All Stories

  1. Current Stage and Future Perspectives for Homology Modeling, Molecular Dynamics Simulations, Machine Learning with Molecular Dynamics, and Quantum Computing for Intrinsically Disordered Proteins and Proteins with Intrinsically Disordered Regions

    Article • Current Protein and Peptide Science, February 2024, Bentham Science Publishers

    Orkid Coskuner-Weber

  2. Current Challenges and Limitations in the Studies of Intrinsically Disordered Proteins in Neurodegenerative Diseases by Computer Simulations

    Article • Current Alzheimer Research, January 2021, Bentham Science Publishers

    Orkid Coskuner-Weber, Prof. Vladimir N. Uversky

  3. Quantum Chemistry Meets Deep Learning for Complex Carbohydrate and Glycopeptide Species I

    Article • Zeitschrift für Physikalische Chemie, April 2019, De Gruyter

    Orkid Coskuner-Weber

  4. Transition Metal Ion Interactions with Disordered Amyloid-β Peptides in the Pathogenesis of Alzheimer’s Disease: Insights from Computational Chemistry Studies

    Article • Journal of Chemical Information and Modeling, April 2019, American Chemical Society (ACS)

    Orkid Coskuner-Weber

  5. Alanine Scanning Effects on the Biochemical and Biophysical Properties of Intrinsically Disordered Proteins: A Case Study of the Histidine to Alanine Mutations in Amyloid-β42

    Article • Journal of Chemical Information and Modeling, January 2019, American Chemical Society (ACS)

    Orkid Coskuner-Weber

  6. Revisiting Cu(II) Bound Amyloid-β40 and Amyloid-β42 Peptides: Varying Coordination Chemistries

    Article • Journal of the Turkish Chemical Society Section A Chemistry, August 2018, Journal of the Turkish Chemical Society, Section A: Chemistry

    Orkid Coskuner-Weber

  7. Insights into the Molecular Mechanisms of Alzheimer’s and Parkinson’s Diseases with Molecular Simulations: Understanding the Roles of Artificial and Pathological Missense Mutations in Intrinsically Disordered Proteins Related to Pathology

    Article • International Journal of Molecular Sciences, January 2018, MDPI AG

    Orkid Coskuner-Weber

  8. Tyrosine Regulates β-Sheet Structure Formation in Amyloid-β42: A New Clustering Algorithm for Disordered Proteins

    Article • Journal of Chemical Information and Modeling, May 2017, American Chemical Society (ACS)

    Orkid Coskuner, Orkid Coskuner-Weber

  9. How accurate are your simulations

    Article • Intrinsically Disordered Proteins, January 2017, Taylor & Francis

    Orkid Coskuner, Prof. Vladimir N. Uversky, Orkid Coskuner-Weber

  10. Adenosine Triphosphate (ATP) Reduces Amyloid-β Protein Misfolding in vitro

    Article • Journal of Alzheimer’s Disease, June 2014, IOS Press

    Orkid Coskuner-Weber

  11. New force field parameters for metalloproteins I: Divalent copper ion centers including three histidine residues and an oxygen-ligated amino acid residue

    Article • Journal of Computational Chemistry, April 2014, Wiley

    Orkid Coskuner, Orkid Coskuner-Weber

  12. Arginine and Disordered Amyloid-β Peptide Structures: Molecular Level Insights into the Toxicity in Alzheimer’s Disease

    Article • ACS Chemical Neuroscience, December 2013, American Chemical Society (ACS)

    Orkid Coskuner, Orkid Coskuner-Weber

  13. Structures and Free Energy Landscapes of the A53T Mutant-Type α-Synuclein Protein and Impact of A53T Mutation on the Structures of the Wild-Type α-Synuclein Protein with Dynamics

    Article • ACS Chemical Neuroscience, July 2013, American Chemical Society (ACS)

