
2018Ordering Protein Contact Matrices, Comput Struct Biotechnol J. 2018 Mar;16:140-56.
-
2018Integrative structure and functional anatomy of a nuclear pore complex, Nature 2018 03;555(7697):475-482.
-
2018Tuning interval Branch-and-Prune for protein structure determination, J Glob Optim. 2018 Sep; 72(1):109–27.
-
2018Recognition of DHN-melanin by a C-type lectin receptor is required for immunity to Aspergillus, Nature 2018 Mar;555(7696):382-386.
-
2018Sequence-specific DNA binding activity of the cross-brace zinc finger motif of the piggyBac transposase, Nucleic Acids Res. 2018 Jan;.
-
2018Integrative structure modeling with the Integrative Modeling Platform, Protein Sci. 2018 01;27(1):245-258.
-
2017Role of Hydrophobins in Aspergillus fumigatus, J Fungi (Basel) 2017 Dec;4(1).
-
2017Integrative structural and dynamical biology with PLUMED-ISDB, Bioinformatics 2017 Dec;33(24):3999-4000.
-
2017Structure of outer membrane protein G in lipid bilayers, Nat Commun 2017 Dec;8(1):2073.
-
2017Structure of the calcium-dependent type 2 secretion pseudopilus., Nat Microbiol 2017 Dec; 2(12): 1686-1695.
-
2017Structural Characterization of Whirlin Reveals an Unexpected and Dynamic Supramodule Conformation of Its PDZ Tandem, Structure 2017 11;25(11):1645-1656.e5.
-
2017Privileged Substructures to Modulate Protein-Protein Interactions, J Chem Inf Model 2017 Oct;57(10):2448-2462.
-
2017The molecular architecture of the yeast spindle pole body core determined by Bayesian integrative modeling, Mol. Biol. Cell 2017 Nov;28(23):3298-3314.
-
2017Conformational switch of harmonin, a submembrane scaffold protein of the hair cell mechanoelectrical transduction machinery, FEBS Letters, 2017, 591 (15), pp.2299 - 2310. ⟨10.1002/1873-3468.12729⟩.
-
2017Sequence Specificity in the Entropy-Driven Binding of a Small Molecule and a Disordered Peptide, J. Mol. Biol. 2017 Sep;429(18):2772-2779.
-
2017A possible desensitized state conformation of the human α7 nicotinic receptor: A molecular dynamics study, Biophys. Chem. 2017 10;229:99-109.
-
2017Molecular Modeling of the Catalytic Domain of CyaA Deepened the Knowledge of Its Functional Dynamics, Toxins (Basel) 2017 06;9(7).
-
2017Simultaneous quantification of protein order and disorder, Nat. Chem. Biol. 2017 03;13(4):339-342.
-
2017Molecular Landscape of the Ribosome Pre-initiation Complex during mRNA Scanning: Structural Role for eIF3c and Its Control by eIF5, Cell Rep 2017 03;18(11):2651-2663.
-
2017Principles of protein structural ensemble determination, Curr. Opin. Struct. Biol. 2017 02;42:106-116.
-
2016A Residue-Resolved Bayesian Approach to Quantitative Interpretation of Hydrogen-Deuterium Exchange from Mass Spectrometry: Application to Characterizing Protein-Ligand Interactions, J Phys Chem B 2017 04;121(15):3493-3501.
-
2016Structure and Function of the Nuclear Pore Complex Cytoplasmic mRNA Export Platform, Cell 2016 11;167(5):1215-1228.e25.
-
2016Modification in hydrophobic packing of HAMP domain induces a destabilization of the auto-phosphorylation site in the histidine kinase CpxA, Biopolymers 2016 Oct;105(10):670-82.
-
2016Building Graphs To Describe Dynamics, Kinetics, and Energetics in the d-ALa:d-Lac Ligase VanA, J Chem Inf Model 2016 09;56(9):1762-75.
-
2016Virtual Screening Approaches towards the Discovery of Toll-Like Receptor Modulators, Int J Mol Sci 2016;17(9).
-
2016Metadynamic metainference: Enhanced sampling of the metainference ensemble using metadynamics, Sci Rep 2016 08;6:31232.
-
2016(1)H, (13)C and (15)N backbone resonance assignments and dynamic properties of the PDZ tandem of Whirlin, Biomol NMR Assign 2016 10;10(2):361-5.
