| A structural biology community assessment of AlphaFold2 applications M Akdel, DEV Pires, EP Pardo, J Jänes, AO Zalevsky, B Mészáros, ... Nature Structural & Molecular Biology 29 (11), 1056-1067, 2022 | 363 | 2022 |
| PanTools: representation, storage and exploration of pan-genomic data S Sheikhizadeh, ME Schranz, M Akdel, D de Ridder, S Smit Bioinformatics 32 (17), i487-i493, 2016 | 71 | 2016 |
| From sequence to function through structure: Deep learning for protein design N Ferruz, M Heinzinger, M Akdel, A Goncearenco, L Naef, C Dallago Computational and Structural Biotechnology Journal 21, 238-250, 2023 | 55 | 2023 |
| Caretta–a multiple protein structure alignment and feature extraction suite M Akdel, J Durairaj, D de Ridder, ADJ van Dijk Computational and structural biotechnology journal 18, 981-992, 2020 | 36 | 2020 |
| Geometricus represents protein structures as shape-mers derived from moment invariants J Durairaj, M Akdel, D de Ridder, ADJ van Dijk Bioinformatics 36 (Supplement_2), i718-i725, 2020 | 30 | 2020 |
| Uncovering new families and folds in the natural protein universe J Durairaj, AM Waterhouse, T Mets, T Brodiazhenko, M Abdullah, ... Nature 622 (7983), 646-653, 2023 | 22 | 2023 |
| What is hidden in the darkness? Deep-learning assisted large-scale protein family curation uncovers novel protein families and folds J Durairaj, AM Waterhouse, T Mets, T Brodiazhenko, M Abdullah, ... bioRxiv, 2023.03. 14.532539, 2023 | 7 | 2023 |
| A structural biology community assessment of AlphaFold 2 applications. bioRxiv. 2021; 2021.2009. 2026.461876 M Akdel, DEV Pires, E Porta Pardo, J Jänes, AO Zalevsky, B Mészáros, ... DOI 10 (2021.09), 26.461876, 0 | 5 | |
| Reinforcement Learning-Driven Linker Design via Fast Attention-based Point Cloud Alignment RM Neeser, M Akdel, D Kovtun, L Naef arXiv preprint arXiv:2306.08166, 2023 | 3 | 2023 |
| What is hidden in the darkness? Characterization of AlphaFold structural space J Durairaj, J Pereira, M Akdel, T Schwede bioRxiv, 2022.10. 11.511548, 2022 | 3 | 2022 |
| Fast and adaptive protein structure representations for machine learning J Durairaj, M Akdel, D Ridder, ADJ Dijk bioRxiv, 2021.04. 07.438777, 2021 | 3 | 2021 |
| Bending and Binding: Predicting Protein Flexibility upon Ligand Interaction using Diffusion Models X Zhang, T Geffner, M McPartlon, M Akdel, D Abramson, G Holt, ... NeurIPS 2023 Generative AI and Biology (GenBio) Workshop, 2023 | 2 | 2023 |
| DiffMaSIF: Surface-based Protein-Protein Docking with Diffusion Models F Sverrisson, M Akdel, D Abramson, J Feydy, A Goncearenco, Y Adeshina, ... Machine Learning in Structural Biology workshop at NeurIPS 2023, 2023 | 1 | 2023 |
| OptiDiff: structural variation detection from single optical mapping reads M Akdel, D de Ridder BioRxiv, 2022.01. 08.475501, 2022 | 1 | 2022 |
| Signal-based optical map alignment M Akdel, H Van De Geest, E Schijlen, IMH Van Rijswijck, EJ Smid, ... Plos one 16 (9), e0253102, 2021 | 1 | 2021 |
| DiffMaSIF: Score-Based Diffusion Models for Protein Surfaces F Sverrisson, M Akdel, D Abramson, J Feydy, A Goncearenco, Y Adeshina, ... | | 2023 |
| Algorithms for biological sequence data M Akdel PQDT-Global, 2022 | | 2022 |
| Representation of Eukaryotic Pangenomes in a Graph Database M Akdel | | 2015 |
| Structure-Based Machine Learning to Investigate Specificity in Plant Sesquiterpene Synthases J Durairaj, M Akdel, J Beekwilder, D de Ridder, ADJ van Dijk Plant and Animal Genome XXIX Conference (January 8-12, 2022), 0 | | |
