Computational Structural Biologist · PhD
Production-grade protein structure prediction pipelines that outperform AlphaFold3. CASP top-ranked, 530+ citations, 30,000+ users, currently accelerating cancer vaccine design at InstaDeep / BioNTech.
Currently at InstaDeep / BioNTech · TCR-pMHC cancer-vaccine pipeline
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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 15 peer-reviewed papers (H-index 9, 530+ 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.
Iterative refinement
Blend physics-based models with ML to close the loop from prediction to validation.
Operational pipelines
Ship pipelines teams can run, monitor, and extend across structure prediction, docking, and MD.
Collaboration-first
Work closely with domain experts so the science stays rigorous while tooling stays approachable.
The mission
Computational structure prediction is no longer the bottleneck - accuracy, dynamics and validation are. I build the pipelines that turn predicted models into decisions a drug-discovery team can act on.
"Proteins are not statues. They are breathing, moving molecular machines. I am building tools to capture the dynamic ensembles that drive biology."
Conventional AI treats proteins as rigid shapes. My protocols integrate Molecular Dynamics to reveal how evolutionarily silent targets truly behave.
Using Local Quality Estimation, we lock certain regions while allowing binding sites to breathe, uncovering cryptic pockets for drug discovery.
"We are moving from predicting a single static snapshot to simulating the full movie of life. This shift is critical for engineering better enzymes and designing smarter drugs for traditionally undruggable targets."
Read Full Research ManifestoNext-generation tools for structure prediction, refinement, and quality assessment.
Reproducible pipeline to fine-tune OpenFold3 on a specific target — data prep, training, and evaluation, with cloud notebooks, Docker, and full documentation.
Refinement of 3D protein models using molecular dynamics simulations and quality assessment.
Quality assessment of protein-protein complex models using deep learning and structural features.
Template-based ligand binding site prediction using structural alignment and quality assessment.
Integrated web resource for high-performance protein structure and function prediction.
Adiyaman, R., Edmunds, N. S., Genc, A. G., Alharbi, S. M. A., & McGuffin, L. J.
Adiyaman, R., & McGuffin, L. J.
Adiyaman, R., & McGuffin, L. J.
Adiyaman, R., & McGuffin, L. J.
Taylor, K. A., Elgheznawy, A., Adiyaman, R., et al.
McGuffin, L. J., Alhaddad, S. N., Behzadi, B., Edmunds, N. S., Genc, A. G., & Adiyaman, R.
Fadini, A., Adiyaman, R., Alhaddad, S. N., et al.
McGuffin, L. J., Edmunds, N. S., Genc, A. G., Alharbi, S. M. A., Salehe, B. R., & Adiyaman, R.
Edmunds, N. S., Alharbi, S. M. A., Genc, A. G., Adiyaman, R., & McGuffin, L. J.
McGuffin, L. J., Adiyaman, R., Maghrabi, A. H. A., et al.
McGuffin, L. J., Aldowsari, F. M. F., Alharbi, S. M. A., & Adiyaman, R.
Sahli, K. A., Flora, G. D., ... Adiyaman, R., et al.
Kryshtafovych, A., ... Adiyaman, R. (CASP-COVID participants), et al.
Yucesan, G., Yilmaz, A., & Adiyaman, R.
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.
Thesis: 'In Silico Optimisation of Zinc Binding Proteins for Biosensor Applications'. Computational protein engineering using molecular docking and mutagenesis. GPA 3.86/4.00.
Dissertation: 'GaAs/GaAlAs Quantum Well'. Research on semiconductor quantum well structures.
Coursework in classical mechanics, relativity, and quantum mechanics. Foundation for computational physics and simulation methods.
End-to-end TCR-pMHC structure prediction pipeline supporting BioNTech's personalised cancer vaccine programme. Integrates AlphaFold2, Boltz-2, and Chai-1 with a hybrid scoring system (FoldX, Rosetta, DockQ, PatchDockQ, ilDDT) for candidate ranking.
Co-led IntFOLD server (30,000+ users, 400,000+ jobs/yr). MultiFOLD3 outperformed AlphaFold3 in quaternary structure prediction by integrating Boltz-2, Chai-1, Protenix and geometric-based rescoring in CAMEO.
Led CASP16 submission achieving 2nd place in protein-ligand pose ranking. Surpasses AlphaFold3 server method in protein-ligand interaction prediction via blind + template docking and affinity scoring.
Quality assessment system for protein binders engineered with 16,000+ features combining physics-based and ML scores (DockQ, QS, PatchDockQ, PatchQS, ilDDT, aa-local-lddt, ics). Contributed to CASP15/16 EMA rankings.
MD-based refinement protocol that improves 3D predictions beyond AlphaFold2 accuracy. Integrates local quality estimation with MD recycling; published in Bioinformatics Advances 2023.
Top-10 (CASP13) and top-5 (CASP13) refinement methods; best server at CASP14. MD restraint strategies lifted predicted structures toward native and improved ligand-site fidelity. 4 first-author papers.
Five surprising truths about refinement, assembly, and validation in the post-AlphaFold era.
Why we need to move beyond static snapshots to capture the full range of conformational dynamics.
Integrating deep learning with molecular dynamics and local quality estimation to model mutants and novel folds.
How dynamic modelling will accelerate therapeutic discovery and the design of next-generation enzymes.
We will publish discussions with experts in protein engineering, AI in drug discovery, and computational biology. Follow the channel for upcoming releases.
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MD-based refinement guided by per-residue local quality estimation - CASP14 target T1095.
End-to-end quality-assessment pipeline for protein-complex models.
Template-based vs template-free protocols - CASP16 target L2000.
Protein modelling in the CASP-Commons COVID experiment.
Predicted ligand-binding residues from structural alignment.
Structures in focus
The recognition event at the heart of the personalised cancer-vaccine pipeline.
Spike receptor-binding domain bound to its human receptor - CASP-COVID modelling.
A classic quaternary assembly - the MultiFOLD / ModFOLDdock problem domain.
Structure renders: RCSB PDB - public domain.
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Send Email →I am always open to research collaborations, consulting on protein design pipelines, and partnering on structural biology products. Whether you have a question or a project in mind, reach out.
Email me directly
recepadiyaman2244@gmail.com