-
2016Structure of Complement C3(H2O) Revealed By Quantitative Cross-Linking/Mass Spectrometry And Modeling, Mol. Cell Proteomics 2016 08;15(8):2730-43.
-
2016Molecular Basis of the Interaction of the Human Protein Tyrosine Phosphatase Non-receptor Type 4 (PTPN4) with the Mitogen-activated Protein Kinase p38γ., J Biol Chem 2016 08; 291(32): 16699-708.
-
2016Automated structure modeling of large protein assemblies using crosslinks as distance restraints, Nat. Methods 2016 Jun;13(6):515-20.
-
2016Free energy landscapes of sodium ions bound to DMPC-cholesterol membrane surfaces at infinite dilution, Phys Chem Chem Phys 2016 Apr;18(13):9036-41.
-
2016Metainference: A Bayesian inference method for heterogeneous systems, Sci Adv 2016 Jan;2(1):e1501177.
-
2016Dissecting protein architecture with communication blocks and communicating segment pairs, BMC Bioinformatics 2016 Jan;17 Suppl 2:13.
-
2016Structure determination of helical filaments by solid-state NMR spectroscopy, Proc. Natl. Acad. Sci. U.S.A. 2016 Jan;113(3):E272-81.
-
2015The molecular architecture of the Dam1 kinetochore complex is defined by cross-linking based structural modelling, Nat Commun 2015 Nov;6:8673.
-
2015The chaperone αB-crystallin uses different interfaces to capture an amorphous and an amyloid client, Nat. Struct. Mol. Biol. 2015 Oct;.
-
2015Efficient Sampling of High-Dimensional Free-Energy Landscapes with Parallel Bias Metadynamics, J Chem Theory Comput 2015 Nov;11(11):5062-7.
-
2015Ligand Discovery for the Alanine-Serine-Cysteine Transporter (ASCT2, SLC1A5) from Homology Modeling and Virtual Screening, PLoS Comput. Biol. 2015 Oct;11(10):e1004477.
-
2015Neisseria meningitidis Type IV Pili Composed of Sequence Invariable Pilins Are Masked by Multisite Glycosylation, PLoS Pathog. 2015 Sep;11(9):e1005162.
-
2015Improved large-scale prediction of growth inhibition patterns using the NCI60 cancer cell line panel., Bioinformatics 2016 Jan; 32(1): 85-95.
-
2015Architecture of the Human and Yeast General Transcription and DNA Repair Factor TFIIH, Mol. Cell 2015 Sep;59(5):794-806.
-
2015Solid-state NMR Study of the YadA Membrane-Anchor Domain in the Bacterial Outer Membrane, Angew. Chem. Int. Ed. Engl. 2015 Aug;.
-
2015Chemically Aware Model Builder (camb): an R package for property and bioactivity modelling of small molecules., J Cheminform 2015 ; 7(): 45.
-
2015Specific Ion Binding at Phospholipid Membrane Surfaces, J Chem Theory Comput 2015 Sep;11(9):4495-9.
-
2015Structural Model of the Bilitranslocase Transmembrane Domain Supported by NMR and FRET Data, PLoS ONE 2015;10(8):e0135455.
-
2015A Structural Model of the Human α7 Nicotinic Receptor in an Open Conformation, PLoS ONE 2015;10(7):e0133011.
-
2015Biogenesis and structure of a type VI secretion membrane core complex, Nature 2015 Jul;523(7562):555-60.
-
2015Comparing the Influence of Simulated Experimental Errors on 12 Machine Learning Algorithms in Bioactivity Modeling Using 12 Diverse Data Sets, J Chem Inf Model 2015 Jul;55(7):1413-25.
-
2015Synthesis of Spirocyclic Pyrazolones by Oxidative C-N Bond Formation, J. Org. Chem. 2015 Jun;80(12):6509-14.
-
2015Temperature Accelerated Molecular Dynamics with Soft-Ratcheting Criterion Orients Enhanced Sampling by Low-Resolution Information, J Chem Theory Comput 2015 Jul;11(7):3446-54.
-
2015NMR Exchange Format: a unified and open standard for representation of NMR restraint data, Nat. Struct. Mol. Biol. 2015 Jun;22(6):433-4.
-
2015The catalytic domains of Clostridium sordellii lethal toxin and related large clostridial glucosylating toxins specifically recognize the negatively charged phospholipids phosphatidylserine and phosphatidic acid, Cell. Microbiol. 2015 Oct;17(10):1477-93.
