Institute of Biological Information Processing (IBI)

Poster (Other) ma, p. (Corresponding author)FZJ* ; Olubiyi, O.FZJ* ; Strodel, B.FZJ* ; Weiergräber, O. H.FZJ*
Conformational polymorphism in Atg8 family proteins
201321st Annual Meeting of the German Crystallographic Society (DGK), DGK 2013, Heinrich-Heine-Universität DüsseldorfFreiberg, Heinrich-Heine-Universität Düsseldorf, Germany, 21 Mar 2013 - 21 Mar 20132013-03-212013-03-21 Fulltext BibTeX | EndNote: XML, Text | RIS

Journal Article ma, p.FZJ* ; Schwarten, M.FZJ* ; Schneider, L.FZJ* ; Boeske, A. ; Henke, N. ; Lisak, D. ; Weber, S.FZJ* ; Mohrluder, J.FZJ* ; Stoldt, M.FZJ* ; Strodel, B.FZJ* ; Methner, A. ; Hoffmann, S.FZJ* ; Weiergraber, O. H.FZJ* ; Willbold, D. (Corresponding author)FZJ*
Interaction of Bcl-2 with the autophagy-related GABAA receptor-associated protein (GABARAP): biophysical characterization and functional implications
The journal of biological chemistry 288, 37204-37215 (2013) [10.1074/jbc.M113.528067]2013 Files Fulltext BibTeX | EndNote: XML, Text | RIS

Journal Article Ma, P. ; Schillinger, O.FZJ* ; Schwarten, M.FZJ* ; Lecher, J.FZJ* ; Hartmann, R.FZJ* ; Stoldt, M.FZJ* ; Mohrlüder, J.FZJ* ; Olubiyi, O. ; Strodel, B.FZJ* ; Willbold, D.FZJ* ; Weiergräber, O. H. (Corresponding author)FZJ*
Conformational Polymorphism in Autophagy-Related Protein GATE-16
Biochemistry 54(35), 5469 - 5479 (2015) [10.1021/acs.biochem.5b00366]2015 Files BibTeX | EndNote: XML, Text | RIS

Poster Mandrysch, A. ; Kovacic, F.FZJ* ; Poojari, C. ; Strodel, B.FZJ* ; Jaeger, K.-E.FZJ*
Thermal adaptation of esterases through the evolution of loop regions
2015FEMS 6th Congress of European Microbiologists, MaastrichtMaastricht, Netherlands, 7 Jun 2015 - 11 Jun 20152015-06-072015-06-11 BibTeX | EndNote: XML, Text | RIS

Journal Article Möckel, C.FZJ* ; Kubiak, J. ; Schillinger, O. ; Kühnemuth, R. ; Della Corte, D. ; Schröder, G. F.FZJ* ; Willbold, D.FZJ* ; Strodel, B. (Corresponding author)FZJ* ; Seidel, C. A. M. (Corresponding author)FZJ* ; Neudecker, P. (Corresponding author)FZJ*
Integrated NMR, Fluorescence, and Molecular Dynamics Benchmark Study of Protein Mechanics and Hydrodynamics
The journal of physical chemistry <Washington, DC> / B B, Condensed matter, materials, surfaces, interfaces & biophysical 123(7), 1453 - 1480 (2019) [10.1021/acs.jpcb.8b08903]2019 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Musselman, C.Extern* ; Kanelis, V.Extern* ; Lecomte, S. ; Strodel, B. (Corresponding author)FZJ*
Editorial for the special issue “A Celebration of Women in Biophysical Chemistry”
Biophysical chemistry 292, 106929 - (2023) [10.1016/j.bpc.2022.106929]2023 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Nasica-Labouze, J. ; Nguyen, P. H. ; Sterpone, F. ; Berthoumieu, O. ; Buchete, N.-V. ; Coté, S. ; De Simone, A. ; Doig, A. J. ; Faller, P. ; Garcia, A. ; Laio, A. ; Li, M. S. ; Melchionna, S. ; Mousseau, N. ; Mu, Y. ; Paravastu, A. ; Pasquali, S. ; Rosenman, D. J. ; Strodel, B.FZJ* ; Tarus, B. ; Viles, J. H. ; Zhang, T. ; Wang, C. ; Derreumaux, P. (Corresponding author)
Amyloid β Protein and Alzheimer’s Disease: When Computer Simulations Complement Experimental Studies
Chemical reviews 115(9), 3518 - 3563 (2015) [10.1021/cr500638n]2015 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Nguyen, P. H. ; Ramamoorthy, A. ; Sahoo, B. R. ; Zheng, J. ; Faller, P. ; Straub, J. E. ; Dominguez, L. ; Shea, J.-E. ; Dokholyan, N. V. ; De Simone, A. ; Ma, B. ; Nussinov, R. ; Najafi, S. ; Ngo, S. T. ; Loquet, A. ; Chiricotto, M. ; Ganguly, P. ; McCarty, J. ; Li, M. S. ; Hall, C. ; Wang, Y. ; Miller, Y. ; Melchionna, S. ; Habenstein, B. ; Timr, S. ; Chen, J. ; Hnath, B. ; Strodel, B.FZJ* ; Kayed, R. ; Lesné, S. ; Wei, G. ; Sterpone, F. ; Doig, A. J. ; Derreumaux, P. (Corresponding author)
Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer’s Disease, Parkinson’s Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis
Chemical reviews 121(4), 2545 - 2647 (2021) [10.1021/acs.chemrev.0c01122]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Olagunju, M. O.FZJ* ; Loschwitz, J.FZJ* ; Olubiyi, O. O. ; Strodel, B. (Corresponding author)FZJ*
Multiscale MD simulations of wild‐type and sickle hemoglobin aggregation
Proteins 90(11), 1811 - 1824 (2022) [10.1002/prot.26352]2022 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Conference Presentation Olubiyi, O.FZJ* ; Strodel, B.FZJ*
Effects of an amyloid-inhibiting D-peptide on the conformation of Alzheimer's Abeta peptide.
2011Computer Simulation and Theory of Macromolecules 2011
Seminar, Hünfeld, DeutschlandHünfeld, Deutschland, 15 Apr 20112011-04-15 BibTeX | EndNote: XML, Text | RIS

