Mustafa (Safa) K.

Postdoctoral Researcher

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Detmold, Germany

Experience

Jul 2023 - Jul 2025
2 years 1 month
Bethesda, United States

Postdoctoral Researcher

National Institutes of Health (NIH), NHLBI

  • Led peptide inhibitor design against UPF1 using RFdiffusion, ProteinMPNN, and AlphaFold2/3; validated candidates with molecular dynamics simulations
  • Screened over 1 million compounds for ataxia fusion proteins via AutoDock Vina; confirmed top hits using GROMACS MD simulations
  • Developed RNA-seq analysis pipelines for nonsense-mediated decay (NMD) studies including isoform quantification and motif discovery
  • Modeled protein-RNA interactions using AlphaFold3 multimers integrated with BioGRID/STRING databases
  • Established computational workflows for transcriptomics and RNA regulation in iPSC-derived human models
Aug 2019 - May 2023
3 years 10 months
Braunschweig, Germany

PhD Researcher

Technische Universität Braunschweig

  • Investigated Legionella pneumophila virulence factors integrating structural biology and interactomics approaches
  • Utilized AlphaFold and Rosetta for modeling pathogen-host interactions; identified druggable targets for therapeutic intervention
  • Purified effector proteins and validated ligand binding using nanoDSF and surface plasmon resonance (SPR)
  • Applied human lung explants to connect molecular mechanisms with tissue-level responses to infection
  • Integrated AP-MS proteomics data with computational modeling to map host-pathogen interaction networks
Apr 2017 - Jul 2019
2 years 4 months
İstanbul, Turkey

Research Assistant

Türkisch-Deutsche Universität

  • Developed computational models for amyloid formation and disordered protein behavior
  • Designed peptide and protein variants using homology modeling, molecular docking, and high-performance computing
  • Established molecular modeling workflows for protein structure-function analysis
Feb 2016 - May 2016
4 months
Turkey

Project Assistant

TÜBİTAK Marmara Technopark (MARTEK)

  • Performed pharmacological assays and biosensor studies for preclinical drug testing
  • Supported automation-based in vivo and ex vivo drug validation protocols
Jun 2014 - Sep 2014
4 months
Portugal

Research Intern

Instituto Gulbenkian de Ciência (IGC)

  • Conducted pharmacological assays and in vivo studies on therapeutic candidates
  • Contributed to synthetic biology and high-throughput screening pipelines
Jun 2013 - Sep 2013
4 months
İstanbul, Turkey

Research Intern

Bogazici University

  • Performed molecular biology assays for drug testing and validation

Summary

Computational biologist with 8+ years of experience bridging experimental biology and computational innovation. Expertise in protein design, structural bioinformatics, and transcriptomics applied to therapeutic discovery. Successfully led projects from molecular modeling to validation in human model systems. Proven ability to integrate multi-omics data, develop computational pipelines, and translate findings into biological insights for undruggable targets.

Skills

Protein Design

  • Alphafold2/3
  • Rfdiffusion
  • Proteinmpnn
  • Rosetta Suite

Structural Biology

  • Molecular Dynamics
  • Pymol/chimerax
  • Gromacs

Computational Methods

  • Python/r Programming
  • Hpc/cloud Computing
  • Bioinformatics Pipelines
  • Bash Scripting

Transcriptomics

  • Rna-seq Analysis
  • Isoform Quantification
  • Motif Discovery
  • Nmd Studies

Experimental Techniques

  • Protein Purification
  • Nanodsf/spr
  • Mass Spectrometry
  • Mammalian/ipsc Culture

Specialized Knowledge

  • Host-pathogen Interactions
  • Drug Discovery Pipelines
  • Multi-omics Integration
  • Undruggable Targets

Technical Skills

  • Protein Design: Alphafold2/3, Rfdiffusion, Proteinmpnn, Rosetta
  • Structural Analysis: Pymol, Chimerax, Gromacs, Autodock Vina
  • Transcriptomics: Rna-seq, Isoform Quantification, Motif Discovery
  • Programming: Python, R, Bash Scripting
  • Computational: Hpc, Cloud Computing, Bioinformatics Pipelines

Languages

German
Native
Turkish
Native
English
Advanced

Education

Aug 2019 - May 2023

Technische Universität Braunschweig

PhD in Biology, Protein interaction and inhibition of L. pneumophila Mip and immunometabolism · Biology · Braunschweig, Germany

Oct 2015 - Jun 2018

Gebze Technical University

M.Sc. Molecular Biology & Genetics, Molecular characterization and identification of the interaction partner of the peptidyl · Molecular Biology & Genetics · Turkey

Oct 2011 - Jun 2015

Gebze Technical University

B.Sc. Molecular Biology & Genetics · Molecular Biology & Genetics · Turkey

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