Laboratory name: ITU Biomolecular Engineering Laboratory
Head of Research Lab: Assoc. Prof. Mert Gür
Laboratory website: https://gurlab.itu.edu.tr/en/homepage
Laboratory Work Areas:
Our lab specializes in applying computational modeling and statistical thermodynamics to problems at the interface of medicine/biology and engineering.
Main research areas:
Biomolecular machines and motors
Nanomachines
Dynein, Kinesin, Microtubule, and Microtubule Associated Proteins
Behçet Disease
SARS-CoV-2 Spike Protein
Computational Simulation and Modeling
Molecular Dynamics
Statistical Mechanics and Thermodynamics
Food Drying
Drug design
Protein Engineering
Important Projects:
16. Self-Coordination of Dyneins during Ciliary Beating
Project Role: PI
Funding Source: TUBITAK (The Scientific and Technological Research Council of Turkey), 2501 - Joint Research Program with National Science Foundation (NSF)
Project Date: 2022- 2025
15. Molecular-scale modeling of dynein microtubule binding and power stroke
Project Role: PI
Funding Source: TUBITAK (The Scientific and Technological Research Council of Turkey)
Project Date: 2022- 2025
14. Modeling the Regulation of Motors by Microtubule-Associated Proteins.
Project Role: PI
Funding Source: Partnership for Advanced Computing in Europe, PRACE (European Union)
Project Date: 2022-2023
13. Identification and Reengineering of Effective Nanobodies Against SARS-CoV-2 Omicron Variant
Project Role: Co-PI
Funding Source: COVID-19 High Performance Computing Consortium (USA)
Project Dates: 2021- 2022
12. The Mechanism and Energetics of Dynein’s Powerstroke (EnDy)
Project Role: PI
Funding Source: DECI-17 (Distributed European Computing Initiative), PRACE-Partnership for Advanced Computing in Europe (European Union)
Project Dates: 2021 – 2022
11. Modeling the Mechanism of the Mechanochemical Cycle of the Cytoplasmic Dynein Motor Protein
Project Role: PI
Funding Source: Istanbul Technical University (ITU) BAP
Project Dates: 2021 – 2022
10. Designing Cell Penetrating Peptide Based Drug Candidates for Behcet’s Disease
Project Role: PI
Funding Source: TUBITAK
Project Dates: 2020 – 2023
9. Development of an Early Detection System for Hereditary Colon and Breast Cancers and its Integration into e-Nabız Personal Health Record System
Project Role: PI
Funding Source: TUBITAK
Project Dates: 2020 – 2023
8. Exploring Nanobody Inhibitory Mechanism against SARS-CoV-2 Spike Glycoprotein Using Molecular Dynamics Simulations, (UC Berkeley – ITU Collaboration)
Project Role: Co-PI
Funding Source: COVID-19 High Performance Computing Consortium (USA)
Project Dates: 2020 – 2021
7. Exploring Binding and Fusion Mechanism of SARS-CoV-2 Spike Glycoprotein Using Molecular Dynamics Simulations, (UC Berkeley – ITU Collaboration)
Project Role: Co-PI
Funding Source: COVID-19 High Performance Computing Consortium (USA)
Project Dates: 2020 – 2021
6. Modelling the Mechanochemical Cycle of Cytoplasmic Dynein Machinery
Project Role: PI
Funding Source: Partnership for Advanced Computing in Europe, PRACE (European Union)
Project Dates: 2020 – 2021
5. Exploring differences in binding characteristics between HLA-B51 and HLA-B52
Project Role: Yürütücü
Funding Source: NVIDIA Hardware Grant Program
Project Dates: 2019 – 2019
4. Modeling the Effects of Mutation and Peptide Binding on Thermodynamic Properties of Cyclophilin 40 Enzyme
Project Role: PI
Funding Source: Istanbul Technical University BAP
Project Dates: 2018 – 2019
3. Modeling the Mechanics and Energetics of the Cytoplasmic Dynein Motor Protein Mechanochemical
Cycle Project Role: PI
Funding Source: TUBITAK
Project Dates: 2016 – 2019
2. Effect of Cell Membrane on the Function of Membrane Proteins Targeted by Therapeutic Drugs Against Neurological Disorders
Role: PI
Funding Source: Turkish Academy of Science (TÜBA)
Project Dates: 2016 – 2019
1. Investigation and Modeling of Functional Mechanisms of Cell Membrane Proteins Targeting Neurological Drugs
Project Role: PI
Funding Source: TUBITAK
Project Dates: 2015 – 2017