Poster Olubiyi, O.FZJ* ; Strodel, B.FZJ*
Interactions of Alzheimer's Aß Peptide with the D-peptide D3 and Lipid Bilayers
2010Computer Simulation and Theory of Macromolecules 2010
Seminar, Hünfeld, DeutschlandHünfeld, Deutschland, 16 Apr 20102010-04-16 BibTeX | EndNote: XML, Text | RIS

Poster Olubiyi, O.FZJ* ; Poojari, C.FZJ* ; Osborne, K.FZJ* ; Strodel, B.FZJ*
Multiscale Modelling of Amyloid Aggregation
2010Multiscale Molecular Modelling: Molecular Dynamics, Computational Statistical Mechanics, and Simulation Algorithms
Seminar, Edinburgh, UKEdinburgh, UK, 30 Jun 20102010-06-30 BibTeX | EndNote: XML, Text | RIS

Talk (non conference) Olubiyi, O.FZJ* ; Strodel, B.FZJ*
Molecular simulation studies on the prevention of amyloid aggregation of Alzheimer's Aβ peptide by D-peptides
2011THE BRAIN: Young Researchers Transatlantic Academy
Seminar, Philadelphia, PA, USAPhiladelphia, PA, USA, 12 Jun 20112011-06-12 BibTeX | EndNote: XML, Text | RIS

Poster Olubiyi, O.FZJ* ; Strodel, B.FZJ*
Computational investigation of Abeta (Aβ) peptide folding: Effect of pH and an amyloid inhibiting D-peptide on the structural propensities of Aβ
2011Amyloid Fibrils, Prions and Precursors: Molecules for Targeted Intervention
Seminar, Halle (Saale), DeutschlandHalle (Saale), Deutschland, 25 Aug 20112011-08-25 BibTeX | EndNote: XML, Text | RIS

Poster Olubiyi, O.FZJ* ; Strodel, B.FZJ*
Computational study of Alzheimer's disease abeta peptide aggregation inhibition by a D-peptide.
2011Computer Simulation and Theory of Macromolecules 2011
Seminar, Hünfeld, DeutschlandHünfeld, Deutschland, 15 Apr 20112011-04-15 BibTeX | EndNote: XML, Text | RIS

Journal Article Olubiyi, O. (Corresponding author)FZJ* ; Strodel, B.FZJ*
Structures of the Amyloid β-Peptides Aβ1-40 and Aβ1-42 as Influenced by pH and a D-Peptide
The journal of physical chemistry <Washington, DC> / B 116(10), 3280-3291 (2012) [10.1021/jp2076337]2012 BibTeX | EndNote: XML, Text | RIS

Journal Article Olubiyi, O. ; Frenzel, D.FZJ* ; Bartnik, D. ; Glück, J. ; Brener, O. ; Nagel-Steger, L.FZJ* ; Funke, S. A. ; Willbold, D. (Corresponding Author)FZJ* ; Strodel, B.FZJ*
Amyloid Aggregation Inhibitory Mechanism of Arginine-rich D-peptides
Current medicinal chemistry 21, 1448-1457 (2014)2014 Files Fulltext BibTeX | EndNote: XML, Text | RIS

