@inproceedings{GasseBowlyCappartetal., author = {Gasse, Maxime and Bowly, Simon and Cappart, Quentin and Charfreitag, Jonas and Charlin, Laurent and Ch{\´e}telat, Didier and Chmiela, Antonia and Dumouchelle, Justin and Gleixner, Ambros and Kazachkov, Aleksandr M. and Khalil, Elias and Lichocki, Pawel and Lodi, Andrea and Lubin, Miles and Maddison, Chris J. and Christopher, Morris and Papageorgiou, Dimitri J. and Parjadis, Augustin and Pokutta, Sebastian and Prouvost, Antoine and Scavuzzo, Lara and Zarpellon, Giulia and Yang, Linxin and Lai, Sha and Wang, Akang and Luo, Xiaodong and Zhou, Xiang and Huang, Haohan and Shao, Shengcheng and Zhu, Yuanming and Zhang, Dong and Quan, Tao and Cao, Zixuan and Xu, Yang and Huang, Zhewei and Zhou, Shuchang and Binbin, Chen and Minggui, He and Hao, Hao and Zhiyu, Zhang and Zhiwu, An and Kun, Mao}, title = {The Machine Learning for Combinatorial Optimization Competition (ML4CO): results and insights}, series = {Proceedings of Conference on Neural Information Processing Systems}, booktitle = {Proceedings of Conference on Neural Information Processing Systems}, language = {en} } @article{KoltaiWuNoeetal., author = {Koltai, Peter and Wu, Hao and No{\´e}, Frank and Sch{\"u}tte, Christof}, title = {Optimal data-driven estimation of generalized Markov state models for non-equilibrium dynamics}, series = {Computation}, volume = {6}, journal = {Computation}, number = {1}, publisher = {MDPI}, address = {Basel, Switzerland}, doi = {10.3390/computation6010022}, pages = {22}, language = {en} } @article{KlusNueskeKoltaietal., author = {Klus, Stefan and N{\"u}ske, Feliks and Koltai, Peter and Wu, Hao and Kevrekidis, Ioannis and Sch{\"u}tte, Christof and No{\´e}, Frank}, title = {Data-driven model reduction and transfer operator approximation}, series = {Journal of Nonlinear Science}, volume = {28}, journal = {Journal of Nonlinear Science}, number = {3}, doi = {10.1007/s00332-017-9437-7}, pages = {985 -- 1010}, language = {en} } @article{PrinzWuSarichetal.2011, author = {Prinz, J.-H. and Wu, Hao and Sarich, Marco and Keller, B. and Fischbach, M. and Held, M. and Chodera, J. and Sch{\"u}tte, Christof and No{\´e}, Frank}, title = {Markov models of molecular kinetics}, series = {J. Chem. Phys.}, volume = {134}, journal = {J. Chem. Phys.}, doi = {10.1063/1.3565032}, pages = {174105}, year = {2011}, language = {en} } @article{SchimunekSeidlElezetal.2023, author = {Schimunek, Johannes and Seidl, Philipp and Elez, Katarina and Hempel, Tim and Le, Tuan and No{\´e}, Frank and Olsson, Simon and Raich, Llu{\´i}s and Winter, Robin and Gokcan, Hatice and Gusev, Filipp and Gutkin, Evgeny M. and Isayev, Olexandr and Kurnikova, Maria G. and Narangoda, Chamali H. and Zubatyuk, Roman and Bosko, Ivan P. and Furs, Konstantin V. and Karpenko, Anna D. and Kornoushenko, Yury V. and Shuldau, Mikita and Yushkevich, Artsemi and Benabderrahmane, Mohammed B. and Bousquet-Melou, Patrick and Bureau, Ronan and Charton, Beatrice and Cirou, Bertrand C. and Gil, G{\´e}rard and Allen, William J. and Sirimulla, Suman and Watowich, Stanley and Antonopoulos, Nick and Epitropakis, Nikolaos and Krasoulis, Agamemnon and Itsikalis, Vassilis and Theodorakis, Stavros and Kozlovskii, Igor and Maliutin, Anton and Medvedev, Alexander and Popov, Petr and Zaretckii, Mark and Eghbal-Zadeh, Hamid and Halmich, Christina and Hochreiter, Sepp and Mayr, Andreas and Ruch, Peter and Widrich, Michael and Berenger, Francois and Kumar, Ashutosh and Yamanishi, Yoshihiro and Zhang, Kam Y. J. and Bengio, Emmanuel and Bengio, Yoshua and Jain, Moksh J. and Korablyov, Maksym and Liu, Cheng-Hao and Marcou, Gilles and Glaab, Enrico and Barnsley, Kelly and Iyengar, Suhasini M. and Ondrechen, Mary Jo and Haupt, V. Joachim and Kaiser, Florian and Schroeder, Michael and Pugliese, Luisa and Albani, Simone and Athanasiou, Christina and Beccari, Andrea and Carloni, Paolo and D'Arrigo, Giulia and Gianquinto, Eleonora and Goßen, Jonas and Hanke, Anton and Joseph, Benjamin P. and Kokh, Daria B. and Kovachka, Sandra and Manelfi, Candida and Mukherjee, Goutam and Mu{\~n}iz-Chicharro, Abraham and Musiani, Francesco and Nunes-Alves, Ariane and Paiardi, Giulia and Rossetti, Giulia and Sadiq, S. Kashif and Spyrakis, Francesca and Talarico, Carmine and Tsengenes, Alexandros and Wade, Rebecca C. and Copeland, Conner and Gaiser, Jeremiah and Olson, Daniel R. and Roy, Amitava and Venkatraman, Vishwesh and Wheeler, Travis J. and Arthanari, Haribabu and Blaschitz, Klara and Cespugli, Marco