-
2015CoMoDo: Identifying Dynamic Protein Domains Based on Covariances of Motion, J Chem Theory Comput 2015 Jun;11(6):2841-54.
-
2015Deciphering the unconventional peptide binding to the PDZ domain of MAST2, Biochem. J. 2015 Jul;469(1):159-68.
-
2015Proteochemometric modelling coupled to in silico target prediction: an integrated approach for the simultaneous prediction of polypharmacology and binding affinity/potency of small molecules., J Cheminform 2015 ; 7(): 15.
-
2015Improved reliability, accuracy and quality in automated NMR structure calculation with ARIA, J. Biomol. NMR 2015 Aug;62(4):425-38.
-
2015Identification of binding sites and favorable ligand binding moieties by virtual screening and self-organizing map analysis, BMC Bioinformatics 2015 Mar;16:93.
-
2015Prediction of PARP Inhibition with Proteochemometric Modelling and Conformal Prediction, Mol Inform 2015 Jun;34(6-7):357-66.
-
2015Strategies to interfere with PDZ-mediated interactions in neurons: What we can learn from the rabies virus., Prog Biophys Mol Biol 2015 Oct; 119(1): 53-9.
-
2015An algorithm to enumerate all possible protein conformations verifying a set of distance constraints., BMC Bioinformatics 2015 Jan; 16(): 23.
-
2015Prediction of the potency of mammalian cyclooxygenase inhibitors with ensemble proteochemometric modeling, J Cheminform 2015;7:1.
-
2015Accuracy of current all-atom force-fields in modeling protein disordered states, J. Chem. Theory Comput. 11 (2015) 2.
-
2015Tackling sampling challenges in biomolecular simulations, Methods Mol. Biol. 2015;1215:151-71.
-
2014An automatic tool to analyze and cluster macromolecular conformations based on self-organizing maps, Bioinformatics 2015 May;31(9):1490-2.
-
2014Modelling ligand selectivity of serine proteases using integrative proteochemometric approaches improves model performance and allows the multi-target dependent interpretation of features, Integr Biol (Camb) 2014 Nov;6(11):1023-33.
-
2014Principal Component Analysis reveals correlation of cavities evolution and functional motions in proteins, J. Mol. Graph. Model. 2015 Feb;55:13-24.
-
2014Quantitative and dynamic analysis of PTEN phosphorylation by NMR, Methods 2015 May;77-78:82-91.
-
2014Regulation of the catalytic activity of the human phosphatase PTPN4 by its PDZ domain., FEBS J 2014 Nov; 281(21): 4852-65.
-
2014Structural and mechanistic insights into the bacterial amyloid secretion channel CsgG, Nature 2014 Dec;516(7530):250-3.
-
2014Uncertainty in integrative structural modeling, Curr. Opin. Struct. Biol. 2014 Oct;28:96-104.
-
2014Molecular architecture of the 40S⋅eIF1⋅eIF3 translation initiation complex, Cell 2014 Aug;158(5):1123-35.
-
2014Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex, Mol. Cell Proteomics 2014 Nov;13(11):2927-43.
-
2014Molecular architecture of photoreceptor phosphodiesterase elucidated by chemical cross-linking and integrative modeling, J. Mol. Biol. 2014 Nov;426(22):3713-28.
-
2014Determining protein complex structures based on a Bayesian model of in vivo Förster resonance energy transfer (FRET) data, Mol. Cell Proteomics 2014 Nov;13(11):2812-23.
-
2014Cys-scanning disulfide crosslinking and bayesian modeling probe the transmembrane signaling mechanism of the histidine kinase, PhoQ, Structure 2014 Sep;22(9):1239-1251.
-
2014Molecular architecture and function of the SEA complex, a modulator of the TORC1 pathway, Mol. Cell Proteomics 2014 Nov;13(11):2855-70.
-
2014Solid-state NMR structure determination from diagonal-compensated, sparsely nonuniform-sampled 4D proton-proton restraints, J. Am. Chem. Soc. 2014 Aug;136(31):11002-10.
-
2014Proteochemometric modeling in a Bayesian framework, J Cheminform 2014;6:35.
-
2014Temperature-accelerated molecular dynamics gives insights into globular conformations sampled in the free state of the AC catalytic domain, Proteins 2014 Oct;82(10):2483-96.
