TIMUCIN LAB

Gebze Technical University

Kocaeli, 41400, Türkiye

emelt@gtu.edu.tr

Welcome to the Timucin Lab, led by Emel Timucin at the Department of Molecular Biology and Genetics, Gebze Technical University. We are a computational research group that uses molecular dynamics simulations, protein structure prediction, and bioinformatics to understand how proteins behave and how that behavior can be tuned for therapeutic ends.

Our work spans several directions:

Molecular dynamics & enhanced sampling — probing conformational dynamics of proteins and protein–protein complexes.
Structure prediction & benchmarking — assessing modern predictors (AlphaFold, Boltz, Chai, and others) on challenging targets such as antibody–antigen and protein–peptide complexes.
Variant interpretation — structure-informed prediction of the functional impact of missense mutations, including our AlphaFold-based pathogenicity predictor, AFFIPred.
Enzymes in non-native environments — how lipases and other enzymes fold, oligomerize, and stay active in deep eutectic solvents.

Join us. We are looking for graduate students (PhD and MSc) who are curious about proteins, simulation, and computational biology. If that sounds like you, please get in touch at emelt@gtu.edu.tr.

“Somewhere, something incredible is waiting to be known.” — Carl Sagan

selected publications

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

Bib

@article{sardag2026enhanced,
  title = {Enhanced and Classical MD Simulations Map Aggregation-Prone Regions in the Olfactomedin Domain of Myocilin},
  author = {Sardag, I. and Duvenci, Z. S. and Timucin, E.},
  journal = {Journal of Chemical Information and Modeling},
  volume = {66},
  number = {1},
  pages = {653--667},
  year = {2026}
}

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

Bib

@article{unsal2026confidence,
  title = {Confidence scoring for deep learning-predicted antibody-antigen complexes: AntiConf as a precision-driven metric},
  author = {Ünsal, S. and Holland, B. and Sardag, I. and Timucin, E.},
  journal = {Briefings in Bioinformatics},
  volume = {27},
  number = {2},
  year = {2026}
}

AFFIPred: AlphaFold2 structure-based Functional Impact Prediction of missense variations

M. S. Pir and E. Timucin

Protein Sci, 2025

Bib

@article{pir2025affipred,
  title = {AFFIPred: AlphaFold2 structure-based Functional Impact Prediction of missense variations},
  author = {Pir, M. S. and Timucin, E.},
  journal = {Protein Sci},
  volume = {34},
  number = {2},
  pages = {e70030},
  year = {2025}
}

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

Bib

@article{shehata2023brave,
  title = {Brave new surfactant world revisited by thermoalkalophilic lipases: computational insights into the role of SDS as a substrate analog},
  author = {Shehata, M. and Unlu, A. and Iglesias-Fernandez, J. and Osuna, S. and Sezerman, O. U. and Timucin, E.},
  journal = {Phys Chem Chem Phys},
  volume = {25},
  number = {3},
  pages = {2234--2247},
  year = {2023}
}

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

Bib

@article{kebabci2022toward,
  title = {Toward Compilation of Balanced Protein Stability Data Sets: Flattening the DeltaDeltaG Curve through Systematic Enrichment},
  author = {Kebabci, N. and Timucin, A. C. and Timucin, E.},
  journal = {J Chem Inf Model},
  volume = {62},
  number = {5},
  pages = {1345--1355},
  year = {2022}
}

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

Bib

@article{le2021molecular,
  title = {Molecular modelling of the FOXO4-TP53 interaction to design senolytic peptides for the elimination of senescent cancer cells},
  author = {Le, H. H. and Cinaroglu, S. S. and Manalo, E. C. and Ors, A. and Gomes, M. M. and Duan Sahbaz, B. and Bonic, K. and Origel Marmolejo, C. A. and Quentel, A. and Plaut, J. S. and Kawashima, T. E. and Ozdemir, E. S. and Malhotra, S. V. and Ahiska, Y. and Sezerman, U. and Bayram Akcapinar, G. and Saldivar, J. C. and Timucin, E. and Fischer, J. M.},
  journal = {EBioMedicine},
  volume = {73},
  pages = {103646},
  year = {2021}
}

Comprehensive evaluation of the MM-GBSA method on bromodomain-inhibitor sets

S. S. Cinaroglu and E. Timucin

Brief Bioinform, 2020

Bib

@article{cinaroglu2020comprehensive,
  title = {Comprehensive evaluation of the MM-GBSA method on bromodomain-inhibitor sets},
  author = {Cinaroglu, S. S. and Timucin, E.},
  journal = {Brief Bioinform},
  volume = {21},
  number = {6},
  pages = {2112--2125},
  year = {2020}
}

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

Bib

@article{shehata2020lipase,
  title = {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},
  author = {Shehata, M. and Unlu, A. and Sezerman, U. and Timucin, E.},
  journal = {J Phys Chem B},
  volume = {124},
  number = {40},
  pages = {8801--8810},
  year = {2020}
}

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

Bib

@article{cinaroglu2019comparative,
  title = {Comparative Assessment of Seven Docking Programs on a Nonredundant Metalloprotein Subset of the PDBbind Refined},
  author = {Cinaroglu, S. S. and Timucin, E.},
  journal = {J Chem Inf Model},
  volume = {59},
  number = {9},
  pages = {3846--3859},
  year = {2019}
}