and Durmaz, Vedat and Fackeldey, Konstantin and Fischer, Patrick D. and Gorgulla, Christoph and Gruber, Christian and Gruber, Karl and Hetmann, Michael and Kinney, Jamie E. and Padmanabha Das, Krishna M. and Pandita, Shreya and Singh, Amit and Steinkellner, Georg and Tesseyre, Guilhem and Wagner, Gerhard and Wang, Zi-Fu and Yust, Ryan J. and Druzhilovskiy, Dmitry S. and Filimonov, Dmitry A. and Pogodin, Pavel V. and Poroikov, Vladimir and Rudik, Anastassia V. and Stolbov, Leonid A. and Veselovsky, Alexander V. and De Rosa, Maria and De Simone, Giada and Gulotta, Maria R. and Lombino, Jessica and Mekni, Nedra and Perricone, Ugo and Casini, Arturo and Embree, Amanda and Gordon, D. Benjamin and Lei, David and Pratt, Katelin and Voigt, Christopher A. and Chen, Kuang-Yu and Jacob, Yves and Krischuns, Tim and Lafaye, Pierre and Zettor, Agn{\`e}s and Rodr{\´i}guez, M. Luis and White, Kris M. and Fearon, Daren and Von Delft, Frank and Walsh, Martin A. and Horvath, Dragos and Brooks III, Charles L. and Falsafi, Babak and Ford, Bryan and Garc{\´i}a-Sastre, Adolfo and Yup Lee, Sang and Naffakh, Nadia and Varnek, Alexandre and Klambauer, G{\"u}nter and Hermans, Thomas M.}, title = {A community effort in SARS-CoV-2 drug discovery}, series = {Molecular Informatics}, volume = {43}, journal = {Molecular Informatics}, number = {1}, doi = {https://doi.org/10.1002/minf.202300262}, pages = {e202300262}, year = {2023}, language = {en} } @article{TrepteSeckerKostovaetal., author = {Trepte, Philipp and Secker, Christopher and Kostova, Simona and Maseko, Sibusiso B. and Gang Choi, Soon and Blavier, Jeremy and Minia, Igor and Silva Ramos, Eduardo and Cassonnet, Patricia and Golusik, Sabrina and Zenkner, Martina and Beetz, Stephanie and Liebich, Mara J. and Scharek, Nadine and Sch{\"u}tz, Anja and Sperling, Marcel and Lisurek, Michael and Wang, Yang and Spirohn, Kerstin and Hao, Tong and Calderwood, Michael A. and Hill, David E. and Landthaler, Markus and Olivet, Julien and Twizere, Jean-Claude and Vidal, Marc and Wanker, Erich E.}, title = {AI-guided pipeline for protein-protein interaction drug discovery identifies a SARS-CoV-2 inhibitor}, series = {bioRxiv}, journal = {bioRxiv}, doi = {10.1101/2023.06.14.544560}, language = {en} } @article{TrepteSeckerOlivetetal., author = {Trepte, Philipp and Secker, Christopher and Olivet, Julien and Blavier, Jeremy and Kostova, Simona and Maseko, Sibusiso B and Minia, Igor and Silva Ramos, Eduardo and Cassonnet, Patricia and Golusik, Sabrina and Zenkner, Martina and Beetz, Stephanie and Liebich, Mara J and Scharek, Nadine and Sch{\"u}tz, Anja and Sperling, Marcel and Lisurek, Michael and Wang, Yang and Spirohn, Kerstin and Hao, Tong and Calderwood, Michael A and Hill, David E and Landthaler, Markus and Choi, Soon Gang and Twizere, Jean-Claude and Vidal, Marc and Wanker, Erich E}, title = {AI-guided pipeline for protein-protein interaction drug discovery identifies a SARS-CoV-2 inhibitor}, series = {Molecular Systems Biology}, volume = {20}, journal = {Molecular Systems Biology}, number = {4}, publisher = {Springer Science and Business Media LLC}, issn = {1744-4292}, doi = {https://doi.org/10.1038/s44320-024-00019-8}, pages = {428 -- 457}, abstract = {Protein-protein interactions (PPIs) offer great opportunities to expand the druggable proteome and therapeutically tackle various diseases, but remain challenging targets for drug discovery. Here, we provide a comprehensive pipeline that combines experimental and computational tools to identify and validate PPI targets and perform early-stage drug discovery. We have developed a machine learning approach that prioritizes interactions by analyzing quantitative data from binary PPI assays or AlphaFold-Multimer predictions. Using the quantitative assay LuTHy together with our machine learning algorithm, we identified high-confidence interactions among SARS-CoV-2 proteins for which we predicted three-dimensional structures using AlphaFold-Multimer. We employed VirtualFlow to target the contact interface of the NSP10-NSP16 SARS-CoV-2 methyltransferase complex by ultra-large virtual drug screening. Thereby, we identified a compound that binds to NSP10 and inhibits its interaction with NSP16, while also disrupting the methyltransferase activity of the complex, and SARS-CoV-2 replication. Overall, this pipeline will help to prioritize PPI targets to accelerate the discovery of early-stage drug candidates targeting protein complexes and pathways.}, language = {en} }