I sometimes create educational animations in Quantum Chemistry using manim.
Check out my content on YouTube.
Quantum Chemistry | Waves and Particles - A quick video that starts of a series of videos on quantum chemistry with waves and particles that we are going to go about understanding the ideas through fun animations.
Running & Cycling
As an avid runner and cyclist since high school, I enjoy regular & irregular runs and rides.
More running and biking routes can be found on Strava.
Research
Publications
PocketVina Enables Scalable and Highly Accurate Physically Valid Docking through Multi-Pocket Conditioning
GPU-accelerated protein–ligand docking with automated pocket detection, exploring through multi-pocket conditioning. The method achieves physically valid binding poses while enabling high-throughput virtual screening at a speed of 1.5 seconds per protein–ligand pair. A Sarıgün, B Uyar, V Franke, A Akalin
• [arXiv, 2025] | [GitHub Repo] | [Colab Demo]
CompassDock: Comprehensive Accurate Assessment Approach for Deep Learning-Based Molecular Docking in Inference and Fine-Tuning
The CompassDock framework is a comprehensive and accurate assessment approach for deep learning-based molecular docking. It evaluates key factors such as the physico-chemical properties and bioactivity favorability of ligands. A Sarıgün, V Franke, B Uyar, A Akalin
• Oral Presentation at Helmholtz AI Conference, 2024, Düsseldorf, Germany
• Accepted to NeurIPS MLSB, 2024, Vancouver, Canada
• [arXiv, 2024] | [GitHub Repo] | [PyPI Installation] | [Colab Demo]
Flexynesis: A deep learning framework for bulk multi-omics data integration for precision oncology and beyond
A deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction.
B Uyar, T Savchyn, R Wurmus, A Sarıgün, MM Shaik, V Franke, A Akalin
• [bioRxiv, 2024] | [GitHub Repo]
Target Specific De Novo Design of Drug Candidate Molecules with Graph Transformer-based Generative Adversarial Networks
A new deep learning model architecture for de novo drug design to treat drug-resistant diseases using Generative Adversarial Networks and a combination of transformer and graph neural network approaches.
A Ünlü, E Çevrim, A Sarıgün, MG Yiğit, H Çelikbilek, O Bayram, HA Güvenilir, A Koyaş, DC Kahraman, A Olğaç, AS Rifaioğlu, E Banoğlu, T Doğan
• [arXiv, 2023] | [Main GitHub Repo] | [Old GitHub Repo] | [Hugging Face Demo]
FEXBind: Fast Explainable Binding Free Energy Prediction by Leveraging Molecular Mechanic Features and Molecular Structure with Graph Neural Networks, Undergraduate Research Project (June 2023) Ankara, Turkey
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Preformatted
i = 0;
while (!deck.isInOrder()) {
print 'Iteration ' + i;
deck.shuffle();
i++;
}
print 'It took ' + i + ' iterations to sort the deck.';
Quantum Chemistry | Waves and Particles - A quick video that starts of a series of videos on quantum chemistry with waves and particles that we are going to go about understanding the ideas through fun animations.
