• E-postNathalie.Reuter@uib.no
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    Høyteknologisenteret, Datablokk, 5.etasje
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Protein Dynamics, Molecular Modeling, Amphitropic Proteins

MOL204 - Applied bioinformatics I
MOL217 - Applied bioinformatics II

  • Vis forfatter(e) 2021. Phospholipids in Motion: High-Resolution 31 P NMR Field Cycling Studies. Journal of Physical Chemistry B. 8827-8838.
  • Vis forfatter(e) 2021. Membrane models for molecular simulations of peripheral membrane proteins. Advances in Physics: X.
  • Vis forfatter(e) 2021. Martini 3: a general purpose force field for coarse-grained molecular dynamics. Nature Methods. 382-388.
  • Vis forfatter(e) 2020. Visual exploration of large normal mode spaces to study protein flexibility. Computers & graphics. 73-83.
  • Vis forfatter(e) 2020. The Arabidopsis (ASHH2) CW domain binds monomethylated K4 of the histone H3 tail through conformational selection. The FEBS Journal. 4458-4480.
  • Vis forfatter(e) 2020. Levels of proteinase 3 and neutrophil elastase in plasma, BAL and biopsies in COPD. European Respiratory Journal.
  • Vis forfatter(e) 2020. Dynamics-function relationship in the catalytic domains of N-terminal acetyltransferases. Computational and Structural Biotechnology Journal. 532-547.
  • Vis forfatter(e) 2020. Classification and phylogeny for the annotation of novel eukaryotic GNAT acetyltransferases. PLoS Computational Biology. 1-29.
  • Vis forfatter(e) 2020. Capturing Choline–Aromatics Cation−π Interactions in the MARTINI Force Field. Journal of Chemical Theory and Computation.
  • Vis forfatter(e) 2019. Peptidomimetic inhibitors targeting the membrane-binding site of the neutrophil proteinase 3. Biochimica et Biophysica Acta - Biomembranes. 1502-1509.
  • Vis forfatter(e) 2019. Interfacial Aromatics Mediating Cation−π Interactions with Choline-Containing Lipids Can Contribute as Much to Peripheral Protein Affinity for Membranes as Aromatics Inserted below the Phosphates. The Journal of Physical Chemistry Letters. 3972-3977.
  • Vis forfatter(e) 2019. Cation‐π Interactions between Methylated Ammonium Groups and Tryptophan in the CHARMM36 Additive Force Field. Journal of Chemical Theory and Computation. 7-12.
  • Vis forfatter(e) 2018. Structure and dynamics of the N-terminal acetyltransferase family: a computational study.
  • Vis forfatter(e) 2018. Search and subvert: Minimalist bacterial phosphatidylinositol-specific phospholipase C enzymes. Chemical Reviews. 8435-8473.
  • Vis forfatter(e) 2018. D-peptides as inhibitors of PR3-membrane interactions. Biochimica et Biophysica Acta - Biomembranes. 458-466.
  • Vis forfatter(e) 2018. Conservation of intrinsic dynamics in proteins-what have computational models taught us? Current Opinion in Structural Biology. 75-81.
  • Vis forfatter(e) 2018. A model for hydrophobic protrusions on peripheral membrane proteins. PLoS Computational Biology. 1-26.
  • Vis forfatter(e) 2017. Molecular determinants of the N-Terminal acetyltransferase Naa60 anchoring to the Golgi membrane. Journal of Biological Chemistry. 6821-6837.
  • Vis forfatter(e) 2017. Interactions stabilizing the C-terminal helix of human phospholipid scramblase 1 in lipid bilayers: A computational study. Biochimica et Biophysica Acta - Biomembranes. 1200-1210.
  • Vis forfatter(e) 2016. Similarity in Shape Dictates Signature Intrinsic Dynamics Despite No Functional Conservation in TIM Barrel Enzymes. PLoS Computational Biology. 26 sider.
  • Vis forfatter(e) 2016. Role of noncovalent interactions in protein peripheral membrane binding. Computational perspectives.
  • Vis forfatter(e) 2016. Proteinase 3 is a phosphatidylserine-binding protein that affects the production and function of microvesicles. Journal of Biological Chemistry. 10476-10489.
