Curriculum Vitae
Recep Adiyaman, PhD
Structural Bioinformatics Scientist | Protein Structure, MD Refinement, Drug Design
Reading, UK
Pioneering the shift from static snapshots to dynamic ensembles. Integrating AI with Molecular Dynamics to model mutants, de novo designs, and drug resistance.
Experience
Collaborative Researcher (Part-Time)
InstaDeep — London, UK
- Built structural immunology pipeline with BioNTech to accelerate cancer vaccine target discovery.
- Bridged experimental readouts and computational prediction for faster candidate prioritisation.
Research Fellow
McGuffin Lab, University of Reading — Reading, UK
- Lead developer for IntFOLD/MultiFOLD refinement; integrated MD recycling to exceed AlphaFold2 accuracy.
- Created FunFOLD5 for ligand interactions; blind + template docking outperform AlphaFold3 in targeted tasks.
- Advanced ensemble prediction, QA, ligand site, disorder, and PPI pipelines for deployable tools.
PhD Researcher
University of Reading — Reading, UK
- Developed ReFOLD2/3 MD restraint strategies; top-10 in CASP13 refinement, improving structure and ligand-site fidelity.
- Published MD-based refinement and quality estimation work; co-led benchmarking of refinement protocols.
Teaching Assistant
University of Reading — Reading, UK
- Delivered bioinformatics practicals (BLAST, PDB/CATH, PyMOL) to ~150 students per cohort.
Skills
Protein / MD
Data / ML
Collaboration
Education
PhD, Biological Sciences
University of Reading — Reading, UK
MD-based refinement of predicted 3D protein models with restraint strategies; developed ReFOLD2/3 (CASP13 top-ranked). Supervisor: Prof. Liam McGuffin.
MSc, Bioengineering
Yildiz Technical University — Istanbul, Turkey
GPA 3.86/4.00. In silico optimisation of zinc-binding proteins for biosensors (Supervisors: Gundog Yucesan, Alper Yilmaz).
MSc, Physics
Trakya University — Edirne, Turkey
Research on GaAs/GaAlAs quantum wells; GPA 67/100.
BSc, Physics
Trakya University — Edirne, Turkey
Coursework in classical mechanics, relativity, and quantum mechanics; GPA 2.78/4.00.
Selected Publications
Improvement of protein tertiary and quaternary structure predictions using the ReFOLD refinement method and the AlphaFold2 recycling process
Bioinformatics Advances, 2023
Citations: 9
Using local protein model quality estimates to guide a molecular dynamics-based refinement strategy
Homology Modeling: Methods and Protocols (Springer US), 2023
Citations: 1
ReFOLD3: refinement of 3D protein models with gradual restraints based on predicted local quality and residue contacts
Nucleic Acids Research, 2021
Citations: 16
Methods for the Refinement of Protein Structure 3D Models
International Journal of Molecular Sciences, 2019
Citations: 68
Prediction of protein structures, functions and interactions using the IntFOLD7, MultiFOLD and ModFOLDdock servers
Nucleic Acids Research, 2023
Citations: 38
Estimation of model accuracy in CASP15 using the ModFOLDdock server
Proteins: Structure, Function, and Bioinformatics, 2023
Citations: 12
IntFOLD: An integrated web resource for high-performance protein structure and function prediction
Nucleic Acids Research, 2019
Citations: 130
ModFOLD8: Accurate global and local quality estimates for 3D protein models
Nucleic Acids Research, 2021
Citations: 69
Structural, functional, and mechanistic insights uncover the fundamental role of orphan connexin-62 in platelets
Blood, 2021
Citations: 11
Modelling SARS‐CoV‐2 proteins in the CASP‐commons experiment
Proteins: Structure, Function, and Bioinformatics, 2021
Citations: 19
Design and synthesis of small peptide sequences to detect concentrations of free transition metal ions
Abstracts of Papers of the American Chemical Society, 2014
Conference abstract
Talks & Posters
- ReFOLD4 for refinement of AlphaFold2 predictions — ISMB 2023 (3D-SIG)
- MD-based refinement guided by local quality — University of Reading BioSci Symposium
- ReFOLD2/3 refinement posters — CASP13/14/16, ISMB 2021, 3D-SIG
References
Prof. Liam McGuffin
School of Biological Sciences, University of Reading
l.j.mcguffin@reading.ac.uk
Assist. Prof. Alper Yilmaz
Yildiz Technical University Bioengineering Department
alperyilmaz@gmail.com