Journal Article Olubiyi, O. (Corresponding author) ; Strodel, B.FZJ*
Topology and parameter data of thirteen non-natural amino acids for molecular simulations with CHARMM22
Data in Brief 9, 642 - 647 (2016) [10.1016/j.dib.2016.09.051]2016 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Olubiyi, O. (Corresponding author)FZJ* ; Olagunju, M. O.FZJ* ; Strodel, B.FZJ*
Rational Drug Design of Peptide-Based Therapies for Sickle Cell Disease
Molecules 24(24), 4551 - (2019) [10.3390/molecules24244551]2019 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Olubiyi, O.FZJ* ; Olagunju, M.FZJ* ; Keutmann, M.FZJ* ; Loschwitz, J.FZJ* ; Strodel, B. (Corresponding author)FZJ*
High Throughput Virtual Screening to Discover Inhibitors of the Main Protease of the Coronavirus SARS-CoV-2
Molecules 25(14), 3193 - (2020) [10.3390/molecules25143193]2020 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Proceedings Olubiyi, O. O. ; Funke, A. ; Willbold, D.FZJ* ; Strodel, B. (Corresponding Author)FZJ*
Modelling the Inhibition of Amyloid-β Aggregation causing Alzheimer's Disease using D-Peptides
201357th Annual Meeting of the Biophysical-Society, PhiladelphiaPhiladelphia, USA, 2 Feb 2013 - 6 Feb 20132013-02-022013-02-06 New York, NY : Rockefeller Univ. Press (2013) [10.1016/j.bpj.2012.11.2176]2013 BibTeX | EndNote: XML, Text | RIS

Poster Osborne, K.FZJ* ; Strodel, B.FZJ*
Coarse Grained Simulation of Amyloid Aggregation
2010Multiscale modelling of lipid bilayers under equilibrium and non-equilibrium conditions
Seminar, Lausanne, SwitzerlandLausanne, Switzerland, 27 Oct 20102010-10-27 BibTeX | EndNote: XML, Text | RIS

Journal Article Owen, M. (Corresponding author)FZJ* ; Csizmadia, I. G. ; Viskolcz, B. ; Strodel, B.FZJ*
Protein Stability and Unfolding Following Glycine Radical Formation
Molecules 22(4), 655 (2017) [10.3390/molecules22040655] special issue: "Biomolecular Simulations"2017 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Owen, M. C. (Corresponding author) ; Strodel, B.FZJ* ; Csizmadia, I. G. ; Viskolcz, B.
Radical Formation Initiates Solvent-Dependent Unfolding and β-Sheet Formation in a Model Helical Peptide
The journal of physical chemistry <Washington, DC> / B 120(22), 4878 - 4889 (2016) [10.1021/acs.jpcb.6b00174]2016 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Owen, M. C. ; Kulig, W. ; Poojari, C. ; Rog, T. ; Strodel, B. (Corresponding author)FZJ*
Physiologically-relevant levels of sphingomyelin, but not GM1, induces a β-sheet-rich structure in the amyloid-β(1-42) monomer
Biochimica et biophysica acta / Biomembranes Biomembranes [...] 1860(9), 1709 - 1720 (2018) [10.1016/j.bbamem.2018.03.026]2018 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Owen, M. C. (Corresponding author) ; Kulig, W. ; Rog, T. ; Vattulainen, I. ; Strodel, B. (Corresponding author)FZJ*
Cholesterol Protects the Oxidized Lipid Bilayer from Water Injury: An All-Atom Molecular Dynamics Study
The journal of membrane biology 251(3), 521 - 534 (2018) [10.1007/s00232-018-0028-9]2018 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Owen, M. C. ; Gnutt, D. ; Gao, M. ; Wärmländer, S. K. T. S. ; Jarvet, J. ; Gräslund, A. ; Winter, R. ; Ebbinghaus, S. ; Strodel, B. (Corresponding author)FZJ*
Effects of in vivo conditions on amyloid aggregation
Chemical Society reviews 48(14), 3946 - 3996 (2019) [10.1039/C8CS00034D]2019 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Paul, A. ; Samantray, S. ; Anteghini, M. ; Khaled, M.FZJ* ; Strodel, B. (Corresponding author)FZJ*
Thermodynamics and kinetics of the amyloid-β peptide revealed by Markov state models based on MD data in agreement with experiment
Chemical science 12(19), 6652 - 6669 (2021) [10.1039/D0SC04657D]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Petrovic, D.FZJ* ; Frank, D. ; Kamerlin, S. C. L. ; Hoffmann, K. (Corresponding author) ; Strodel, B. (Corresponding author)FZJ*
Shuffling Active Site Sub-State Populations Impacts Catalytic Activity: The Case of Glucose Oxidase
ACS catalysis 7, 6188–6197 (2017) [10.1021/acscatal.7b01575]2017 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Petrović, D. ; Wang, X.FZJ* ; Strodel, B. (Corresponding author)FZJ*
How accurately do force fields represent protein side chain ensembles?
Proteins 86(9), 935 - 944 (2018) [10.1002/prot.25525]2018 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Petrović, D. (Corresponding author) ; Bokel, A. ; Allan, M. ; Urlacher, V. B. ; Strodel, B. (Corresponding author)FZJ*
Simulation-Guided Design of Cytochrome P450 for Chemo- and Regioselective Macrocyclic Oxidation
Journal of chemical information and modeling 58(4), 848 - 858 (2018) [10.1021/acs.jcim.8b00043]2018 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Pfaff, L. ; Gao, J. ; Li, Z. ; Jäckering, A.FZJ* ; Weber, G. ; Mican, J. ; Chen, Y. ; Dong, W. ; Han, X. ; Feiler, C. G. ; Ao, Y.-F. ; Badenhorst, C. P. S. ; Bednar, D. ; Palm, G. J. ; Lammers, M. ; Damborsky, J. ; Strodel, B. (Corresponding author)FZJ* ; Liu, W. ; Bornscheuer, U. T. ; Wei, R.
Multiple Substrate Binding Mode-Guided Engineering of a Thermophilic PET Hydrolase
ACS catalysis 12(15), 9790 - 9800 (2022) [10.1021/acscatal.2c02275]2022 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Poster Poojari, C.FZJ* ; Strodel, B.FZJ*
Modelling transmembrane structures of Alzheimer's A1-42 peptide: Peptide insertion and A-membrane interactions
2011Amyloid Fibrils, Prions and Precursors: Molecules for Targeted Intervention
Seminar, Halle (Saale), DeutschlandHalle (Saale), Deutschland, 25 Aug 20112011-08-25 BibTeX | EndNote: XML, Text | RIS

