Curriculum Vitae
Recep Adiyaman, PhD
Computational Structural Biologist | Protein Structure Prediction & Drug Design
Coventry, UK
Computational structural biologist with 9+ years of research experience in protein structure prediction, molecular dynamics simulation, and AI/ML-driven drug design. Developer of multiple internationally benchmarked tools (IntFOLD, ReFOLD, FunFOLD, MultiFOLD, ModFOLDdock2Q) that consistently rank among the top methods at CASP blind prediction experiments. Published 14 peer-reviewed papers (H-index 9, 470+ citations) in journals including Nucleic Acids Research, Blood, and Bioinformatics Advances. Currently combining deep learning structure predictors (AlphaFold2/3, Boltz-2, Chai-1) with physics-based methods for cancer vaccine design in collaboration with InstaDeep/BioNTech. Experienced in Python, PyTorch, HPC/SLURM environments, and end-to-end bioinformatics pipeline development.
Experience
Collaborative Researcher (Part-Time)
InstaDeep (BioNTech Group) — London, UK
- Designed and developed a protein structure prediction pipeline for structural immunology, integrating TCR-pMHC modelling using AlphaFold2, Boltz-2, and Chai-1 to support BioNTech's personalised cancer vaccine programme.
- Contributed the --min-pep-length parameter to the OpenStructure framework, improving peptide quality assessment accuracy.
- Engineered a hybrid scoring system combining physics-based energy terms (FoldX, Rosetta) with ML-based features (DockQ, QS, PatchDockQ, PatchQS, ilDDT, aa-local-lddt, ics scores) for candidate ranking and selection.
- Collaborated with cross-functional teams spanning computational biology, experimental immunology, and vaccine development.
Research Fellow
McGuffin Lab, University of Reading — Reading, UK
- Co-led the development and maintenance of IntFOLD integrated server for 3D protein model prediction, serving 30,000+ users and 400,000+ jobs every year.
- Built ModFOLDdock2Q, a model quality assessment method utilising over 16,000 engineered features, achieving significant performance for identification of better protein binders.
- Led ReFOLD4 development — MD-based refinement protocol that improves 3D predictions beyond AlphaFold2 accuracy by integrating local quality estimation with MD simulations (Bioinformatics Advances, 2023).
- Led FunFOLD5 development for CASP16, achieving 2nd place in protein-ligand pose ranking and surpassing AlphaFold3 server method in protein-ligand interaction prediction.
- Contributed to MultiFOLD3, which outperformed AlphaFold3 in quaternary structure prediction by integrating Boltz-2, Chai-1, Protenix and geometric-based rescoring in CAMEO.
- ReFOLD3 ranked top-5 in CASP13 for difficult refinement targets; became top-performing refinement server at CASP14 (NAR Web Server Issue, 2021).
- Published 10+ papers across Nucleic Acids Research, Bioinformatics Advances, Proteins, and Haematologica.
Teaching Assistant
University of Reading — Reading, UK
- Delivered practical demonstrations for undergraduate bioinformatics and programming modules.
- Supported student learning in Python scripting, sequence analysis (BLAST, HHpred), and structural biology concepts (PyMOL, ChimeraX).
PhD Researcher
University of Reading — Reading, UK
- Developed ReFOLD2 (top-10 CASP13) and ReFOLD3 (top-5 CASP13, best server CASP14) using MD restraint strategies to lift predicted structures toward native.
- Extended refinement methods to protein-ligand binding site prediction; published 4 first-author papers.
Skills
Protein Structure & MD
Docking & Drug Design
ML & AI
Programming & Infrastructure
Bioinformatics Tools
Collaboration & Impact
Education
PhD, Structural Bioinformatics
University of Reading — Reading, UK
Thesis: 'The Molecular Dynamics Based Refinement of Predicted 3D Models Using Different Restraint Strategies'. Developed ReFOLD2 (top-10 CASP13) and ReFOLD3 (top-5 CASP13, best server CASP14). 4 first-author papers. Supervisor: Prof. Liam McGuffin.
MSc, Bioengineering
Yildiz Technical University — Istanbul, Turkey
Thesis: 'In Silico Optimisation of Zinc Binding Proteins for Biosensor Applications'. Computational protein engineering using molecular docking and mutagenesis. GPA 3.86/4.00.
MSc, Physics
Trakya University — Edirne, Turkey
Dissertation: 'GaAs/GaAlAs Quantum Well'. Research on semiconductor quantum well structures.
BSc, Physics
Trakya University — Edirne, Turkey
Coursework in classical mechanics, relativity, and quantum mechanics. Foundation for computational physics and simulation methods.
Selected Publications
Improvement of protein tertiary and quaternary structure predictions using the ReFOLD refinement method and the AlphaFold2 recycling process
Using local protein model quality estimates to guide a molecular dynamics-based refinement strategy
ReFOLD3: Refinement of 3D protein models with gradual restraints based on predicted local quality and residue contacts
Methods for the Refinement of Protein Structure 3D Models
Inter-platelet communication driving thrombus formation is regulated by extracellular calpain-1 cleavage of connexin 62
Prediction and quality assessment of protein quaternary structure models using the MultiFOLD2 and ModFOLDdock2 servers
Highlights of model quality assessment in CASP16
Prediction of protein structures, functions and interactions using the IntFOLD7, MultiFOLD and ModFOLDdock servers
Estimation of model accuracy in CASP15 using the ModFOLDdock server
IntFOLD: An integrated web resource for high-performance protein structure and function prediction
ModFOLD8: Accurate global and local quality estimates for 3D protein models
Structural, functional, and mechanistic insights uncover the fundamental role of orphan connexin-62 in platelets
Modeling SARS-CoV-2 proteins in the CASP-commons experiment
Design and synthesis of small peptide sequences to detect concentrations of free transition metal ions
Talks & Posters
- ReFOLD4 for the refinement of AlphaFold2 predictions — ISMB 2023, 3D-SIG (Oral)
- MD-Based Refinement of Protein Models with Local Quality Assessment — University of Reading Symposium (Oral)
- Design of metal ion-binding small peptides — 1st National Biosensor Congress, Turkey (Oral)
- 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
alyilmaz@yildiz.edu.tr