All Stories

  1. Liquid-Liquid Phase Separation Associated with Intrinsically Disordered Proteins: Experimental and Computational Tools

    Article • Current Protein and Peptide Science, December 2025, Bentham Science Publishers

    Orkid Coskuner-Weber

  2. Metagenomics studies in aquaculture systems: Big data analysis, bioinformatics, machine learning and quantum computing

    Article • Computational Biology and Chemistry, October 2025, Elsevier

    Orkid Coskuner-Weber

  3. Effects of pathological mutations on the CHCHD2 monomer structure: A study by AlphaFold3 linked to the generation of conformational ensembles

    Article • Computers in Biology and Medicine, September 2025, Elsevier

    Orkid Coskuner-Weber

  4. Implicit Solvent Models and Their Applications in Biophysics

    Article • Biomolecules, August 2025, MDPI AG

    Orkid Coskuner-Weber

  5. Implicit Solvent Models and Their Applications in Biophysics

    Article • July 2025, MDPI AG

    Orkid Coskuner-Weber

  6. BioMatics 1.0: A Wasserstein Distance Approach for Next-Generation Multiple Sequence Alignment

    Article • July 2025, Springer Science + Business Media

    Orkid Coskuner-Weber

  7. Impacts of pathogenic mutations on the structures of the CHCHD10 monomer: An AlphaFold3 study linked to the generation of conformational ensembles

    Article • International Journal of Biological Macromolecules, July 2025, Elsevier

    Orkid Coskuner-Weber

  8. Three new Microbacterium species isolated from the Marmara Sea mucilage event: Microbacterium istanbulense sp. nov., Microbacterium bandirmense sp. nov., Microbacterium marmarense sp. nov

    Article • Systematic and Applied Microbiology, May 2025, Elsevier

    Orkid Coskuner-Weber

  9. Unraveling Genomic and Pathogenic Features of Aeromonas ichthyocola sp. nov., Aeromonas mytilicola sp. nov., and Aeromonas mytilicola subsp. aquatica subsp. nov.

    Article • Animals, March 2025, MDPI AG

    Orkid Coskuner-Weber

  10. Electromagnetic radiation and biophoton emission in neuronal communication and neurodegenerative diseases

    Article • Progress in Biophysics and Molecular Biology, March 2025, Elsevier

    Orkid Coskuner-Weber

  11. Integrating chemical artificial intelligence and cognitive computing for predictive analysis of biological pathways: a case for intrinsically disordered proteins

    Article • Biophysical Reviews, February 2025, Springer Science + Business Media

    Orkid Coskuner-Weber

  12. Disordered peptide-based design of intrinsically disordered polymers for biomedical applications

    Article • International Journal of Polymer Analysis and Characterization, February 2025, Taylor & Francis

    Orkid Coskuner-Weber

  13. Effects of the Amyotrophic Lateral Sclerosis-related Q108P Mutation on the Structural Ensemble Characteristics of CHCHD10

    Article • Current Protein and Peptide Science, January 2025, Bentham Science Publishers

    Orkid Coskuner-Weber

  14. Molecular Crowding by Computational Approaches

    Article • January 2025, Springer Science + Business Media

    Orkid Coskuner-Weber

  15. Key genes and pathways in the molecular landscape of pancreatic ductal adenocarcinoma: A bioinformatics and machine learning study

    Article • Computational Biology and Chemistry, December 2024, Elsevier

    Orkid Coskuner-Weber

  16. Disordered Peptide-Based Design of Intrinsically Disordered Polymers for Biomedical Applications

    Article • October 2024, MDPI AG

    Orkid Coskuner-Weber

  17. Structures prediction and replica exchange molecular dynamics simulations of α-synuclein: A case study for intrinsically disordered proteins

    Article • International Journal of Biological Macromolecules, September 2024, Elsevier

    Orkid Coskuner-Weber

  18. Intrinsically Disordered Proteins by Homology Modeling and Replica Exchange Molecular Dynamics Simulations: A Case Study of Amyloid-β42

    Article • Journal of the Turkish Chemical Society Section A Chemistry, August 2024, Journal of the Turkish Chemical Society, Section A: Chemistry

    Orkid Coskuner-Weber

  19. Structural Properties of Rat Intestinal Fatty Acid-Binding Protein with its Dynamics: Insights into Intrinsic Disorder

    Article • Protein and Peptide Letters, June 2024, Bentham Science Publishers

    Orkid Coskuner-Weber

  20. 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

  21. The impacts of the mitochondrial myopathy-associated G58R mutation on the dynamic structural properties of CHCHD10

    Article • Journal of Biomolecular Structure and Dynamics, June 2023, Taylor & Francis

    Orkid Coskuner-Weber

  22. Intrinsically Disordered Synthetic Polymers in Biomedical Applications

    Article • Polymers, May 2023, MDPI AG

    Orkid Coskuner-Weber

  23. Frontotemporal Dementia-Related V57E Mutation Impairs Mitochondrial Function and Alters the Structural Properties of CHCHD10

    Article • ACS Chemical Neuroscience, May 2023, American Chemical Society (ACS)

    Orkid Coskuner-Weber

  24. Paving the Way for Synthetic Intrinsically Disordered Polymers for Soft Robotics

    Article • Polymers, February 2023, MDPI AG

    Orkid Coskuner-Weber

  25. Effects of the Jokela type of spinal muscular atrophy‐related G66V mutation on the structural ensemble characteristics of CHCHD10

