Abdulkadır Kocak

Gebze Technical University — Turkey

Computer Science · Physical Sciences

15h-index516citations61works2.42yr avg
OpenAlex↗ORCID↗Google Scholar↗Lab page↗

Accepting Students?

No reports yet. Know if this professor is taking students?

Research Topics

Computational Drug Discovery Methods(10), Advanced Chemical Physics Studies(8), Machine Learning in Materials Science(7), Protein Structure and Dynamics(6), Metal-Organic Frameworks: Synthesis and Applications(5)

Publications61 total

Data-Efficient Equivariant NNPs Enable DFT-Accurate Simulations and Implicit Solvation Free Energies
The Journal of Physical Chemistry B·2025Open Access
Data-Efficient Equivariant NNPs Enable DFT-Accurate Simulations and Solvation Free Energies
2025Open Access
A Retrospective Analysis of the Predictive Role of RDW, MPV, and MPV/PLT Values in 28-Day Mortality of Geriatric Sepsis Patients: Associations with APACHE II and SAPS II Scores
Medicina·2025· 2 citedOpen Access
Modeling Gas Adsorption and Mechanistic Insights into Flexibility in Isoreticular Metal–Organic Frameworks Using High-Dimensional Neural Network Potentials
Langmuir·2025· 9 citedOpen Access
DeepConf: Leveraging ANI-ML Potentials for Exploring Local Minima with Application to Bioactive Conformations
Journal of Chemical Information and Modeling·2025· 3 citedOpen Access
DeepConf: Leveraging ANI-ML Potentials for Exploring Local Minima with A Focus on Bioactive Conformations
2024Open Access
DeepConf: Leveraging ANI-ML Potentials for Exploring Local Minima with A Focus on Bioactive Conformations
2024Open Access
Benchmarking ANI potentials as a rescoring function and screening FDA drugs for SARS-CoV-2 Mpro
Journal of Computer-Aided Molecular Design·2024· 5 citedOpen Access
Modeling Gas Adsorption and Mechanistic Insights into Flexibility in Isoreticular Metal–Organic Frameworks using High-Dimensional Neural Network Potentials
2023· 2 citedOpen Access
Computational analysis of substrate recognition of Sars-Cov-2 Mpro main protease
Computational Biology and Chemistry·2023· 6 cited
Exploring potential <i>Plasmodium</i> kinase inhibitors: a combined docking, MD and QSAR studies
Journal of Biomolecular Structure and Dynamics·2023· 3 cited
Exploring epigenetic drugs as potential inhibitors of SARS-CoV-2 main protease: a docking and MD simulation study
Journal of Biomolecular Structure and Dynamics·2023· 3 citedOpen Access
Revisiting MMPBSA by Adoption of MC-Based Surface Area/Volume, ANI-ML Potentials, and Two-Valued Interior Dielectric Constant
The Journal of Physical Chemistry B·2023· 15 citedOpen Access
Exploring potential <i>Plasmodium</i> kinase inhibitors: a combined docking, MD and QSAR studies
Figshare·2023Open Access
The performance of <scp>ANI‐ML</scp> potentials for ligand‐n(<scp>H<sub>2</sub>O</scp>) interaction energies and estimation of hydration free energies from end‐point <scp>MD</scp> simulations
Journal of Computational Chemistry·2022· 6 cited
Accurate Binding Free Energy Method from End-State MD Simulations
Journal of Chemical Information and Modeling·2022· 50 citedOpen Access
An accurate binding free energy method from endstate MD simulations
Zenodo (CERN European Organization for Nuclear Research)·2022Open Access
A neural network potential for the IRMOF series and its application for thermal and mechanical behaviors
Physical Chemistry Chemical Physics·2022· 22 cited
Development and Application of a Single Neural Network Potential for IRMOF-n (n=1,4,6,7,10)
2021Open Access
Molecular dynamics simulations reveal the plausible agonism/antagonism mechanism by steroids on androgen receptor mutations
Journal of Molecular Graphics and Modelling·2021· 15 cited
page 1 of 4Next →

Frequent Co-authors

Müslüm Yıldız(13), Ömer Tayfuroğlu(12), Ricardo B. Metz(8), Yunus Zorlu(7), Ebru Akkus(5), Hülya Anıl(5), Koray Harmancı(5), Hakan Yılmaz(4), Özlem Faiz(3), Ö. Andaç(3), Özcan Bör(3), W. L. Pearson(2), Gokhan Altinay(2), Zachary Sallese(2), Muhammad Affawn Ashraf(2), Jennifer S. Daluz(2), Christopher Copeland(2), Yakup Canıtez(2), Şükrü Çekiç(2), Uğur Çelik(2)