  • Vis forfatter(e) 2016. Improving the force field description of tyrosine-choline cation-π interactions: QM investigation of Phenol-N(Me)4 Interactions. Journal of Chemical Theory and Computation. 5585-5595.
  • Vis forfatter(e) 2016. A Role for Weak Electrostatic Interactions in Peripheral Membrane Protein Binding. Biophysical Journal. 1367-1378.
  • Vis forfatter(e) 2015. Quantifying transient interactions between bacillus phosphatidylinositol-specific phospholipase-C and phosphatidylcholine-rich vesicles. Journal of the American Chemical Society. 14-17.
  • Vis forfatter(e) 2015. Membrane docking of the synaptotagmin 7 C2A domain: computation reveals interplay between electrostatic and hydrophobic contributions. Biochemistry. 5696-5711.
  • Vis forfatter(e) 2015. Comparing the intrinsic dynamics of multiple protein structures using elastic network models. Biochimica et Biophysica Acta - General Subjects. 911-922.
  • Vis forfatter(e) 2015. Biochemical and cellular analysis of Ogden syndrome reveals downstream Nt-acetylation defects. Human Molecular Genetics. 1956-1976.
  • Vis forfatter(e) 2014. WEBnm@ v2.0: Web server and services for comparing protein flexibility. BMC Bioinformatics.
  • Vis forfatter(e) 2014. Two homologous neutrophil serine proteases bind to POPC vesicles with different affinities: When aromatic amino acids matter. Biochimica et Biophysica Acta - Biomembranes. 3191-3202.
  • Vis forfatter(e) 2014. Synthesis and biological evaluation of pseudopeptide inhibitors of Proteinase 3.
  • Vis forfatter(e) 2014. Reversible ketomethylene-based inhibitors of human neutrophil proteinase 3. Journal of Medicinal Chemistry. 9396-9408.
  • Vis forfatter(e) 2014. In silico, in vitro and in vivo models reveal functional impairment of the Ogden syndrome N-terminal acetyltransferase Naa10 S37P mutant.
  • Vis forfatter(e) 2014. In silico design, synthesis, and assays of specific substrates for proteinase 3: Influence of fluorogenic and charged groups. Journal of Medicinal Chemistry. 1111-1115.
  • Vis forfatter(e) 2014. Evolution of oligomeric state through allosteric pathways that mimic ligand binding. Science.
  • Vis forfatter(e) 2014. Characterization of immunological cross-reactivity between enterotoxigenic Escherichia coli heat-stable toxin and human guanylin and uroguanylin. Infection and Immunity. 2913-2922.
  • Vis forfatter(e) 2014. Automated Enzyme Function Inference in Archaea Genomes:comparison of PRIAM and EFICAZ.
  • Vis forfatter(e) 2013. Visual cavity analysis in molecular simulations. BMC Bioinformatics.
  • Vis forfatter(e) 2013. Probing for π-Cation Interactions in the Binding of B. Thuringiensis Phosphatidylinositol-Specific Phospholipase C Phosphatidylcholine-Rich Vesicles.
  • Vis forfatter(e) 2013. Probing for pi-cation interactions in the binding of B. thuringiensis phohosphatidylinositol-specific phospholipase C phosphatidylcholine-rich vesicles. Biophysical Journal. 363A-364A.
  • Vis forfatter(e) 2013. Expert system for mining and sifting novel enzyme sequences in metagenomics data.
  • Vis forfatter(e) 2013. Examining the flexibility of tim barrel proteins based on their structural topology. Biophysical Journal. 227A-228A.
  • Vis forfatter(e) 2013. Evaluation of protein elastic network models based on an analysis of collective motions. Journal of Chemical Theory and Computation. 5618-5628.
  • Vis forfatter(e) 2013. Does changing the predicted dynamics of a phospholipase C alter activity and membrane binding? Biophysical Journal. 185-195.
  • Vis forfatter(e) 2013. Comparing normal modes of protein structures using Webnm@ 2.0. Biophysical Journal. 228A-228A.
  • Vis forfatter(e) 2013. Comparing aminoglycoside binding sites in bacterial ribosomal RNA and aminoglycoside modifying enzymes. Proteins: Structure, Function, and Bioinformatics. 63-80.