    Article • Proteins Structure Function and Bioinformatics, January 2023, Wiley

    Orkid Coskuner-Weber

  26. Intrinsically disordered proteins and proteins with intrinsically disordered regions in neurodegenerative diseases

    Article • Biophysical Reviews, June 2022, Springer Science + Business Media

    Orkid Coskuner-Weber

  27. Structures of the Wild-Type and S59L Mutant CHCHD10 Proteins Important in Amyotrophic Lateral Sclerosis–Frontotemporal Dementia

    Article • ACS Chemical Neuroscience, March 2022, American Chemical Society (ACS)

    Orkid Coskuner-Weber

  28. From Quantum Mechanics, Classical Mechanics, and Bioinformatics to Artificial Intelligence Studies in Neurodegenerative Diseases

    Article • January 2022, Springer Science + Business Media

    Orkid Coskuner-Weber

  29. Insights into the structural properties of SARS-CoV-2 main protease

    Article • Current Research in Structural Biology, January 2022, Elsevier

    Orkid Coskuner-Weber

  30. Methods to study the effect of solution variables on the conformational dynamics of intrinsically disordered proteins

    Article • January 2022, Elsevier

    Orkid Coskuner-Weber

  31. Secondary structure dependence on simulation techniques and force field parameters: from disordered to ordered proteins

    Article • Biophysical Reviews, October 2021, Springer Science + Business Media

    Orkid Coskuner-Weber

  32. Challenges and limitations in the studies of glycoproteins: A computational chemist's perspective

    Article • Proteins Structure Function and Bioinformatics, September 2021, Wiley

    Orkid Coskuner-Weber

  33. Challenges and Limitations in the Studies of Glycoproteins: A Computational Chemist’s Perspective

    Article • July 2021, Wiley

    Orkid Coskuner-Weber

  34. Structures of MERS‐CoV macro domain in aqueous solution with dynamics: Impacts of parallel tempering simulation techniques and CHARMM36m and AMBER99SB force field parameters

    Article • Proteins Structure Function and Bioinformatics, May 2021, Wiley

    Orkid Coskuner-Weber

  35. Secondary structure dependence of amyloid‐β(1–40) on simulation techniques and force field parameters

    Article • Chemical Biology & Drug Design, February 2021, Wiley

    Orkid Coskuner-Weber

  36. 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

  37. Molecular simulations of IDPs: From ensemble generation to IDP interactions leading to disorder-to-order transitions

    Article • January 2021, Elsevier

    Orkid Coskuner-Weber

  38. Epitope region identification challenges of intrinsically disordered proteins in neurodegenerative diseases: Secondary structure dependence of α‐synuclein on simulation techniques and force field parameters

    Article • Chemical Biology & Drug Design, January 2020, Wiley

    Orkid Coskuner-Weber

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

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

    Orkid Coskuner-Weber

  40. 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

  41. 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

  42. Intrinsically disordered proteins in various hypotheses on the pathogenesis of Alzheimer's and Parkinson's diseases

    Article • January 2019, Elsevier

    Orkid Coskuner-Weber

  43. 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

  44. 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

  45. BMP-2 and BMP-9 binding specificities with ALK-3 in aqueous solution with dynamics

    Article • Journal of Molecular Graphics and Modelling, October 2017, Elsevier

    Orkid Coskuner, Orkid Coskuner-Weber

  46. 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

  47. How accurate are your simulations

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

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

  48. Divalent copper ion bound amyloid-β(40) and amyloid-β(42) alloforms are less preferred than divalent zinc ion bound amyloid-β(40) and amyloid-β(42) alloforms

    Article • JBIC Journal of Biological Inorganic Chemistry, September 2016, Springer Science + Business Media

    Orkid Coskuner, Orkid Coskuner-Weber

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

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

    Orkid Coskuner-Weber

  50. 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

  51. 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

  52. 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

  53. 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

  54. 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

  55. 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

  56. 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

  57. 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

  58. 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

  59. Metallic Systems

    Article • May 2011, Taylor & Francis

    Orkid Coskuner-Weber

  60. Aqueous Solutions of Metal Ions

    Article • April 2011, Taylor & Francis

    Orkid Coskuner-Weber

  61. Carbohydrate and Trivalent Iron Ion Interactions in the Gas Phase and in Aqueous Solution

    Article • April 2011, Taylor & Francis

    Orkid Coskuner-Weber

  62. 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

  63. Dynamic and Structural Properties of Aqueous Arsenic Solutions

    Article • ChemPhysChem, June 2009, Wiley

    Orkid Coskuner, Orkid Coskuner-Weber

  64. 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

  65. Ligand Exchange Reactions in the Formation of Diphosphine-Protected Gold Clusters

    Article • The Journal of Physical Chemistry C, August 2008, American Chemical Society (ACS)

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

  66. 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

  67. 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

  68. 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

  69. Water Dissociation in the Presence of Metal Ions

    Article • Angewandte Chemie, October 2007, Wiley

    Orkid Coskuner, Orkid Coskuner-Weber

  70. 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

  71. Hydrophobic Interactions of Xenon by Monte Carlo Simulations

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

    Orkid Coskuner, Orkid Coskuner-Weber

  72. Hydrophobic Interactions by Monte Carlo Simulations

    Article • Zeitschrift für Physikalische Chemie, March 2006, De Gruyter

    Orkid Coskuner, Orkid Coskuner-Weber