I. Web Applications & Computational Frameworks

1. ADEPT (Automated Dynamics-aware Evolutionary Profiling Tool)

• Description: An open-access web server for variant interpretation. ADEPT processes standard CSV inputs of per-residue RMSF and evolutionary conservation data to compute dynamics-aware metrics, uncoupling structural rigidity from functional mechanics. Features secure, client-side processing.

• Links:

  • Web Server: karagolresearch.com/adept

  • Source Code: GitHub Repository

 

2. VariantT (Directional Variant Tension Framework)

• Description: A web-based application that quantifies substitution asymmetry and models evolutionary constraints. Users can input multiple sequence alignments (MSAs), adjust statistical parameters, and visualize global tension scores to bridge protein design with evolutionary inference.

• Link: karagolresearch.com/variantt

 

3. Evolutionary Statistics Toolkit

• Description: A streamlined web application for sequence analysis utilizing a client-side architecture, allowing researchers to run evolutionary statistical analyses locally without uploading sensitive genomic data to external servers.

• Link: alperkaragol.com/toolkitdocu

 

4. TitanSim (Computational Azotosome Builder)

• Description: A computational simulation framework and builder focused on membrane modeling and structural analysis (specifically modeling hypothetical lipid-like structures like azotosomes).

• Link: Available via Karagöl Toolkits/GitHub.

 

II. Sequence Analysis & Formatting Scripts

5. Alignment Substitution Analyzer (AlignSubs)

• Description: A targeted computational tool used to parse multiple sequence alignments and rigorously quantify substitution rates and residue variation across large biological datasets.

 

6. HGVS to FASTA Variant Format Converter

• Description: A streamlined utility built to automate the conversion of clinical genetic variant nomenclature (HGVS standard) directly into FASTA sequences for rapid downstream structural modeling and sequence analysis.

 

7. Hydrophilicity Plot Generator

• Description: A computational plotting tool that analyzes amino acid sequences to generate predictive hydrophilicity maps, which are critical for predicting protein folding, solubility, and membrane-spanning regions.

 

8. Truncated Isoforms Analyzer

• Description: A bioinformatics script/tool set designed to map and analyze truncated protein isoforms, aiding in the understanding of alternative splicing and pathological protein expressions.

 

III. Medical AI, Imaging & Clinical Databases

9. Brain CT & MRI AI Recognition Pipeline

• Description: A specialized AI pipeline and hackathon-winning framework designed to automate the recognition of anomalies in neuroimaging (CT and MRI), acting as a clinical decision-support mechanism.

 

10. NeuroAcoustic Analysis Platform

• Description: A computational platform aimed at the intersection of neurology and acoustic data, designed to process and analyze complex neuro-acoustic signals for clinical diagnostic applications.

 

11. Factor IX (FIX) Variant Database

• Description: A specialized genetic variant database for human coagulation factor IX, developed as a clinical service for biochemists and physicians in collaboration with the Structural Immunology Group at UCL.

• Link: GitHub Repository (FIX_database)

 

12. CT Stroke Detection Pipeline

• Description: An AI-driven medical imaging pipeline designed to detect strokes from CT scans, developed for the TEKNOFEST Artificial Intelligence in Healthcare Competition.

• Link: alperkaragol.com/ctstrokedetection

 

IV. Mobile Platforms & Educational Interactives

13. Graphiet and Seqiet

• Description: A cross-platform mobile bioinformatics pipeline currently in development for analyzing and visualizing sequence data natively on mobile devices.

 

14. Transporter Interactive Pages (Serotonin & Glutamate)

• Description: Web-based interactive structural visualization pages that allow students and researchers to explore the molecular dynamics, binding pockets, and structural transitions of critical neurotransmitter transporters.

 

15. The Game of Residues

• Description: An interactive, educational software tool/game designed to teach the chemical properties of amino acids, residue interactions, and the foundational rules of protein folding.

 

16. Molecular Dynamics on Cloud Computing

• Description: Cloud-based scripts and environments structured to democratize access to high-performance molecular dynamics simulations without requiring expensive on-premise computing clusters.