Ventures & IP
My commercial portfolio focuses on translating computational biology, deep learning for protein engineering, and structural bioinformatics into scalable biotech and clinical solutions. Below is an overview of active corporate ventures, proprietary software packages, and intellectual property.
Corporate Ventures
Co-founder | Ophyra Biotechnology
Core Technology: De novo protein design leveraging computational tools for hyperstable beta-barrel cages and synthetic chaperones.
Co-founder | MAGEN Bioanalytics
Core Technology: Proprietary epidemiological tracking algorithms.
Co-founder | Netiva Medical
Core Technology: Vector based computational models and real-time computer vision for health environments focusing hospital infection control.
Patents & Intellectual Property
Method for Designing pH-Specific Proteins
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Status: Patent Pending | Application No: 2024/018998
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Description: A foundational computational method utilizing evolutionary-informed sequential single base substitutions to engineer environment-responsive (pH-specific) proteins. This serves as a core mechanism for developing targeted "bio-betters."
Not-disclosed
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Status: Invention Disclosure Under Review | Institution: Istanbul University Technology Transfer Application and Research Center
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Description: An environment-responsive therapeutic mechanism designed to induce apoptosis specifically within the acidic microenvironments of cancer tissues.
Regulation of Immune Activation via STING Truncated Isoform
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Status: Early Publication Approved | Application No: 2024/018993
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Description: A therapeutic approach for the treatment of autoimmune diseases and inflammation, modulating the immune system and inflammatory response utilizing a specifically engineered STING truncated isoform.
Inhibition of SNARE Complex Formation and VAMP2 Dimerization
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Status: Early Publication Approved | Application No: 2024/018735
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Description: A targeted mechanism utilizing a VAMP2 truncated isoform for applications in pain management, neuromuscular blockade, and precise synaptic modulation.
Not-disclosed
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Status: Invention Disclosure Under Review | Institution: Istanbul University Technology Transfer Application and Research Center
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Description: -
Software
15. GMX_MMPBSA on Colab & HPC/Jupyter
Availability: GitHub
14. TitanSim: Computational Azotosome Builder
Availability: Live on tanerkaragol.com
13. NeuroAcoustic Analysis (NeuroSync)
Availability: Live on tanerkaragol.com
12. hydrophilicity-plot (Python Package)
Description: Kyte-Doolittle hydrophilicity plot tool for FASTA single/multiple protein sequences.
11. AlignSubs (Python Package)
Description: Alignment Substitution Analyzer for nucleotide and amino acid substitutions.
10. adept-evo (Python Package)
Description: Automated Dynamics-Aware Evolutionary Profiling Tool (ADEPT).
9. karagol-rama (Python Package)
Description: Karagol-Ramachandran plots. Silicon-backbone Ramachandran-equivalent dihedral analysis for MD simulations.
8. lipid-plots (Python Package)
Description: MD analysis tools for lipid membrane geometry, evaluating packing defects, depth-disorder, and tilt-torsion.
7. Factor IX Variant Database
Description: Genetic variants in the human coagulation factor 9 as a service for clinicians and biochemists. Perkins S.J, Karagöl T., Karagöl A., Spencer H. (2025, soon be available) © Copyright 2003-2024, Structural Immunology Group, University College London.
6. KernelNodes
Description: A web-based program to identify evolutionary node networks of proteins, for causal mutational pathways and functional domain screening.
5. Stroke Detection from CT Images
Description: AI-driven pipeline developed for the Aerospace and Technology Festival, Artificial Intelligence in Healthcare Competition.
Availability: https://www.alperkaragol.com/ctstrokedetection
4. PyMOL Scripts for Variation Analysis (2023-2024)
Description: Custom scripts for structural visualization and variation analysis.
3. Evolutionary Statistics Toolkit (2024)
Description: A simplified sequence analysis web toolkit featuring client-side processing.
Availability: Live Web Site
2. HGVS Missense Variants to FASTA Format Converter
Availability: GitHub, Live Web Site, Pyhton
1. Molecular Dynamics Simulations on Cloud Computing
Description: Blog Post detailing cloud computing methodologies for molecular dynamics.
For source code and further repository details, please visit my GitHub account: https://github.com/karagol-taner