Conference Presentation Poojari, C.FZJ* ; Strodel, B.FZJ*
Modelling transmembrane structures of Alzheimer's Aß1-42 peptide
2011Computer Simulation and Theory of Macromolecules 2011
Seminar, Hünfeld, DeutschlandHünfeld, Deutschland, 15 Apr 20112011-04-15 BibTeX | EndNote: XML, Text | RIS

Talk (non conference) Poojari, C.FZJ* ; Strodel, B.FZJ*
Modelling transmembrane structures of Alzheimer's A1-42 peptide
2011THE BRAIN: Young Researchers Transatlantic Academy
Seminar, Philadelphia PA. USAPhiladelphia PA. USA, 12 Jun 20112011-06-12 BibTeX | EndNote: XML, Text | RIS

Talk (non conference) Poojari, C.FZJ* ; Strodel, B.FZJ*
Modelling transmembrane structures of Alzheimer's A1-42 peptide
2011.
Seminar, Philadelphia, Drexel, Univ.Philadelphia, Drexel, Univ., 21 Jun 20112011-06-21 BibTeX | EndNote: XML, Text | RIS

Poster Poojari, C.FZJ* ; Strodel, B.FZJ*
Transmembrane structures for Alzheimer's Abt oligomers
2011Biophysical Society Meeting 2011
Seminar, Baltimore, USABaltimore, USA, 6 Mar 20112011-03-06 BibTeX | EndNote: XML, Text | RIS

Poster Poojari, C.FZJ* ; Strodel, B.FZJ*
Modellling the insertion of the Alzheimer's peptide into lipid bilayers and the resulting Abeta-membrane interactions
2011Membrane Proteins: Structure and Function
Seminar, Oxford,UKOxford,UK, 6 Apr 20112011-04-06 BibTeX | EndNote: XML, Text | RIS

Poster Poojari, C.FZJ* ; Strodel, B.FZJ*
Modelling transmembrane structures of Alzheimer's A1-42 peptide
2011Computer Simulation and Theory of Macromolecules 2011
Seminar, Hünfeld, DeutschlandHünfeld, Deutschland, 15 Apr 20112011-04-15 BibTeX | EndNote: XML, Text | RIS

Journal Article Poojari, C. (Corresponding author)FZJ* ; Kukol, A. ; Strodel, B.FZJ*
How the amyloid-β peptide and membranes affect each other: An extensive simulation study
Biochimica et biophysica acta / Biomembranes 1828(2), 327 - 339 (2013) [10.1016/j.bbamem.2012.09.001]2013 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Poojari, C.FZJ*ICS-6* ; Xiao, D. ; Batista, V. S. ; Strodel, B. (Corresponding author)FZJ*
Membrane Permeation Induced by Aggregates of Human Islet Amyloid Polypeptides
Biophysical journal 105, 2323-2332 (2013) [10.1016/j.bpj.2013.09.045]2013 Files Fulltext BibTeX | EndNote: XML, Text | RIS