-
2014Elucidating the mechanism of substrate recognition by the bacterial Hsp90 molecular chaperone, J. Mol. Biol. 2014 Jun;426(12):2393-404.
-
2014Distinct docking and stabilization steps of the Pseudopilus conformational transition path suggest rotational assembly of type IV pilus-like fibers, Structure 2014 May;22(5):685-96.
-
2014Conformational changes in acetylcholine binding protein investigated by temperature accelerated molecular dynamics, PLoS ONE 2014;9(2):e88555.
-
2014The free energy profile of tubulin straight-bent conformational changes, with implications for microtubule assembly and drug discovery, PLoS Comput. Biol. 2014 Feb;10(2):e1003464.
-
2014Functional motions modulating VanA ligand binding unraveled by self-organizing maps, J Chem Inf Model 2014 Jan;54(1):289-301.
-
2014Modeling of proteins and their assemblies with the Integrative Modeling Platform, Methods Mol. Biol. 2014;1091:277-95.
-
2014Extending in silico mechanism-of-action analysis by annotating targets with pathways: application to cellular cytotoxicity readouts, Future Med Chem 2014;6(18):2029-56.
-
2013Free-energy landscape of protein oligomerization from atomistic simulations, Proc. Natl. Acad. Sci. U.S.A. 2013 Dec;110(49):E4708-13.
-
2013Stabilization of the integrase-DNA complex by Mg2+ ions and prediction of key residues for binding HIV-1 integrase inhibitors, Proteins 2014 Mar;82(3):466-78.
-
2013Identification of cinnamic acid derivatives as novel antagonists of the prokaryotic proton-gated ion channel GLIC, J. Med. Chem. 2013 Jun;56(11):4619-30.
-
2013Structural basis for alternating access of a eukaryotic calcium/proton exchanger, Nature 2013 Jul;499(7456):107-10.
-
2013Combined approaches for drug design points the way to novel proline racemase inhibitor candidates to fight Chagas’ disease, PLoS ONE 2013;8(4):e60955.
-
2013Funnel metadynamics as accurate binding free-energy method, Proc. Natl. Acad. Sci. U.S.A. 2013 Apr;110(16):6358-63.
-
2013Crystal structure of a eukaryotic phosphate transporter, Nature 2013 Apr;496(7446):533-6.
-
2013Methylations of tryptophan-modified naphthoquinone affect its inhibitory potential toward Aβ aggregation, J Phys Chem B 2013 Feb;117(6):1780-9.
-
2012Ordered phosphorylation events in two independent cascades of the PTEN C-tail revealed by NMR, J. Am. Chem. Soc. 2012 Dec;134(50):20533-43.
-
2012A convective replica-exchange method for sampling new energy basins, J Comput Chem 2013 Jan;34(2):132-40.
-
2012Contact-based ligand-clustering approach for the identification of active compounds in virtual screening, Adv Appl Bioinform Chem 2012;5:61-79.
-
2012Optimization of designed armadillo repeat proteins by molecular dynamics simulations and NMR spectroscopy, Protein Sci. 2012 Sep;21(9):1298-314.
-
2012CSB: a Python framework for structural bioinformatics, Bioinformatics 2012 Nov;28(22):2996-7.
-
2012High selectivity of the γ-aminobutyric acid transporter 2 (GAT-2, SLC6A13) revealed by structure-based approach, J. Biol. Chem. 2012 Nov;287(45):37745-56.
-
2012Interference with the PTEN-MAST2 interaction by a viral protein leads to cellular relocalization of PTEN, Sci Signal 2012 Aug;5(237):ra58.
-
2012pH-dependent molecular dynamics of vesicular stomatitis virus glycoprotein G, Proteins 2012 Nov;80(11):2601-13.
-
2012Photocontrol of reversible amyloid formation with a minimal-design peptide, J Phys Chem B 2012 Aug;116(30):8961-73.
-
2012Efficient Simulation of Explicitly Solvated Proteins in the Well-Tempered Ensemble, J Chem Theory Comput 2012 Jul;8(7):2189-92.
-
2012Efficient modeling of symmetric protein aggregates from NMR data, Angew. Chem. Int. Ed. Engl. 2012 Jul;51(28):6916-9.
-
2012Differential role of calmodulin and calcium ions in the stabilization of the catalytic domain of adenyl cyclase CyaA from Bordetella pertussis, Proteins 2012 Apr;80(4):1028-40.
