Ismail Hakki Akgün

Performing Effective Calculations of Protein-Ligand Binding Free Energy with the Help of Molecular Dynamics Methods

Ismail Hakki Akgün · Current Journal of Applied Science and Technology · 2025

Aims: In our study, we aimed to calculate the binding free energies using molecular dynamics methods with the help of biased sampling approach using the binding site residues in protein - ligand complexes. Methodology: Molecular modeling and dynamics methods such as Steered Molec...

Open access Research Article 10.9734/cjast/2025/v44i24482

VLVS: A Knime Based Virtual Library Generation and Screening Workflow

Ismail Hakki Akgün · Journal of Pharmaceutical Research International · 2021

Objective: Tocreate an easy-to-use structure-based screening workflow using KNIME and open source software to prepare and screen virtual libraries in order to discover novel bioactive or drug molecules. Materials and Methods: In the preparation of the workflow we mentioned in the...

Open access Research Article 10.9734/jpri/2020/v32i4831121

Screening of Natural Product and Natural Product like Molecules against SARS–CoV–2 Main Protease Using Molecular Modeling Methods

Ismail Hakki Akgün · Journal of Pharmaceutical Research International · 2021

Objective: To determine possible MPro enzyme inhibitors by using structure-based virtual screening methods, in the ZINC Biogenic Data Set containing natural products and natural product-like molecules. Materials and Methods: QVina, an AutoDockVina derivative, was used in virtual...

Open access Research Article 10.9734/jpri/2020/v32i4831123