Journal Article Poojari, C.FZJ*ICS-6* ; Strodel, B. (Corresponding Author)FZJ*
Stability of Transmembrane Amyloid ß-Peptide and Membrane Integrity Tested by Molecular Modeling of Site-Specific Aß$_{42}$ Mutations
PLoS one 8(11), e78399 (2013) [10.1371/journal.pone.0078399]2013 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Samantray, S.FZJ* ; Yin, F.FZJ* ; Kav, B.FZJ* ; Strodel, B. (Corresponding author)FZJ*
Different Force Fields Give Rise to Different Amyloid Aggregation Pathways in Molecular Dynamics Simulations
Journal of chemical information and modeling 60(12), 6462 - 6475 (2020) [10.1021/acs.jcim.0c01063]2020 Embargoed OpenAccess Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Samantray, S. (Corresponding author)FZJ* ; Olubiyi, O. O. (Corresponding author)FZJ* ; Strodel, B. (Corresponding author)FZJ*
The Influences of Sulphation, Salt Type, and Salt Concentration on the Structural Heterogeneity of Glycosaminoglycans
International journal of molecular sciences 22(21), 11529 - (2021) [10.3390/ijms222111529]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Samantray, S.FZJ* ; Strodel, B. (Corresponding author)FZJ*
The Effects of Different Glycosaminoglycans on the Structure and Aggregation of the Amyloid-β (16–22) Peptide
The journal of physical chemistry <Washington, DC> / B 125(21), 5511 - 5525 (2021) [10.1021/acs.jpcb.1c00868]2021 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Schäffler, M.FZJ* ; Khaled, M.FZJ* ; Strodel, B. (Corresponding author)FZJ*
ATRANET – Automated generation of transition networks for the structural characterization of intrinsically disordered proteins
Methods 206, 18 - 26 (2022) [10.1016/j.ymeth.2022.07.013]2022 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Schäffler, M.FZJ* ; Samantray, S. ; Strodel, B. (Corresponding author)FZJ*
Transition Networks Unveil Disorder-to-Order Transformations in Aβ Caused by Glycosaminoglycans or Lipids
International journal of molecular sciences 24(14), 11238 - (2023) [10.3390/ijms241411238]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Schillinger, O.FZJ* ; Panwalkar, V.FZJ* ; Strodel, B.FZJ* ; Dingley, A. (Corresponding author)FZJ*
Molecular Dynamics Simulations Reveal Key Roles of the Interleukin-6 Alpha Receptor in the Assembly of the Human Interleukin-6 Receptor Complex
The journal of physical chemistry letters 121, 8113-8122 (2017) [10.1021/acs.jpcb.7b05732]2017 Files BibTeX | EndNote: XML, Text | RIS

Preprint Schumann, W.FZJ* ; Strodel, B. (Corresponding author)FZJ*
Allosteric communication induced by GTP binding sets off a closed-to-open transition in a bacterial dynamin-like protein
[10.1101/2023.01.16.524228] Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Schumann, W. ; Loschwitz, J.FZJ* ; Reiners, J. ; Degrandi, D. ; Legewie, L. ; Stühler, K. ; Pfeffer, K. ; Poschmann, G. ; Smits, S. H. J. ; Strodel, B. (Corresponding author)FZJ*
Integrative modeling of guanylate binding protein dimers
Protein science 32(12), e4818 (2023) [10.1002/pro.4818]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Poster (Other) Schwarten, M. (Corresponding Author)FZJ* ; ma, p.FZJ* ; Schneider, L. ; Boeske, A. ; Henke, N. ; Lisak, D. ; Weber, S.FZJ* ; Mohrlüder, J.FZJ* ; Stoldt, M.FZJ* ; Strodel, B.FZJ* ; Methner, A. ; Hoffmann, S.FZJ* ; Weiergräber, O. H.FZJ* ; Willbold, D.FZJ*
The autophagy-related protein GABARAP directly interacts with the anti-apoptotic regulator BcI-2
2014Gordon Research Conference: Autophagy in Stress, Development & Disease, Il CioccoIl Ciocco, Italy, 16 Mar 2014 - 21 Mar 20142014-03-162014-03-21 BibTeX | EndNote: XML, Text | RIS

Contribution to a book Schwarten, M.FZJ* ; Weiergräber, O. H.FZJ* ; Petrović, D.FZJ* ; Strodel, B.FZJ* ; Willbold, D. (Corresponding author)FZJ*
Structural Studies of Autophagy-Related Proteins
2019Autophagy / Ktistakis, Nicholas (Editor) Chapter 2 ; ISSN: 1064-3745=1940-6029 ; ISBN: 978-1-4939-8872-3=978-1-4939-8873-0 ; doi:10.1007/978-1-4939-8873-0 New York, NY : Springer New York, Methods in Molecular Biology 1880, 17 - 56 (2019) [10.1007/978-1-4939-8873-0_2]2019 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Sengupta, U. ; Strodel, B. (Corresponding author)FZJ*
Markov models for the elucidation of allosteric regulation
Philosophical transactions of the Royal Society of London / B Biological sciences Series B 373(1749), 20170178 - (2018) [10.1098/rstb.2017.0178]2018 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Sengupta, U. ; Carballo-Pacheco, M. ; Strodel, B. (Corresponding author)FZJ*
Automated Markov state models for molecular dynamics simulations of aggregation and self-assembly
The journal of chemical physics 150(11), 115101 - (2019) [10.1063/1.5083915]2019 Embargoed OpenAccess Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Sharma, O. P. (Corresponding author) ; Vadlamudi, Y. ; Liao, Q.FZJ* ; Strodel, B.FZJ* ; Suresh Kumar, M.
Molecular modeling, dynamics, and an insight into the structural inhibition of cofactor independent phosphoglycerate mutase isoform 1 from Wuchereria bancrofti using cheminformatics and mutational studies
Journal of biomolecular structure & dynamics 31(7), 765-778 (2013) [10.1080/07391102.2012.709460]2013 BibTeX | EndNote: XML, Text | RIS

