publications

in reversed chronological order

2026

  1. Peptide Design for Targeting BTB Domain Homodimerization of BACH2: Complementary In Silico and In Vitro Approaches
    E. Acar, H. Basaga, E. Timucin, and 1 more author
    ACS Omega, 2026
  2. Pathogenicity Prediction of Missense Variations in Hereditary Cancer Genes
    C. B. Akyerli, G. Gerdan, A. Bülbül, and 3 more authors
    International Journal of Molecular Sciences, 2026
  3. Enhanced and Classical MD Simulations Map Aggregation-Prone Regions in the Olfactomedin Domain of Myocilin
    I. Sardag, Z. S. Duvenci, and E. Timucin
    Journal of Chemical Information and Modeling, 2026
  4. The Pretransplant EASIX Score Predicts Transplant-Related Mortality in Children Undergoing Hematopoietic Stem Cell Transplantation for Non-Malignant Disorders
    V. Uygun, V. Hazar, K. Yalçin, and 8 more authors
    Clinical Transplantation, 2026
  5. Confidence scoring for deep learning-predicted antibody-antigen complexes: AntiConf as a precision-driven metric
    S. Ünsal, B. Holland, I. Sardag, and 1 more author
    Briefings in Bioinformatics, 2026

2025

  1. Determination of the Roles of H. pylori Outer Membrane Virulence Factors and Pyroptosis-Associated NLRP3, ASC, Caspase-1, Gasdermin D, IL-1beta, and IL-18 in Ulcer and Gastritis Pathogenesis
    Y. Buyukcolak-Cebeci, E. Timucin, S. Akcelik-Deveci, and 4 more authors
    Biology (Basel), 2025
  2. Exploring the role of microbiome in cystic fibrosis clinical outcomes through a mediation analysis
    S. S. Koldas, O. U. Sezerman, and E. Timucin
    mSystems, 2025
  3. Insights into the solution structure of the actin-binding tail domain of metavinculin by small angle X-ray scattering and molecular dynamics simulations
    Z. A. Oztug Durer, H. I. Ince, Z. S. Duvenci, and 5 more authors
    Int J Biol Macromol, 2025
  4. AFFIPred: AlphaFold2 structure-based Functional Impact Prediction of missense variations
    M. S. Pir and E. Timucin
    Protein Sci, 2025
  5. Computational modeling of the anti-inflammatory complexes of IL37
    I. Sardag, Z. S. Duvenci, S. Belkaya, and 1 more author
    Journal of Molecular Graphics & Modelling, 2025
  6. A Novel NUP85 Variant Expanding the Phenotypic Spectrum of NUP85-Associated Steroid-Resistant Nephrotic Syndrome
    E. D. K. Sükür, E. Timucin, T. Bastug, and 1 more author
    Clinical Genetics, 2025

2024

  1. Identification of interaction partners of outer inflammatory protein A: Computational and experimental insights into how Helicobacter pylori infects host cells
    S. Akcelik-Deveci, E. Kilic, N. Mansur-Ozen, and 3 more authors
    PLoS One, 2024
  2. Rational design of monomeric IL37 variants guided by stability and dynamical analyses of IL37 dimers
    I. Sardag, Z. S. Duvenci, S. Belkaya, and 1 more author
    Comput Struct Biotechnol J, 2024

2023

  1. Computational completion of the Aurora interaction region of N-Myc in the Aurora a kinase complex
    P. Altiner, S. S. Cinaroglu, A. C. Timucin, and 1 more author
    Sci Rep, 2023
  2. Evaluation of AlphaFold structure-based protein stability prediction on missense variations in cancer
    H. Keskin Karakoyun, S. K. Yuksel, I. Amanoglu, and 5 more authors
    Front Genet, 2023
  3. Follicular homocysteine as a marker of oocyte quality in PCOS and the role of micronutrients
    T. Kucuk, P. E. Horozal, A. Karakulak, and 2 more authors
    J Assist Reprod Genet, 2023
  4. Effect of the switch status of Helicobacter pylori outer inflammatory protein A on gastric diseases
    S. Oktem-Okullu, T. Karaman, S. Akcelik-Deveci, and 5 more authors
    AMB Express, 2023
  5. Brave new surfactant world revisited by thermoalkalophilic lipases: computational insights into the role of SDS as a substrate analog
    M. Shehata, A. Unlu, J. Iglesias-Fernandez, and 3 more authors
    Phys Chem Chem Phys, 2023
  6. A small non-interface surface epitope in human IL18 mediates the dynamics and self-assembly of IL18-IL18BP heterodimers
    Y. Y. Yazici, S. Belkaya, and E. Timucin
    Comput Struct Biotechnol J, 2023

