Abdulkadir Kocak

Gebze, 41400, Turkey

Last Updated: 09/26/2026

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Found 19 publications

Data-Efficient Equivariant NNPs Enable DFT-Accurate Simulations and Implicit Solvation Free Energies.

Data-Efficient Equivariant NNPs Enable DFT-Accurate Simulations and Implicit Solvation Free Energies.

Journal: The journal of physical chemistry. B

Published: November 28, 2025

Modeling Gas Adsorption and Mechanistic Insights into Flexibility in Isoreticular Metal-Organic Frameworks Using High-Dimensional Neural Network Potentials.

Modeling Gas Adsorption and Mechanistic Insights into Flexibility in Isoreticular Metal-Organic Frameworks Using High-Dimensional Neural Network Potentials.

Journal: Langmuir : the ACS journal of surfaces and colloids

Published: March 14, 2025

DeepConf: Leveraging ANI-ML Potentials for Exploring Local Minima with Application to Bioactive Conformations.

DeepConf: Leveraging ANI-ML Potentials for Exploring Local Minima with Application to Bioactive Conformations.

Journal: Journal of chemical information and modeling

Published: March 04, 2025

Benchmarking ANI potentials as a rescoring function and screening FDA drugs for SARS-CoV-2 Mpro.

Benchmarking ANI potentials as a rescoring function and screening FDA drugs for SARS-CoV-2 Mpro.

Journal: Journal of computer-aided molecular design

Published: January 03, 2024

Exploring potential Plasmodium kinase inhibitors: a combined docking, MD and QSAR studies.

Exploring potential Plasmodium kinase inhibitors: a combined docking, MD and QSAR studies.

Journal: Journal of biomolecular structure & dynamics

Published: August 21, 2023

Computational analysis of substrate recognition of Sars-Cov-2 Mpro main protease.

Computational analysis of substrate recognition of Sars-Cov-2 Mpro main protease.

Journal: Computational biology and chemistry

Published: August 11, 2023

Exploring epigenetic drugs as potential inhibitors of SARS-CoV-2 main protease: a docking and MD simulation study.

Exploring epigenetic drugs as potential inhibitors of SARS-CoV-2 main protease: a docking and MD simulation study.

Journal: Journal of biomolecular structure & dynamics

Published: July 17, 2023

Revisiting MMPBSA by Adoption of MC-Based Surface Area/Volume, ANI-ML Potentials, and Two-Valued Interior Dielectric Constant.

Revisiting MMPBSA by Adoption of MC-Based Surface Area/Volume, ANI-ML Potentials, and Two-Valued Interior Dielectric Constant.

Journal: The journal of physical chemistry. B

Published: May 12, 2023

Accurate Binding Free Energy Method from End-State MD Simulations.

Accurate Binding Free Energy Method from End-State MD Simulations.

Journal: Journal of chemical information and modeling

Published: August 16, 2022

The performance of ANI-ML potentials for ligand-n(H2 O) interaction energies and estimation of hydration free energies from end-point MD simulations.

The performance of ANI-ML potentials for ligand-n(H2 O) interaction energies and estimation of hydration free energies from end-point MD simulations.

Journal: Journal of computational chemistry

Published: July 15, 2022

A neural network potential for the IRMOF series and its application for thermal and mechanical behaviors.

A neural network potential for the IRMOF series and its application for thermal and mechanical behaviors.

Journal: Physical chemistry chemical physics : PCCP

Published: May 05, 2022

Molecular dynamics simulations reveal the plausible agonism/antagonism mechanism by steroids on androgen receptor mutations.

Molecular dynamics simulations reveal the plausible agonism/antagonism mechanism by steroids on androgen receptor mutations.

Journal: Journal of molecular graphics & modelling

Published: September 25, 2021

Showing 1-12 of 19

Last Updated: 09/26/2026