Dr. Janani Durairaj

Pereira, Joana, Pantolini, Lorenzo, Durairaj, Janani, & Schwede, Torsten. (2025). Large-scale protein clustering in the age of deep learning [Journal-article]. Current Opinion in Structural Biology, 94. https://doi.org/10.1016/j.sbi.2025.103078

Robin, Xavier, Škrinjar, Peter, Waterhouse, Andrew, Studer, Gabriel, Tauriello, Gerardo, Durairaj, Janani, & Schwede, Torsten. (2025). Benchmarking of macromolecular complexes with the Continuous Automated Model Evaluation (CAMEO) [Posted-content]. In Authorea. Authorea. https://doi.org/10.22541/au.174638718.83117953/v1

Träger, Lena, Degen, Morris, Pereira, Joana, Durairaj, Janini, Dias Teixeira, Raphael, Hiller, Sebastian, & Huguenin-Dezot, Nicolas. (2025). Structural basis for cooperative ssDNA binding by bacteriophage protein filament P12. Nucleic Acids Research, 53(5). https://doi.org/10.1093/nar/gkaf132

Schwede, Torsten, Studer, Gabriel, Robin, Xavier, Bienert, Stefan, Durairaj, Janani, & Tauriello, Gerardo. (2025). Comparing macromolecular complexes - a fully automated benchmarking suite [Posted-content]. In Research Square. Springer Science and Business Media LLC. https://doi.org/10.21203/rs.3.rs-5920881/v1

Škrinjar, Peter, Eberhardt, Jérôme, Durairaj, Janani, & Schwede, Torsten. (2025). Have protein-ligand co-folding methods moved beyond memorisation? [Posted-content]. In bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2025.02.03.636309

Durairaj, Janani, Adeshina, Yusuf, Cao, Zhonglin, Zhang, Xuejin, Oleinikovas, Vladas, Duignan, Thomas, McClure, Zachary, Robin, Xavier, Studer, Gabriel, Kovtun, Daniel, Rossi, Emanuele, Zhou, Guoqing, Veccham, Srimukh, Isert, Clemens, Peng, Yuxing, Sundareson, Prabindh, Akdel, Mehmet, Corso, Gabriele, Stärk, Hannes, et al. (2024). PLINDER: The protein-ligand interactions dataset and evaluation resource [Posted-content]. In bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2024.07.17.603955

Palermo, G., Accordi, G., Gadioli, D., Zhang, Y., Vitali, E., Guindani, B., Ardagna, D., Silvano, C., Beccari, A. R., Bonanni, D., Talarico, C., Lughini, F., Biswas, A. D., Martinovic, J., Golasowski, M., Silva, P., Bohm, A., Beranek, J., Krenek, J., et al. (2024). LIGATE - LIgand Generator and portable drug discovery platform AT Exascale [Proceedings-article]. 20th ACM International Conference on Computing Frontiers, 2, 107–109. https://doi.org/10.1145/3637543.3656335

Durairaj, Janani, Follonier, Océane M., Leuzinger, Karoline, Alexander, Leila T., Wilhelm, Maud, Pereira, Joana, Hillenbrand, Caroline A., Weissbach, Fabian H, Schwede, Torsten, Hirsch, Hans H., & Greber, Urs F. (2024). Structural implications of BK polyomavirus sequence variations in the major viral capsid protein Vp1 and large T-antigen: a computational study. mSphere, 9(4), Online ahead of print. https://doi.org/10.1128/msphere.00799-23

Pantolini, Lorenzo, Studer, Gabriel, Pereira, Joana, Durairaj, Janani, Tauriello, Gerardo, & Schwede, Torsten. (2024). Embedding-based alignment: combining protein language models with dynamic programming alignment to detect structural similarities in the twilight-zone [Journal-article]. Bioinformatics, 40(1). https://doi.org/10.1093/bioinformatics/btad786

Leemann, Michèle, Sagasta, Ander, Eberhardt, Jerome, Schwede, Torsten, Robin, Xavier, & Durairaj, Janani. (2023). Automated benchmarking of combined protein structure and ligand conformation prediction. Proteins: Structure, Function and Bioinformatics, 91(12), 1912–1924. https://doi.org/10.1002/prot.26605