    Orkid Coskuner, Orkid Coskuner-Weber

  14. Structures of the E46K Mutant-Type α-Synuclein Protein and Impact of E46K Mutation on the Structures of the Wild-Type α-Synuclein Protein

    Article • ACS Chemical Neuroscience, March 2013, American Chemical Society (ACS)

    Orkid Coskuner, Orkid Coskuner-Weber

  15. Structures and Free Energy Landscapes of the Wild-Type and A30P Mutant-Type α-Synuclein Proteins with Dynamics

    Article • ACS Chemical Neuroscience, March 2013, American Chemical Society (ACS)

    Orkid Coskuner, Orkid Coskuner-Weber

  16. The Structures of the E22Δ Mutant-Type Amyloid-β Alloforms and the Impact of E22Δ Mutation on the Structures of the Wild-Type Amyloid-β Alloforms

    Article • ACS Chemical Neuroscience, February 2013, American Chemical Society (ACS)

    Professor George Perry, Orkid Coskuner, Orkid Coskuner-Weber

  17. Probing and Trapping a Sensitive Conformation: Amyloid-β Fibrils, Oligomers, and Dimers

    Article • Journal of Alzheimer’s Disease, September 2012, IOS Press

    Orkid Coskuner-Weber

  18. Structures and free energy landscapes of aqueous zinc(II)-bound amyloid-β(1–40) and zinc(II)-bound amyloid-β(1–42) with dynamics

    Article • JBIC Journal of Biological Inorganic Chemistry, June 2012, Springer Science + Business Media

    Professor George Perry, Orkid Coskuner, Orkid Coskuner-Weber

  19. Amyloid-β peptide structure in aqueous solution varies with fragment size

    Article • The Journal of Chemical Physics, November 2011, American Institute of Physics

    Orkid Coskuner, Professor George Perry, Orkid Coskuner, Orkid Coskuner-Weber

  20. Single Ion and Dimerization Studies of the Al(III) Ion in Aqueous Solution

    Article • The Journal of Physical Chemistry A, October 2010, American Chemical Society (ACS)

    Orkid Coskuner, Orkid Coskuner-Weber

  21. Dynamic and Structural Properties of Aqueous Arsenic Solutions

    Article • ChemPhysChem, June 2009, Wiley

    Orkid Coskuner, Orkid Coskuner-Weber

  22. Identification of Active Sites of Biomolecules II: Saccharide and Transition Metal Ion in Aqueous Solution

    Article • The Journal of Physical Chemistry A, March 2009, American Chemical Society (ACS)

    Dr. Denis E Bergeron, Orkid Coskuner, Orkid Coskuner-Weber

  23. Glycosidic linkage conformation of methyl-α-mannopyranoside

    Article • The Journal of Chemical Physics, July 2008, American Institute of Physics

    Dr. Denis E Bergeron, Orkid Coskuner, Orkid Coskuner-Weber

  24. Identification of Active Sites of Biomolecules. 1. Methyl-α-mannopyranoside and FeIII

    Article • The Journal of Physical Chemistry A, April 2008, American Chemical Society (ACS)

    Dr. Denis E Bergeron, Orkid Coskuner, Orkid Coskuner-Weber

  25. Coordination Studies of Al-EDTA in Aqueous Solution

    Article • The Journal of Physical Chemistry A, March 2008, American Chemical Society (ACS)

    Orkid Coskuner, Orkid Coskuner-Weber

  26. Water Dissociation in the Presence of Metal Ions

    Article • Angewandte Chemie, October 2007, Wiley

    Orkid Coskuner, Orkid Coskuner-Weber

  27. Preferred conformation of the glycosidic linkage of methyl-β-mannose

    Article • The Journal of Chemical Physics, July 2007, American Institute of Physics

    Orkid Coskuner, Orkid Coskuner-Weber

  28. Hydrophobic Interactions of Xenon by Monte Carlo Simulations

    Article • Zeitschrift für Physikalische Chemie, June 2007, De Gruyter

    Orkid Coskuner, Orkid Coskuner-Weber