Journal Article - Online First Smorodina, E. ; Kav, B. ; Fatafta, H.FZJ* ; Strodel, B. (Corresponding author)FZJ*
Effects of ion type and concentration on the structure and aggregation of the amyloid peptide A β16−22$$ {\boldsymbol{\beta}}_{16-22} $$
Proteins 16-22, prot.26635 (2023) [10.1002/prot.26635]2023 BibTeX | EndNote: XML, Text | RIS

Journal Article Strodel, B.FZJ* ; Bauer, M. S. ; Fejer, S. N. ; Koslover, E. F. ; Wales, D. J.
Interpolation Schemes for Peptide Rearrangements
The journal of chemical physics 132, 054101 (2010) [10.1063/1.3273617]2010 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Talk (non conference) (Invited) Strodel, B.FZJ*
Amyloid Aggregation
2009Besuch der "Computational Biomolecular Dynamics Group" von Bert de Groot, Max-Planck-Institut für Biophysikalische Chemie, Göttingen
Seminar, GöttingenGöttingen, 6 May 20092009-05-06 BibTeX | EndNote: XML, Text | RIS

Conference Presentation Strodel, B.FZJ*
Multiscale Modelling of Protein Aggregation
2009CECAM Workshop "Linking Systems Biology and Biomolecular Simulations
Seminar, Lausanne, SchweizLausanne, Schweiz, 16 Nov 20092009-11-16 BibTeX | EndNote: XML, Text | RIS

Journal Article Strodel, B.FZJ* ; Lee, J. W. L. ; Whittleston, C. S. ; Wales, D. J.
Transmembrane Structures for Alzheimer’s Aß1-42 Oligomers
Journal of the American Chemical Society 132, 13300 - 13312 (2010) [10.1021/ja103725c]2010 BibTeX | EndNote: XML, Text | RIS

Conference Presentation (Invited) Strodel, B.FZJ*
Telluride Science Workshop: Protein and Peptide Interactions in Cellular Environments
2010Transmembrane structures for Alzheimer's Aß1-42 oligomers
Seminar, Telluride, USATelluride, USA, 9 Jul 20102010-07-09 BibTeX | EndNote: XML, Text | RIS

Talk (non conference) Strodel, B.FZJ*
Analysis of Molecular Dynamics Simulations
2010Autumn School "Biomolecular Structure and Function - Computational Approaches
Seminar, EssenEssen, 29 Nov 20102010-11-29 BibTeX | EndNote: XML, Text | RIS

Poster Strodel, B.FZJ*
Interactions of Alzheimer's Abeta-Peptide with Lipid Bilayers
2010ISQBP 2010 President´s meeting
Seminar, Cetraro, ItalyCetraro, Italy, 14 Jun 20102010-06-14 BibTeX | EndNote: XML, Text | RIS

Journal Article Strodel, B.FZJ* ; Khalili, M. ; Trygubenko, S. ; Fejer, S. N. ; Wales, D. J. ; Małolepsza, E. (Corresponding author)
Symmetrization of the AMBER and CHARMM force fields
Journal of computational chemistry 31(7), 1402-1409 (2010) [10.1002/jcc.21425]2010 Files Fulltext BibTeX | EndNote: XML, Text | RIS

Journal Article Strodel, B. (Corresponding author)FZJ* ; Fitzpatrick, A. W. ; Vendruscolo, M. ; Dobson, C. M. ; Wales, D. J.
Characterizing the First Steps of Amyloid Formation for the ccβ Peptide
The journal of physical chemistry <Washington, DC> / B 112(32), 9998 - 10004 (2008) [10.1021/jp801222x]2008 Files Fulltext BibTeX | EndNote: XML, Text | RIS

Journal Article Strodel, B. (Corresponding author)FZJ* ; Whittleston, C. S. ; Wales, D. J.
Thermodynamics and kinetics of aggregation for the GNNQQNY peptide.
Journal of the American Chemical Society 129(51), 16005 - 16014 (2007) [10.1021/ja075346p]2007 Files Fulltext BibTeX | EndNote: XML, Text | RIS

Contribution to a book Strodel, B.FZJ* ; Wales, D. ; Leitner, D. M. (Corresponding author)
Pathways and Rates for Structural Transformations of Peptides and Proteins. In Energy Flow in Proteins.
2009Proteins : energy, heat and signal flow Boca Raton : CRC Press/Taylor & Francis Group : 5, 315-340 (2009)2009 Fulltext BibTeX | EndNote: XML, Text | RIS