-
2012ARIA for solution and solid-state NMR, Methods Mol. Biol. 2012;831:453-83.
-
2011The redundancy of NMR restraints can be used to accelerate the unfolding behavior of an SH3 domain during molecular dynamics simulations, BMC Struct. Biol. 2011;11:46.
-
2011Peptides targeting the PDZ domain of PTPN4 are efficient inducers of glioblastoma cell death, Structure 2011 Oct;19(10):1518-24.
-
2011Structural basis for inhibiting β-amyloid oligomerization by a non-coded β-breaker-substituted endomorphin analogue, ACS Chem. Biol. 2011 Nov;6(11):1265-76.
-
2011Pharmacological and structural characterization of long-sarafotoxins, a new family of endothelin-like peptides: Role of the C-terminus extension, Biochimie 2012 Feb;94(2):461-70.
-
2011A chirality-based metrics for free-energy calculations in biomolecular systems, J Comput Chem 2011 Sep;32(12):2627-37.
-
2011Assessing the Quality of the OPEP Coarse-Grained Force Field, J Chem Theory Comput 2011 Jun;7(6):1928-34.
-
2011Grid computing for improving conformational sampling in NMR structure calculation, Bioinformatics 2011 Jun;27(12):1713-4.
-
2011ATP binding enables broad antibiotic selectivity of aminoglycoside phosphotransferase(3′)-IIIa: an elastic network analysis, J. Mol. Biol. 2011 Jun;409(3):450-65.
-
2011Mechanism of reactant and product dissociation from the anthrax edema factor: a locally enhanced sampling and steered molecular dynamics study, Proteins 2011 May;79(5):1649-61.
-
2011Bayesian estimation of NMR restraint potential and weight: a validation on a representative set of protein structures, Proteins 2011 May;79(5):1525-37.
-
2010Amyloid fibril polymorphism is under kinetic control, J. Am. Chem. Soc. 2010 Oct;132(42):14960-70.
-
2010Multiple routes and milestones in the folding of HIV-1 protease monomer, PLoS ONE 2010 Oct;5(10):e13208.
-
2010Activation of the edema factor of Bacillus anthracis by calmodulin: evidence of an interplay between the EF-calmodulin interaction and calcium binding, Biophys. J. 2010 Oct;99(7):2264-72.
-
2010Structural insights into serine-rich fimbriae from Gram-positive bacteria, J. Biol. Chem. 2010 Oct;285(42):32446-57.
-
2010Complete phenotypic recovery of an Alzheimer’s disease model by a quinone-tryptophan hybrid aggregation inhibitor, PLoS ONE 2010;5(6):e11101.
-
2010Simultaneous use of solution, solid-state NMR and X-ray crystallography to study the conformational landscape of the Crh protein during oligomerization and crystallization, Adv Appl Bioinform Chem 2010;3:25-38.
-
2010Use of allostery to identify inhibitors of calmodulin-induced activation of Bacillus anthracis edema factor, Proc. Natl. Acad. Sci. U.S.A. 2010 Jun;107(25):11277-82.
-
2010Linking well-tempered metadynamics simulations with experiments, Biophys. J. 2010 May;98(9):L44-6.
-
2010Molecular basis of cyclooxygenase enzymes (COXs) selective inhibition, Proc. Natl. Acad. Sci. U.S.A. 2010 Mar;107(12):5411-6.
-
2010Attenuation of rabies virulence: takeover by the cytoplasmic domain of its envelope protein, Sci Signal 2010 Jan;3(105):ra5.
-
2009ATP conformations and ion binding modes in the active site of anthrax edema factor: a computational analysis, Proteins 2009 Dec;77(4):971-83.
-
2009Automatic clustering of docking poses in virtual screening process using self-organizing map, Bioinformatics 2010 Jan;26(1):53-60.
-
2009DARPin-assisted crystallography of the CC2-LZ domain of NEMO reveals a coupling between dimerization and ubiquitin binding, J. Mol. Biol. 2010 Jan;395(1):89-104.
-
2009How does a simplified-sequence protein fold?, Biophys. J. 2009 Sep;97(6):1737-46.
-
2009Influence of different assignment conditions on the determination of symmetric homodimeric structures with ARIA, Proteins 2009 May;75(3):569-85.
-
20099,10-Anthraquinone hinders beta-aggregation: how does a small molecule interfere with Abeta-peptide amyloid fibrillation?, Protein Sci. 2009 Apr;18(4):792-800.