  • Vis forfatter(e) 2013. Characterization of cytosolic proliferating cell nuclear antigen (PCNA) in neutrophils: anti-apoptotic role of monomeric PCNA. European Journal of Clinical Investigation. 20-20.
  • Vis forfatter(e) 2013. Cation-π interactions as specific anchors for B. Thuringiensis PhosphoInositol-specific PhosphoLipase-C binding to Phosphatidylcholine bilayer.
  • Vis forfatter(e) 2013. Cation-π interactions as lipid specific anchors for phosphatidylinositol-specific phospholipase-C.
  • Vis forfatter(e) 2013. Cation-pi Interactions As Lipid-Specific Anchors for Phosphatidylinositol-Specific Phospholipase C. Journal of the American Chemical Society. 5740-5750.
  • Vis forfatter(e) 2013. Cation-PI interactions as specific anchors for B. thurigiensis phosphoinositol-specific phospholipase-C binding to phosphatidylcholine bilayer. Biophysical Journal. 536A-536A.
  • Vis forfatter(e) 2013. Aromatic amino acid distribution in peripheral membrane proteins. .
  • Vis forfatter(e) 2012. Structural modeling and kinetic studies of a mutant N-terminal acetyltransferase, hNaa10p Ser37Pro, causing an infantile lethal disorder.
  • Vis forfatter(e) 2012. Specificity and Versatility of Substrate Binding Sites in Four Catalytic Domains of Human N-Terminal Acetyltransferases. PLOS ONE.
  • Vis forfatter(e) 2012. PR3 Interacts Directly to Lipid Bilayers: Evidence from MD Simulations and SPR Experiments. Biophysical Journal. 497A-497A.
  • Vis forfatter(e) 2012. PR3 Interacts Directly to Lipid Bilayers: Evidence from MD Simulations and SPR Experiments.
  • Vis forfatter(e) 2012. Nuclear-to-cytoplasmic Relocalization of the Proliferating Cell Nuclear Antigen (PCNA) during Differentiation Involves a Chromosome Region Maintenance 1 (CRM1)-dependent Export and Is a Prerequisite for PCNA Antiapoptotic Activity in Mature Neutrophils. Journal of Biological Chemistry. 33812-33825.
  • Vis forfatter(e) 2012. Measuring and comparing structural fluctuation patterns in large protein datasets. Bioinformatics. 2431-2440.
  • Vis forfatter(e) 2012. Implicit Surfaces for Interactive Graph Based Cavity Analysis of Molecular Simulations. 9 sider.
  • Vis forfatter(e) 2012. Anchoring of PI-PLC to DMPC Bilayers Involves Specific Cation-PI Interactions. Biophysical Journal. 78A-79A.
  • Vis forfatter(e) 2012. Anchoring of PI-PLC to DMPC Bilayers Involves Specific Cation-PI Interactions.
  • Vis forfatter(e) 2012. An x-linked infantile lethal disorder caused by N-terminal acetyltransferase deficiency.
  • Vis forfatter(e) 2012. A dynamic model of long-range conformational adaptations triggered by nucleotide binding in GroEL-GroES. Proteins: Structure, Function, and Bioinformatics. 2333-2346.
  • Vis forfatter(e) 2011. Principal component and normal mode analysis of proteins; a quantitative comparison using the GroEL subunit. Proteins: Structure, Function, and Bioinformatics. 232-243.
  • Vis forfatter(e) 2011. Molecular analysis of the membrane insertion domain of proteinase 3, the Wegener's autoantigen, in RBL cells: implication for its pathogenic activity. Journal of Leukocyte Biology. 941-950.
  • Vis forfatter(e) 2011. Mechanistic Investigation of Aromatic Amino Acid Hydroxylases. A Density Functional Theory Study.
  • Vis forfatter(e) 2011. Interactive Visual Analysis of Temporal Cluster Structures. Computer Graphics Forum. 711-720.
  • Vis forfatter(e) 2011. Integrating Cluster Formation and Cluster Evaluation in Interactive Visual Analysis. 8 sider.
  • Vis forfatter(e) 2011. Exploring the factors determining the dynamics of different protein folds. Protein Science. 197-209.
  • Vis forfatter(e) 2011. Dynamics, flexibility and ligand induced conformational changes in biological macromolecules: a computational approach. Future Medicinal Chemistry. 2079-2100.