2022

  1. Toward Compilation of Balanced Protein Stability Data Sets: Flattening the DeltaDeltaG Curve through Systematic Enrichment
    N. Kebabci, A. C. Timucin, and E. Timucin
    J Chem Inf Model, 2022
  2. Modeling and dynamical analysis of the full-length structure of factor XII with zinc
    E. Kilinc, A. Can Timucin, S. Selim Cinaroglu, and 1 more author
    J Mol Model, 2022

2021

  1. Molecular modelling of the FOXO4-TP53 interaction to design senolytic peptides for the elimination of senescent cancer cells
    H. H. Le, S. S. Cinaroglu, E. C. Manalo, and 16 more authors
    EBioMedicine, 2021
  2. Bridging the Bridging Imidazolate in the Bimetallic Center of the Cu/Zn SOD1 and ALS
    A. C. Timucin, S. S. Cinaroglu, O. U. Sezerman, and 1 more author
    Front Chem, 2021

2020

  1. Comprehensive evaluation of the MM-GBSA method on bromodomain-inhibitor sets
    S. S. Cinaroglu and E. Timucin
    Brief Bioinform, 2020
  2. Understanding thermal and organic solvent stability of thermoalkalophilic lipases: insights from computational predictions and experiments
    M. Shehata, E. Timucin, A. Venturini, and 1 more author
    J Mol Model, 2020
  3. Lipase and Water in a Deep Eutectic Solvent: Molecular Dynamics and Experimental Studies of the Effects of Water-In-Deep Eutectic Solvents on Lipase Stability
    M. Shehata, A. Unlu, U. Sezerman, and 1 more author
    J Phys Chem B, 2020

2019

  1. Translation and cross-cultural adaptation of the extended version of the Nordic musculoskeletal questionnaire into Turkish
    N. Alaca, E. E. Safran, A. I. Karamanlargil, and 1 more author
    J Musculoskelet Neuronal Interact, 2019
  2. Comparative Assessment of Seven Docking Programs on a Nonredundant Metalloprotein Subset of the PDBbind Refined
    S. S. Cinaroglu and E. Timucin
    J Chem Inf Model, 2019
  3. In silico identification of inhibitors targeting N-Terminal domain of human Replication Protein A
    S. S. Cinaroglu and E. Timucin
    J Mol Graph Model, 2019
  4. Insights into an alternative benzofuran binding mode and novel scaffolds of polyketide synthase 13 inhibitors
    S. S. Cinaroglu and E. Timucin
    J Mol Model, 2019

2018

  1. Thermostability of the PYL-PP2C Heterodimer Is Dependent on Magnesium: In Silico Insights into the Link between Heat Stress Response and Magnesium Deficiency in Plants
    E. Timucin and O. U. Sezerman
    J Chem Inf Model, 2018

2016

  1. RACK1 Is an Interaction Partner of ATG5 and a Novel Regulator of Autophagy
    S. Erbil, O. Oral, G. Mitou, and 8 more authors
    J Biol Chem, 2016
  2. Probing the roles of two tryptophans surrounding the unique zinc coordination site in lipase family I.5
    E. Timucin, A. Cousido-Siah, A. Mitschler, and 2 more authors
    Proteins-Structure Function and Bioinformatics, 2016
  3. Predicting the impact of mutations on the specific activity of Bacillus thermocatenulatus lipase using a combined approach of docking and molecular dynamics
    O. Yukselen, E. Timucin, and U. Sezerman
    J Mol Recognit, 2016

2015

  1. Zinc Modulates Self-Assembly of Bacillus thermocatenulatus Lipase
    E. Timucin and O. U. Sezerman
    Biochemistry, 2015

2014

  1. Direct in vitro selection of titanium-binding epidermal growth factor
    S. Tada, E. Timucin, T. Kitajima, and 2 more authors
    Biomaterials, 2014

2013

  1. Modifying the catalytic preference of tributyrin in Bacillus thermocatenulatus lipase through in-silico modeling of enzyme-substrate complex
    E. Durmaz, S. Kuyucak, and U. O. Sezerman
    Protein Eng Des Sel, 2013
  2. The Conserved Lid Tryptophan, W211, Potentiates Thermostability and Thermoactivity in Bacterial Thermoalkalophilic Lipases
    E. Timucin and O. U. Sezerman
    Plos One, 2013

2011

  1. The drought response displayed by a DRE-binding protein from Triticum dicoccoides
    S. Lucas, E. Durmaz, B. A. Akpinar, and 1 more author
    Plant Physiol Biochem, 2011