-
2009Dynamics and energetics: a consensus analysis of the impact of calcium on EF-CaM protein complex, Biophys. J. 2009 Feb;96(4):1249-63.
-
2008Amyloid aggregation on lipid bilayers and its impact on membrane permeability, J. Mol. Biol. 2009 Mar;387(2):407-15.
-
2008The zinc finger of NEMO is a functional ubiquitin-binding domain, J. Biol. Chem. 2009 Jan;284(5):2902-7.
-
2008Structural biology by NMR: structure, dynamics, and interactions, PLoS Comput. Biol. 2008;4(9):e1000168.
-
2008The unfolded ensemble and folding mechanism of the C-terminal GB1 beta-hairpin, J. Am. Chem. Soc. 2008 Oct;130(42):13938-44.
-
2008Accurate NMR structures through minimization of an extended hybrid energy, Structure 2008 Sep;16(9):1305-12.
-
2008Graphical analysis of NMR structural quality and interactive contact map of NOE assignments in ARIA, BMC Struct. Biol. 2008;8:30.
-
2008The conformational plasticity of calmodulin upon calcium complexation gives a model of its interaction with the oedema factor of Bacillus anthracis, Proteins 2008 Jun;71(4):1813-29.
-
2008The key-role of tyrosine 155 in the mechanism of prion transconformation as highlighted by a study of sheep mutant peptides, Peptides 2008 Jul;29(7):1073-84.
-
20083D structure determination of the Crh protein from highly ambiguous solid-state NMR restraints, J. Am. Chem. Soc. 2008 Mar;130(11):3579-89.
-
2008Electrostatic contribution to the thermodynamic and kinetic stability of the homotrimeric coiled coil Lpp-56: A computational study, Proteins 2008 Feb;70(3):810-22.
-
2008Solution structure of NEMO zinc finger and impact of an anhidrotic ectodermal dysplasia with immunodeficiency-related point mutation, J. Mol. Biol. 2008 Apr;377(5):1419-32.
-
2008Direct detection of N-H[…]O=C hydrogen bonds in biomolecules by NMR spectroscopy, Nat Protoc 2008;3(2):235-41.
-
2008Direct detection of N-H[…]N hydrogen bonds in biomolecules by NMR spectroscopy, Nat Protoc 2008;3(2):242-8.
-
2007Designed armadillo repeat proteins as general peptide-binding scaffolds: consensus design and computational optimization of the hydrophobic core, J. Mol. Biol. 2008 Mar;376(5):1282-304.
-
2007Pathways and intermediates of amyloid fibril formation, J. Mol. Biol. 2007 Dec;374(4):917-24.
-
2007Insight into the folding inhibition of the HIV-1 protease by a small peptide, Biophys. J. 2007 Oct;93(8):2813-21.
-
2006ARIA2: automated NOE assignment and data integration in NMR structure calculation, Bioinformatics 2007 Feb;23(3):381-2.
-
2006DNA recognition by the brinker repressor–an extreme case of coupling between binding and folding, J. Mol. Biol. 2006 Aug;361(4):659-72.
-
2006Interpreting the aggregation kinetics of amyloid peptides, J. Mol. Biol. 2006 Jul;360(4):882-92.
-
2006Comparison of different torsion angle approaches for NMR structure determination, J. Biomol. NMR 2006 Mar;34(3):153-66.
-
2005Prediction of aggregation rate and aggregation-prone segments in polypeptide sequences, Protein Sci. 2005 Oct;14(10):2723-34.
-
2005Organism complexity anti-correlates with proteomic beta-aggregation propensity, Protein Sci. 2005 Oct;14(10):2735-40.
-
2004Membrane localization and flexibility of a lipidated ras peptide studied by molecular dynamics simulations, J. Am. Chem. Soc. 2004 Nov;126(46):15277-86.
-
2004The role of aromaticity, exposed surface, and dipole moment in determining protein aggregation rates, Protein Sci. 2004 Jul;13(7):1939-41.
-
2004Ensemble variance in free energy calculations by thermodynamic integration: theory, optimal “Alchemical” path, and practical solutions, J Comput Chem 2004 May;25(7):985-93.
-
2004Effect of multiple symmetries on the association of R67 DHFR subunits bearing interfacial complementing mutations, Protein Sci. 2004 Jan;13(1):1-14.