Robin, Xavier, Studer, Gabriel, Durairaj, Janani, Eberhardt, Jerome, Schwede, Torsten, & Walters, W. Patrick. (2023). Assessment of protein–ligand complexes in CASP15. Proteins: Structure, Function and Bioinformatics, 91(12), 1811–1821. https://doi.org/10.1002/prot.26601

Mullowney, Michael W., Duncan, Katherine R., Elsayed, Somayah S., Garg, Neha, van der Hooft, Justin J. J., Martin, Nathaniel I., Meijer, David, Terlouw, Barbara R., Biermann, Friederike, Blin, Kai, Durairaj, Janani, Gorostiola González, Marina, Helfrich, Eric J. N., Huber, Florian, Leopold-Messer, Stefan, Rajan, Kohulan, de Rond, Tristan, van Santen, Jeffrey A., Sorokina, Maria, et al. (2023). Artificial intelligence for natural product drug discovery. Nature Reviews Drug Discovery, 22(11), 895–916. https://doi.org/10.1038/s41573-023-00774-7

Palermo, G., Accordi, G., Gadioli, D., Vitali, E., Silvano, C., Guindani, B., Ardagna, D., Beccari, A.R., Bonanni, D., Talarico, C., Lughini, F., Martinovic, J., Silva, P., Bohm, A., Beranek, J., Krenek, J., Jansik, B., Cosenza, B., Crisci, L., et al. (2023). Tunable and Portable Extreme-Scale Drug Discovery Platform at Exascale: the LIGATE Approach. Proceedings of the 20th ACM International Conference on Computing Frontiers 2023, CF 2023, 272–278. https://doi.org/10.1145/3587135.3592172

Li, C., Dong, L., Durairaj, J., Guan, J.-C., Yoshimura, M., Quinodoz, P., Horber, R., Gaus, K., Li, J., Setotaw, Y. B., Qi, J., De Groote, H., Wang, Y., Thiombiano, B., Floková, K., Walmsley, A., Charnikhova, T. V., Chojnacka, A., Correia de Lemos, S., et al. (2023). Maize resistance to witchweed through changes in strigolactone biosynthesis [Journal-article]. Science, 379(6627), 94–99. https://doi.org/10.1126/science.abq4775

Alexander, Leila T, Durairaj, Janani, Kryshtafovych, Andriy, Abriata, Luciano A, Bayo, Yusupha, Bhabha, Gira, Breyton, Cécile, Caulton, Simon G, Chen, James, Degroux, Séraphine, Ekiert, Damian C, Erlandsen, Benedikte S, Freddolino, Peter L, Gilzer, Dominic, Greening, Chris, Grimes, Jonathan M, Grinter, Rhys, Gurusaran, Manickam, Hartmann, Marcus D, et al. (2023). Protein target highlights in CASP15: Analysis of models by structure providers. Proteins, 91(12), 1571–1599. https://doi.org/10.1002/prot.26545

Durairaj, Janani, Alexander, Leila Tamara, Studer, Gabriel, Tauriello, Gerardo, Prandi, Ingrid Guarnetti, Lepore, Rosalba, Chillemi, Giovanni, & Schwede, Torsten. (2023). From Genomes to Variant Interpretations Through Protein Structures. In SpringerBriefs in Applied Sciences and Technology (pp. 41–50). Springer Science and Business Media Deutschland GmbH. https://doi.org/10.1007/978-3-031-30691-4_6

Durairaj, Janani, de Ridder, Dick, & van Dijk, Aalt D.J. (2023). Beyond sequence: Structure-based machine learning [Journal-article]. Computational and Structural Biotechnology Journal, 21, 630–643. https://doi.org/10.1016/j.csbj.2022.12.039

Durairaj, Janani, Waterhouse, Andrew M., Mets, Toomas, Brodiazhenko, Tetiana, Abdullah, Minhal, Studer, Gabriel, Tauriello, Gerardo, Akdel, Mehmet, Andreeva, Antonina, Bateman, Alex, Tenson, Tanel, Hauryliuk, Vasili, Schwede, Torsten, & Pereira, Joana. (2023). Uncovering new families and folds in the natural protein universe. Nature, 622(7983), 646–653. https://doi.org/10.1038/s41586-023-06622-3