  • Vis forfatter(e) 2011. Conformational sampling and nucleotide-dependent transitions of the GroEL subunit probed by unbiased molecular dynamics simulations. PLoS Computational Biology.
  • Vis forfatter(e) 2011. Comparison of PR3 and PI-PLC binding to a DMPC bilayer.
  • Vis forfatter(e) 2010. Structures of human proteinase 3 and neutrophil elastase - so similar yet so different. The FEBS Journal. 2238-2254.
  • Vis forfatter(e) 2010. Proliferating cell nuclear antigen acts as a cytoplasmic platform controlling human neutrophil survival. Journal of Experimental Medicine (JEM). 2631-2645.
  • Vis forfatter(e) 2010. Molecular Dynamics Simulations of Mixed Acidic/Zwitterionic Phospholipid Bilayers. Biophysical Journal. 825-833.
  • Vis forfatter(e) 2010. Interaction of proteinase 3 with its associated partners: implications in the pathogenesis of Wegener's granulomatosis. Current Opinion in Rheumatology. 1-7.
  • Vis forfatter(e) 2010. How does Proteinase 3 interact with lipid bilayers? Physical Chemistry, Chemical Physics - PCCP. 7487-7496.
  • Vis forfatter(e) 2009. Normal mode analysis for proteins. Journal of Molecular Structure: THEOCHEM. 42-48.
  • Vis forfatter(e) 2009. Mutagenesis analysis of the insertion domain of proteinase 3 into membrane: a potential target for anti-inflammatory therapy in vasculitis. APMIS : Acta pathologica, microbiologica et immunologica Scandinavica. Supplementum. 121-121.
  • Vis forfatter(e) 2009. Challenges in pK(a) Predictions for Proteins: The case of Asp213 in Human Proteinase 3. Journal of Physical Chemistry A. 11783-11792.
  • Vis forfatter(e) 2008. Computational prediction of the binding site of proteinase 3 to the plasma membrane. Proteins: Structure, Function, and Bioinformatics. 1655-1669.
  • Vis forfatter(e) 2007. Two-Level Approach to Efficient Visualization of Protein Dynamics. IEEE Transactions on Visualization and Computer Graphics. 1616-1623.
  • Vis forfatter(e) 2007. TMM@: a web application for the analysis of transmembrane helix mobility. BMC Bioinformatics. 8 sider.
  • Vis forfatter(e) 2007. Molecular modeling of the substrate specificity and of the membrane anchoring of Proteinase 3.
  • Vis forfatter(e) 2007. Influence of charge distribution at the active site surface on the substrate specificity of human neutrophil protease 3 and elastase - A kinetic and molecular modeling analysis. Journal of Biological Chemistry. 1989-1997.
  • Vis forfatter(e) 2007. Differences in the substrate binding sites of murine and human proteinase 3 and neutrophil elastase. FEBS Letters. 5685-5690.
  • Vis forfatter(e) 2007. Bioinformatikk anvendt på lokalanestetikas virkningsmekanisme. Den norske tannlegeforenings tidende. 672-675.
  • Vis forfatter(e) 2006. Inspection of the binding sites of proteinase3 for the design of a highly specific substrate. Journal of Medicinal Chemistry. 1248-1260.
  • Vis forfatter(e) 2006. Evaluation of models for the evolution of protein sequences and functions under structural constraint. Biophysical Chemistry. 134-144.
  • Vis forfatter(e) 2006. A novel locust (Schistocerca gregaria) serine protease inhibitor with a high affinity for neutrophil elastase. Biochemical Journal. 467-476.
  • Vis forfatter(e) 2005. WEBnm@: a web application for normal mode analyses of proteins. BMC Bioinformatics.
  • Vis forfatter(e) 2005. Normal mode-based fitting of atomic structure into electron density maps: Application to sarcoplasmic reticulum Ca-ATPase. Biophysical Journal. 818-827.
  • Vis forfatter(e) 2005. Cleavage of p21/WAF1/CIP1 by proteinase 3 modulates differentiation of a monocytic cell line. Journal of Biological Chemistry. 30242-30253.
  • Vis forfatter(e) 2004. The norwegian bioinformatics platform.
  • Vis forfatter(e) 2004. Normal modes of the Ca2+-ATPase based on a comparison between the E1Ca2 and E2TG structures.

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