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P. Ma , O.Schillinger , M. Schwarten , J. Lecher , R. Hartmann , M. Stoldt , J. Mohrlüder , O. Olubiyi , B. Strodel , D. Willbold , and O. H. Weiergräber. Conformational polymorphism in the autophagy-related protein GATE-16. Biochemistry, DOI: 10.1021/acs.biochem.5b00366 (2015)

M. Carballo-Pacheco, A. Ismail, and B. Strodel. Oligomer Formation of Toxic and Functional Amyloid Peptides Studied with Atomistic Simulations. J. Phys. Chem. B, 119, 9696-9705 (2015)

Q. Liao, S.C.L. Kamerlin, and B. Strodel. Development and Application of a Nonbonded Cu2+ Model That Includes the Jahn–Teller Effect. J. Phys. Chem. Lett., 6, 2657–2662 (2015)

J. Nasica-Labouze, P.H. Nguyen, F. Sterpone, O. Berthoumieu, N.V.Buchete, S. Coté, A. De Simone, A.J. Doig, P. Faller, A. Garcia, A. Laio, S.L. Mai, S. Melchionna, N. Mousseau, Y. Mu, A. Paravastu, S. Pasquali, D.J. Rosenman, B. Strodel, B. Tarus, J.H. Viles, T. Zhang, C. Wang, P. Derreumaux. Amyloid β Protein and Alzheimer’s Disease: When Computer Simulations Complement Experimental Studies. Chem. Rev., 115, 3518-3563 (2015)

M. Carballo Pacheco, I. Vancea, and B. Strodel. Extension of the FACTS implicit solvation model to membranes. J. Chem. Theory Comput., 10, 3163-3176 (2014)

F. Hoffmann, I. Vancea, S.G. Kamat, and B. Strodel. Protein structure prediction: assembly of secondary structure elements by basin-hopping. ChemPhysChem., 15, 3378–3390 (2014)

B. Barz, O. Olubiyi, and B. Strodel. Early amyloid β-protein aggregation precedes conformational change. Chem. Commun., 50, 5373-5375 (2014)
This communication is part of themed collection: 2014 Emerging Investigators.

B. Barz, D.J. Wales, and B. Strodel. A Kinetic Approach to the Sequence–Aggregation Relationship in Disease-related Protein Assembly. J. Phys. Chem. B., 118, 1003-1011 (2014)

B.Strodel. Book Review: Protein-Protein Interactions in Drug Discovery. ChemBioChem, 15, 472-473 (2014)

O. Olubiyi, D. Frenzel, D. Bartnik, J.M. Glück, O. Brener, L. Nagel-Steger, S.A. Funke, D. Willbold, and B. Strodel. Amyloid aggregation inhibitory mechanism of arginine-rich D-peptides. Curr. Med. Chem., 21, 1448-1457 (2014)

Ma, P.; Schwarten, M.; Schneider, L.; Boeske, A.; Henke, N.; Lisak, D.; Weber, S.; Mohrluder, J.; Stoldt, M.; Strodel, B.; Methner, A.; Hoffmann, S.; Weiergraber, O. H.; Willbold, D. Interaction of Bcl-2 with the Autophagy-Related Protein GABARAP -- Biophysical Characterization and Functional Implications. J. Biol. Chem., 113, 1-26 (2013)

C. Poojari, D. Xiao, V. S. Batista and B. Strodel. Membrane permeation induced by aggregates of human islet amyloid polypeptides. Biophys. J., 105, 2323-2332 (2013)

C. Poojari and B. Strodel. Stability of transmembrane amyloid β-peptide and membrane integrity tested by molecular modeling of site-specific Aβ42 mutations. PLoS ONE, 8: e78399 (2013)

K. L. Osborne, M. Bachmann and B. Strodel. Thermodynamic analysis of structural transitions during GNNQQNY aggregation. Proteins: Struct. Func. Bioinf., 81:1141–1155 (2013)

F. Hoffmann and B. Strodel. Protein structure prediction using global optimization by basin-hopping with NMR shift restraints. J. Chem. Phys., 138:025102 (2013).

C. Poojari, A. Kukol and B. Strodel. How the amyloid-β peptide and membranes affect each other: an extensive simulation study. BBA-Biomembranes, 1828, 327-339 (2013).

O. P. Sharma, Y. Vadlamudi, Q. Liao, B. Strodel, and M. Suresh Kumar. 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. J. Biomol. Struct. Dyn., 31, 765-778 (2013).

O.O. Olubiyi and B. Strodel. Structures of the Amyloid β-Peptides Aβ1-40 and Aβ1-42 as Influenced by pH and a D-Peptide. J. Phys. Chem. B, 116, 3280-3291 (2012).

P. S. Suresh, O. Olubiyi, C. Thirunavukkarasu, B. Strodel, M. S. Kumar. Molecular modeling of human alkaline sphingomyelinase. Bioinformation, 6, 78-82 (2011).

K. Klenin, B. Strodel, D.J. Wales and W. Wenzel. Modelling Proteins: Conformational Sampling and Reconstruction of Folding Kinetics. BBA-Proteins and Proteomics, 1814, 977-1000 (2011).

B. Strodel, J.W.L. Lee, C.S. Whittleston and D.J. Wales. Transmembrane structures for Alzheimer's Aβ1-42 oligomers. J. Am. Chem. Soc., 132, 13300-13312 (2010).