Review/Journal Article/Contribution to a book Strodel, B. (Corresponding Author)FZJ*
Protein-Protein Interactions in Drug Discovery. Edited by Alexander Dömling.
2014Protein–Protein Interactions in Drug Discovery. Edited by Alexander Dömling. ChemBioChem 15(3), 472 - 473 (2014) [10.1002/cbic.201300761]2014 Files BibTeX | EndNote: XML, Text | RIS

Communication Strodel, B. (Corresponding author)FZJ*
Learning from simulations
Files Fulltext Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Strodel, B.FZJ* ; Coskuner-Weber, O. (Corresponding author)
Transition Metal Ion Interactions with Disordered Amyloid-β Peptides in the Pathogenesis of Alzheimer’s Disease: Insights from Computational Chemistry Studies
Journal of chemical information and modeling 59(5), 1782 - 1805 (2019) [10.1021/acs.jcim.8b00983]2019 Embargoed OpenAccess Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Strodel, B. (Corresponding author)FZJ*
Amyloid aggregation simulations: challenges, advances and perspectives
Current opinion in structural biology 67, 145 - 152 (2021) [10.1016/j.sbi.2020.10.019]2021 Embargoed OpenAccess Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Strodel, B. (Corresponding author)FZJ*
Energy Landscapes of Protein Aggregation and Conformation Switching in Intrinsically Disordered Proteins
Journal of molecular biology 433(20), 167182 - (2021) [10.1016/j.jmb.2021.167182]2021 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Suresh, P. S. ; Olubiyi, O.FZJ* ; Thirunavukkarasu, C. ; Strodel, B.FZJ* ; Kumar, M. S.
Molecular modeling of human alkaline sphingomyelinase
Bioinformation: discovery at the interface of physical and biological sciences 6, 78-82 (2011)2011 BibTeX | EndNote: XML, Text | RIS

Journal Article Taiwo, B. J. (Corresponding author) ; Olubiyi, O. O. (Corresponding author) ; Wang, X.FZJ* ; Fisusi, F. A. ; Akinniyi, G. A. ; Van Heerden, F. R. ; Strodel, B.FZJ*
Schistosomiasis: Snail-vector control, molecular modelling and dynamic studies of bioactive N-acetylglycoside saponins from Tetrapleura tetraptera
Computational biology and chemistry 77, 363 - 372 (2018) [10.1016/j.compbiolchem.2018.09.011]2018 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Tohidifar, L. ; Strodel, B. (Corresponding author)FZJ*
Molecular dynamics studies for enhancing the anticancer drug efficacy: Toward designing a new carbon nanotube-based paclitaxel delivery system
Journal of molecular liquids 323, 114638 - (2021) [10.1016/j.molliq.2020.114638]2021 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Uluca, B.FZJ* ; Viennet, T.FZJ* ; Petrović, D.FZJ* ; Shaykhalishahi, H.FZJ* ; Weirich, F.FZJ* ; Gönülalan, A.FZJ* ; Strodel, B.FZJ* ; Etzkorn, M.FZJ* ; Hoyer, W.FZJ* ; Heise, H. (Corresponding author)FZJ*
DNP-Enhanced MAS NMR: A Tool to Snapshot Conformational Ensembles of α -Synuclein in Different States
Biophysical journal 114(7), 1614 - 1623 (2018) [10.1016/j.bpj.2018.02.011]2018 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Uspenskiy, I. ; Strodel, B.FZJ* ; Stock, G. (Corresponding author)
Classical calculation of transient absorption spectra monitoring ultrafast electron transfer processes
Journal of chemical theory and computation 2(6), 1605 - 1617 (2006) [10.1021/ct6002127]2006 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Uspenskiy, I. ; Strodel, B.FZJ* ; Stock, G. (Corresponding author)
Classical description of the dynamics and time-resolved spectroscopy of nonadiabatic cis-trans photoisomerizations.
Chemical physics 329(1-3), 109 - 117 (2006) [10.1016/j.chemphys.2006.07.047]2006 Files BibTeX | EndNote: XML, Text | RIS

Poster Vancea, I.FZJ* ; Osborne, K.FZJ* ; Strodel, B.FZJ*
Multiscale Modelling of Protein Aggregation
2009Methods of Molecular Simulations 2009
Seminar, Heidelberg, DeutschlandHeidelberg, Deutschland, 7 Dec 20092009-12-07 BibTeX | EndNote: XML, Text | RIS

Poster Vancea, I.FZJ* ; Strodel, B.FZJ*
Structural and Dynamical Properties of Protein-Hydration Waters
2010From Computational Biophysics to Systems Biology (CBSB 2010)
Seminar, Traverse City, Michigan, USATraverse City, Michigan, USA, 5 Jun 20102010-06-05 BibTeX | EndNote: XML, Text | RIS

