| A structural biology community assessment of AlphaFold2 applications M Akdel, DEV Pires, EP Pardo, J Jänes, AO Zalevsky, B Mészáros, ... Nature Structural & Molecular Biology, 1-12, 2022 | 358 | 2022 |
| An analysis of characterized plant sesquiterpene synthases J Durairaj, A Di Girolamo, HJ Bouwmeester, D De Ridder, J Beekwilder, ... Phytochemistry 158, 157-165, 2019 | 57 | 2019 |
| Artificial intelligence for natural product drug discovery MW Mullowney, KR Duncan, SS Elsayed, N Garg, JJJ van der Hooft, ... Nature Reviews Drug Discovery 22 (11), 895-916, 2023 | 41 | 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 | 35 | 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 | 27* | 2023 |
| Maize resistance to witchweed through changes in strigolactone biosynthesis C Li, L Dong, J Durairaj, JC Guan, M Yoshimura, P Quinodoz, R Horber, ... Science 379 (6627), 94-99, 2023 | 25 | 2023 |
| New prediction categories in CASP15 A Kryshtafovych, M Antczak, M Szachniuk, T Zok, RC Kretsch, R Rangan, ... Proteins: Structure, Function, and Bioinformatics, 2023 | 22 | 2023 |
| The tomato cytochrome P450 CYP712G1 catalyses the double oxidation of orobanchol en route to the rhizosphere signalling strigolactone, solanacol Y Wang, J Durairaj, HG Suarez Duran, R van Velzen, K Flokova, CY Liao, ... New Phytologist 235 (5), 1884-1899, 2022 | 20 | 2022 |
| The santalene synthase from Cinnamomum camphora: Reconstruction of a sesquiterpene synthase from a monoterpene synthase A Di Girolamo, J Durairaj, A van Houwelingen, F Verstappen, D Bosch, ... Archives of Biochemistry and Biophysics 695, 108647, 2020 | 14 | 2020 |
| Integrating structure-based machine learning and co-evolution to investigate specificity in plant sesquiterpene synthases J Durairaj, E Melillo, HJ Bouwmeester, J Beekwilder, D de Ridder, ... PLOS Computational Biology 17 (3), e1008197, 2021 | 12 | 2021 |
| Assessment of protein–ligand complexes in CASP15 X Robin, G Studer, J Durairaj, J Eberhardt, T Schwede, WP Walters Proteins: Structure, Function, and Bioinformatics 91 (12), 1811-1821, 2023 | 8 | 2023 |
| Protein target highlights in CASP15: Analysis of models by structure providers LT Alexander, J Durairaj, A Kryshtafovych, LA Abriata, Y Bayo, G Bhabha, ... Proteins: Structure, Function, and Bioinformatics 91 (12), 1571-1599, 2023 | 8 | 2023 |
| Embedding-based alignment: combining protein language models with dynamic programming alignment to detect structural similarities in the twilight-zone L Pantolini, G Studer, J Pereira, J Durairaj, G Tauriello, T Schwede Bioinformatics, btad786, 2024 | 6* | 2024 |
| Beyond sequence: Structure-based machine learning J Durairaj, D de Ridder, ADJ van Dijk Computational and Structural Biotechnology Journal 21, 630-643, 2023 | 6 | 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 |
| Automated benchmarking of combined protein structure and ligand conformation prediction M Leemann, A Sagasta, J Eberhardt, T Schwede, X Robin, J Durairaj Proteins: Structure, Function, and Bioinformatics, 2023 | 2* | 2023 |
| Tunable and Portable Extreme-Scale Drug Discovery Platform at Exascale: the LIGATE Approach G Palermo, G Accordi, D Gadioli, E Vitali, C Silvano, B Guindani, ... arXiv preprint arXiv:2304.09953, 2023 | 2 | 2023 |
| How predicted protein models help to illuminate the full protein universe J Pereira, J Durairaj, L Pantolini, G Studer, X Robin, A Waterhouse, ... Acta Crystallographica Section A: Foundations of Crystallography 78, a76-a76, 2023 | | 2023 |
Aalt D.J. van DijkProfessor Data Analysis in the Life Sciences, University of AmsterdamVerified email at uva.nl