Kryshtafovych, Andriy, Antczak, Maciej, Szachniuk, Marta, Zok, Tomasz, Kretsch, Rachael C, Rangan, Ramya, Pham, Phillip, Das, Rhiju, Robin, Xavier, Studer, Gabriel, Durairaj, Janani, Eberhardt, Jerome, Sweeney, Aaron, Topf, Maya, Schwede, Torsten, Fidelis, Krzysztof, & Moult, John. (2023). New prediction categories in CASP15. Proteins, 91(12), 1550–1557. https://doi.org/10.1002/prot.26515

Wang, Yanting, Durairaj, Janani, Suárez Duran, Hernando G., van Velzen, Robin, Flokova, Kristyna, Liao, Che‐Yang, Chojnacka, Aleksandra, MacFarlane, Stuart, Schranz, M. Eric, Medema, Marnix H., van Dijk, Aalt D. J., Dong, Lemeng, & Bouwmeester, Harro J. (2022). The tomato cytochrome P450 CYP712G1 catalyses the double oxidation of orobanchol en route to the rhizosphere signalling strigolactone, solanacol [Journal-article]. New Phytologist, 235(5), 1884–1899. https://doi.org/10.1111/nph.18272

Akdel, Mehmet, Pires, Douglas E. V., Pardo, Eduard Porta, Jänes, Jürgen, Zalevsky, Arthur O., Mészáros, Bálint, Bryant, Patrick, Good, Lydia L., Laskowski, Roman A., Pozzati, Gabriele, Shenoy, Aditi, Zhu, Wensi, Kundrotas, Petras, Serra, Victoria Ruiz, Rodrigues, Carlos H. M., Dunham, Alistair S., Burke, David, Borkakoti, Neera, Velankar, Sameer, et al. (2022). A structural biology community assessment of AlphaFold2 applications. Nature Structural and Molecular Biology, 29(11), 1056–1067. https://doi.org/10.1038/s41594-022-00849-w

Durairaj, Janani, Melillo, Elena, Bouwmeester, Harro J., Beekwilder, Jules, de Ridder, Dick, & van Dijk, Aalt D. J. (2021). Integrating structure-based machine learning and co-evolution to investigate specificity in plant sesquiterpene synthases [Journal-article]. PLoS Computational Biology, 17(3), e1008197. https://doi.org/10.1371/journal.pcbi.1008197

Durairaj, Janani. (2021). Computational approaches to discover novel enzymes for fragrance and flavour [Dissertation, Wageningen University and Research]. https://doi.org/10.18174/551031

Durairaj, Janani, Akdel, Mehmet, de Ridder, Dick, & van Dijk, Aalt D J. (2020). Geometricus represents protein structures as shape-mers derived from moment invariants [Journal-article]. Bioinformatics, 36(Supplement_2), I718–I725. https://doi.org/10.1093/bioinformatics/btaa839

Di Girolamo, Alice, Durairaj, Janani, van Houwelingen, Adèle, Verstappen, Francel, Bosch, Dirk, Cankar, Katarina, Bouwmeester, Harro, de Ridder, Dick, van Dijk, Aalt D.J., & Beekwilder, Jules. (2020). The santalene synthase from Cinnamomum camphora: Reconstruction of a sesquiterpene synthase from a monoterpene synthase [Journal-article]. Archives of Biochemistry and Biophysics, 695, 108647. https://doi.org/10.1016/j.abb.2020.108647

Akdel, Mehmet, Durairaj, Janani, de Ridder, Dick, & van Dijk, Aalt D.J. (2020). Caretta – A multiple protein structure alignment and feature extraction suite [Journal-article]. Computational and Structural Biotechnology Journal, 18, 981–992. https://doi.org/10.1016/j.csbj.2020.03.011

Durairaj, Janani, Di Girolamo, Alice, Bouwmeester, Harro J., de Ridder, Dick, Beekwilder, Jules, & van Dijk, Aalt DJ. (2019). An analysis of characterized plant sesquiterpene synthases [Journal-article]. Phytochemistry, 158, 157–165. https://doi.org/10.1016/j.phytochem.2018.10.020