M.S. Bauer, B. Strodel, S.N. Fejer, E.F. Koslover and D.J. Wales. Interpolation Schemes for Peptide Rearrangements. J. Chem. Phys., 132, 054101 (2010).

E. Malolepsza, B. Strodel, M. Khalili, S. Trygubenko, S. Fejer and D.J. Wales. Symmetrisation of the AMBER and CHARMM Force Fields. J. Comp. Chem., 31, 1402-1409 (2010).

B. Strodel and D.J. Wales. Frontiers Article: Free Energy Surfaces from an Extended Harmonic Superposition Approach and Kinetics for Alanine Dipeptide. Chem. Phys. Lett., 466, 105-115 (2008).

B. Strodel, A.W. Fitzpatrick, M. Vendruscolo, C.M. Dobson, and D.J. Wales. Characterising the first steps of amyloid formation for the ccβ peptide. J. Phys. Chem. B 112:9998-10004 (2008).

B. Strodel and D.J. Wales. Implicit solvent models and the energy landscape for aggregation of the amyloidogenic KFFE peptide. J. Chem. Theo. Comp. 4:657-672 (2008).

B. Strodel, C.S. Whittleston, and D.J. Wales. Thermodynamics and Kinetics of Aggregation for the GNNQQNY Peptide. J. Am. Chem. Soc. 129:16005-16014 (2007).

Classical calculation of transient absorption spectra monitoring ultrafast electron transfer processes.
I. Uspenskiy, B. Strodel, and G. Stock.
J. Chem. Theo. Comp. 2:1605-1617 (2006).

Classical description of the dynamics and time-resolved spectroscopy of nonadiabatic cis-trans photoisomerizations.
I. Uspenskiy, B. Strodel, and G. Stock.
Chem. Phys. 329:109-117 (2006).

Quantum modeling of transient infrared spectra reflecting photoinduced electron-transfer dynamics.
B. Strodel and G. Stock.
J. Chem. Phys. 124:114105 (2006).

Modeling of decoherence and dissipation in nonadiabatic photoreactions by an effective-scaling nonsecular Redfield algorithm.
B. Balzer and G. Stock.
Chem. Phys. 310:33-41 (2005).

Transient spectral features of a cis-trans photoreaction in the condensed phase: A model study.
B. Balzer and G. Stock.
J. Phys. Chem. A 108:6464-6473 (2004).

Mechanism of a photochemical funnel: a dissipative wave-packet dynamics study.
B. Balzer, S. Hahn, and G. Stock.
Chem. Phys. Lett. 379:351-358 (2003).

Quasiclassical and semiclassical wave-packet dynamics n periodic potentials.
B. Balzer, S. Dilthey, G. Stock, and M. Thoss.
J. Chem. Phys. 119:5795-5804 (2003).

Quasiperiodic orbit analysis of nonadiabatic cis-trans photoisomerization dynamics.
B. Balzer, S. Dilthey, S. Hahn, M. Thoss, and G. Stock.
J. Chem. Phys. 119:4204-4215, (2003).


Book Chapters and Proceedings

Carballo-Pacheco M., Barz B. and Strodel B. Functional Amyloids. Proceedings of the 46th IFF Spring School Functional Soft Matter, 23 February - 06 March 2015, Jülich, Germany.

Barz B. and Strodel B. Thermodynamics and kinetics of amyloid aggregation from atomistic simulations. Proceedings of the Conference Physical Biology of Proteins and Peptides: Theory, Experiment and Simulation, 18 - 20 February 2015, Mexico City, Mexico.

K. L. Osborne, B. Barz, M. Bachmann, and B. Strodel. Thermodynamics of Protein Aggregation. Phys. Proc., 53, 90-95 (2014) Proceedings of the 26th Workshop on Recent Developments in Computer Simulation Studies in Condensed Matter Physics, Feb 25-Mar 1, 2013, Athens, Georgia, USA.

O. O. Olubiyi, B. Strodel. Secondary Structure Propensities of the Amyloid β-Peptide Aβ1-42 as Influenced by pH and a D-Peptide. In `From Computational Biophysics to Systems Biology (CBSB11)', Proceedings, 20-22 July 2011, Julich, Germany, ISBN 978-3-89336-748-1, pp. 145-150 (2012).

K. Osborne, M. Bachmann, B. Strodel. Coarse Grained Simulation of Amyloid Aggregators. In `From Computational Biophysics to Systems Biology (CBSB11)', Proceedings, 20-22 July 2011, Julich, Germany, ISBN 978-3-89336-748-1, pp. 151-155 (2012).

C. Poojari, B. Strodel. Modeling Transmembrane Amyloid-β Structures: Aβ-Membrane Interactions. In `From Computational Biophysics to Systems Biology (CBSB11)', Proceedings, 20-22 July 2011, Julich, Germany, ISBN 978-3-89336-748-1, pp. 157-162 (2012).

D.J. Wales, J.M. Carr, M. Khalili, V. de Souza, B. Strodel, and C.S. Whittleston. Pathways and Rates for Structural Transformations of Peptides and Proteins. In Energy Flow in Proteins. edited by D.Leitner and J.Straub, Taylor and Francis/CRC Press, 315-340 (2009).


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