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AmirSedaghaati/README.md

Amir Sedaghati


How I work

My background started in wet-lab biology — mesenchymal stem cell culture, ELISAs, standard laboratory workflows. During my MSc, my research moved into molecular docking and molecular dynamics, and that shifted my long-term direction toward computational methods. I still build the automation that connects both sides.


Projects

  • alphafold-cadd-workflow — Automated CADD pipeline: AlphaFold structure prediction → Vina docking → Lipinski filtering, orchestrated with Nextflow (TREM2 target)
  • AChE-QSAR-Machine-Learning — Random Forest QSAR pipeline predicting AChE inhibitor bioactivity (pIC50) from ChEMBL data and RDKit Morgan fingerprints
  • pubchem-metabolite-descriptor-fetcher — Python + R pipeline that batch-fetches physicochemical descriptors from PubChem and visualizes drug-likeness against Lipinski/TPSA thresholds
  • cadd-fastapi-service — FastAPI service exposing CADD pipeline stages as REST endpoints for automation tools like n8n (active development)
  • md-trajectory-analysis — RMSD/RMSF analysis of a short GROMACS MD simulation, with PyMOL structure rendering
  • vina-docking-pipeline — Parses, filters, and ranks AutoDock Vina docking output; generates a hit list and affinity chart
  • n8n-automation-examples — Webhook-triggered n8n workflow: PubChem lookup, Lipinski filtering, branching error handling, and Google Sheets logging

Selected results

Contributed to isolating human Wharton's Jelly mesenchymal stem cells and to lentiviral vector production used to engineer them to express erythropoietin (EPO), evaluated in a 4T1 breast cancer mouse model. The engineered cells maintained therapeutic plasma EPO, hemoglobin, and hematocrit levels for over 10 weeks post-transplantation. Published: Current Gene Therapy

Docked walnut husk metabolites against pectate lyase Pel3 using AutoDock 4.2 as the primary method (AutoDock Vina 1.2 as a secondary cross-check), then validated the top hit — Aesculin — with molecular dynamics and τRAMD. MM-PBSA binding free energy ≈ -2.9 kcal/mol, average RAMD residence time ≈0.015 ns — consistent with moderate, reversible binding rather than a strong inhibitor. Published: Biochemical and Biophysical Reports

Network-Based Transcriptomics Identifies Key Hippocampal Targets in Alzheimer’s Disease and Their Modulation by Apigenin, Luteolin, and Berberine. Published: Scientific African


What I'm looking for

A research-oriented position — Bioinformatics Scientist, Computational Biologist, or Computational Drug Discovery Scientist — in a life-science team where computation and wet-lab work are closely linked. Primarily targeting Germany, the Netherlands, Switzerland, Denmark, Norway, and Ireland — though I'd consider a strong opportunity anywhere else, too. Visa sponsorship needed — happy to discuss timeline directly.


Languages

English — IELTS 7.0
German — A2, working toward B1/B2


LinkedIn ORCID Gmail

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  1. alphafold-cadd-workflow alphafold-cadd-workflow Public

    Automated CADD pipeline: AlphaFold structure prediction → Vina docking → Lipinski filtering, orchestrated with Nextflow (TREM2 target)

    Python

  2. AChE-QSAR-Machine-Learning AChE-QSAR-Machine-Learning Public

    A machine learning pipeline utilizing Random Forest to predict Acetylcholinesterase (AChE) inhibitor bioactivity using ChEMBL data and RDKit Morgan fingerprints.

    Python

  3. pubchem-metabolite-descriptor-fetcher pubchem-metabolite-descriptor-fetcher Public

    Python + R pipeline for batch PubChem descriptor retrieval and Lipinski/TPSA drug-likeness visualization

    Python

  4. cadd-fastapi-service cadd-fastapi-service Public

    A deployable REST API that wraps a CADD screening pipeline, compound descriptor retrieval, Lipinski filtering, and docking result parsing exposed as HTTP endpoints via FastAPI and Docker.

    Python

  5. md-trajectory-analysis md-trajectory-analysis Public

    Post-processing and analysis of a short GROMACS MD simulation (RMSD, RMSF, PyMOL rendering)

    Python

  6. vina-docking-pipeline vina-docking-pipeline Public

    Analyzes AutoDock Vina output files and generates binding affinity plots

    Python