Poster Vancea, I.FZJ* ; Strodel, B.FZJ*
Implicit solvation in different dielectric environments with the generalized Born model FACTS
2011Computer Simulation and Theory of Macromolecules 2011
Seminar, Hünfeld, DeutschlandHünfeld, Deutschland, 15 Apr 20112011-04-15 BibTeX | EndNote: XML, Text | RIS

Poster Vancea, I.FZJ* ; Strodel, B.FZJ*
Implicit solvation in different dielectric environments with the generalized Born model FACTS
2011European Biophysics Conference
Seminar, Budapest, HungaryBudapest, Hungary, 23 Aug 20112011-08-23 BibTeX | EndNote: XML, Text | RIS

Journal Article Viennet, T. ; Wördehoff, M. M. ; Uluca, B.FZJ* ; Poojari, C. ; Shaykhalishahi, H. ; Willbold, D.FZJ* ; Strodel, B.FZJ* ; Heise, H.FZJ* ; Buell, A. K. ; Hoyer, W.FZJ* ; Etzkorn, M. (Corresponding author)FZJ*
Structural insights from lipid-bilayer nanodiscs link α-Synuclein membrane-binding modes to amyloid fibril formation
Communications biology 1(1), 44 (2018) [10.1038/s42003-018-0049-z]2018 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Wallin, C. ; Kulkarni, Y. S. ; Abelein, A. ; Jarvet, J. ; Liao, Q. ; Strodel, B.FZJ* ; Olsson, L. ; Luo, J. ; Abrahams, J. P. ; Sholts, S. B. ; Roos, P. M. ; Kamerlin, S. C. L. ; Gräslund, A. ; Wärmländer, S. K. T. S. (Corresponding author)
Characterization of Mn(II) ion binding to the amyloid-ß peptide in Alzheimer’s disease
Journal of trace elements in medicine and biology 38, 183-193 (2016) [10.1016/j.jtemb.2016.03.009]2016 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Weber, J. ; Petrović, D. ; Strodel, B.FZJ* ; Smits, S. H. J. ; Kolkenbrock, S. ; Leggewie, C. ; Jaeger, K.-E. (Corresponding author)FZJ*
Interaction of carbohydrate-binding modules with poly(ethylene terephthalate)
Applied microbiology and biotechnology 103(12), 4801 - 4812 (2019) [10.1007/s00253-019-09760-9]2019 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Contribution to a book Weiergräber, O. H.FZJ* ; Schwarten, M.FZJ* ; Strodel, B.FZJ* ; Willbold, D. (Corresponding author)FZJ*
Investigating Structure and Dynamics of Atg8 Family Proteins
New York, NY [u.a.] : Elsevier, Methods in enzymology 587, 115–142 (2017) [10.1016/bs.mie.2016.09.056]2017 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Weiergräber, O. H. (Corresponding author)FZJ* ; Petrović, D. ; Kislat, A. ; Pattky, M. ; Fabig, J. ; Batra-Safferling, R.FZJ* ; Schulte am Esch, J. ; Hänel, K.FZJ* ; Huhn, C. ; Strodel, B.FZJ* ; Homey, B. ; Willbold, D. (Corresponding author)FZJ*
Structure and Dynamics of Human Chemokine CCL16—Implications for Biological Activity
Biomolecules 12(11), 1588 - (2022) [10.3390/biom12111588]2022 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Willbold, D. (Corresponding author)FZJ* ; Strodel, B.FZJ* ; Schröder, G. F.FZJ* ; Hoyer, W.FZJ* ; Heise, H.FZJ*
Amyloid-type Protein Aggregation and Prion-like Properties of Amyloids
Chemical reviews 121(13), 8285 - 8307 (2021) [10.1021/acs.chemrev.1c00196]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Wolff, M.FZJ* ; Zhang-Haagen, B. ; Decker, C. ; Barz, B. ; Schneider, M. ; Biehl, R.FZJ* ; Radulescu, A.FZJ* ; Strodel, B.FZJ* ; Willbold, D. (Corresponding author)FZJ* ; Nagel-Steger, L. (Corresponding author)FZJ*
Aβ42 pentamers/hexamers are the smallest detectable oligomers in solution
Scientific reports 7, 2493 (2017) [10.1038/s41598-017-02370-3]2017 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Poster Yamin, P.FZJ* ; Strodel, B.FZJ*
Large-scale simulations of Aß aggregation in membranes
2009Expanding the frontiers of molecular dynamics simulations in biology
Seminar, Barcelona, SpanienBarcelona, Spanien, 23 Nov 20092009-11-23 BibTeX | EndNote: XML, Text | RIS

Journal Article Zhang, T.FZJ* ; Loschwitz, J.FZJ* ; Strodel, B.FZJ* ; Nagel-Steger, L.FZJ* ; Willbold, D. (Corresponding author)FZJ*
Interference with Amyloid-β Nucleation by Transient Ligand Interaction
Molecules 24(11), 2129 - (2019) [10.3390/molecules24112129]2019 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Last Modified: 17.06.2022

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