publications

2023

    2022

    1. Markov field models: Scaling molecular kinetics approaches to large molecular machines
      Hempel, Tim, Olsson, Simon, and Noé, Frank
      Current Opinion in Structural Biology 2022
    2. A litmus test for classifying recognition mechanisms of transiently binding proteins
      Chakrabarti, Kalyan S., Olsson, Simon, Pratihar, Supriya, Giller, Karin, Overkamp, Kerstin, Lee, Ko On, Gapsys, Vytautas, Ryu, Kyoung-Seok, Groot, Bert L., Noé, Frank, Becker, Stefan, Lee, Donghan, Weikl, Thomas R., and Griesinger, Christian
      Nature Communications 2022
    3. Motional clustering in supra-\tau_c conformational exchange influences NOE cross-relaxation rate
      Kolloff, Christopher, Mazur, Adam, Marzinek, Jan K., Bond, Peter J., Olsson, Simon, and Hiller, Sebastian
      Journal of Magnetic Resonance 2022
    4. Prediction of the chemical context for Buchwald-Hartwig coupling reactions
      Genheden, Samuel, Mårdh, Agnes, Lahti, Gustav, Engkvist, Ola, Olsson, Simon, and Kogej, Thierry
      Molecular Informatics 2022

    2021

    1. A transferable Boltzmann generator for small-molecules conformers.
      Diez, Juan Viguera, Atance, Sara Romeo, Engkvist, Ola, Mercado, Rocı́o, and Olsson, Simon
      ELLIS Machine Learning for Molecule Discovery Workshop (ML4Molecules) 2021 2021
    2. De novo drug design using reinforcement learning with graph-based deep generative models
      Atance, Sara Romeo, Diez, Juan Viguera, Engkvist, Ola, Olsson, Simon, and Mercado, Rocı́o
      Reinforcement Learning for Real Life (RL4RealLife) Workshop in the 38 th International Conference on Machine Learning, 2021. 2021
    3. Multi-body effects in a coarse-grained protein force field
      Wang, Jiang, Charron, Nicholas, Husic, Brooke, Olsson, Simon, Noé, Frank, and Clementi, Cecilia
      The Journal of Chemical Physics 2021
    4. Camostat mesylate inhibits SARS-CoV-2 activation by TMPRSS2-related proteases and its metabolite GBPA exerts antiviral activity
      Hoffmann, Markus, Hofmann-Winkler, Heike, Smith, Joan C., Krüger, Nadine, Arora, Prerna, Sørensen, Lambert K., Søgaard, Ole S., Hasselstrøm, Jørgen Bo, Winkler, Michael, Hempel, Tim, Raich, Lluı́s, Olsson, Simon, Danov, Olga, Jonigk, Danny, Yamazoe, Takashi, Yamatsuta, Katsura, Mizuno, Hirotaka, Ludwig, Stephan, Noé, Frank, Kjolby, Mads, Braun, Armin, Sheltzer, Jason M., and Pöhlmann, Stefan
      EBioMedicine 2021
    5. Discovery of a hidden transient state in all bromodomain families
      Raich, Lluı́s, Meier, Katharina, Günther, Judith, Christ, Clara D., Noé, Frank, and Olsson, Simon
      Proceedings of the National Academy of Sciences 2021
    6. Molecular mechanism of inhibiting the SARS-CoV-2 cell entry facilitator TMPRSS2 with camostat and nafamostat
      Hempel, Tim, Raich, Lluı́s, Olsson, Simon, Azouz, Nurit P., Klingler, Andrea M., Hoffmann, Markus, Pöhlmann, Stefan, Rothenberg, Marc E., and Noé, Frank
      Chemical Science 2021

    2020

    1. Coarse graining molecular dynamics with graph neural networks
      Husic, Brooke E., Charron, Nicholas E., Lemm, Dominik, Wang, Jiang, Pérez, Adrià, Majewski, Maciej, Krämer, Andreas, Chen, Yaoyi, Olsson, Simon, Fabritiis, Gianni, Noé, Frank, and Clementi, Cecilia
      The Journal of Chemical Physics 2020
    2. Protein Allostery at Atomic Resolution
      Strotz, Dean, Orts, Julien, Kadavath, Harindranath, Friedmann, Michael, Ghosh, Dhiman, Olsson, Simon, Chi, Celestine N., Pokharna, Aditya, Güntert, Peter, Vögeli, Beat, and Riek, Roland
      Angewandte Chemie International Edition 2020

    2019

    1. Boltzmann generators: Sampling equilibrium states of many-body systems with deep learning
      Noé, Frank, Olsson, Simon, Köhler, Jonas, and Wu, Hao
      Science 2019
    2. Dynamic graphical models of molecular kinetics
      Olsson, Simon, and Noé, Frank
      Proceedings of the National Academy of Sciences 2019
    3. Machine Learning of Coarse-Grained Molecular Dynamics Force Fields
      Wang, Jiang, Olsson, Simon, Wehmeyer, Christoph, Pérez, Adrià, Charron, Nicholas E., Fabritiis, Gianni, Noé, Frank, and Clementi, Cecilia
      ACS Central Science 2019
    4. Introduction to Markov state modeling with the PyEMMA software [Article v1.0]
      Wehmeyer, Christoph, Scherer, Martin K., Hempel, Tim, Husic, Brooke E., Olsson, Simon, and Noé, Frank
      Living Journal of Computational Molecular Science 2019

    2018

    1. A scalable approach to the computation of invariant measures for high-dimensional Markovian systems
      Gerber, Susanne, Olsson, Simon, Noé, Frank, and Horenko, Illia
      Scientific Reports 2018

    2017

    1. The Exact Nuclear Overhauser Enhancement: Recent Advances
      Nichols, Parker, Born, Alexandra, Henen, Morkos, Strotz, Dean, Orts, Julien, Olsson, Simon, Güntert, Peter, Chi, Celestine, and Vögeli, Beat
      Molecules 2017
    2. Combining experimental and simulation data of molecular processes via augmented Markov models
      Olsson, Simon, Wu, Hao, Paul, Fabian, Clementi, Cecilia, and Noé, Frank
      Proceedings of the National Academy of Sciences 2017

    2016

    1. Mechanistic Models of Chemical Exchange Induced Relaxation in Protein NMR
      Olsson, Simon, and Noé, Frank
      Journal of the American Chemical Society 2016
    2. The Dynamic Basis for Signal Propagation in Human Pin1-WW
      Olsson, Simon, Strotz, Dean, Vögeli, Beat, Riek, Roland, and Cavalli, Andrea
      Structure 2016
    3. Bayesian inference of protein ensembles from SAXS data
      Antonov, L. D., Olsson, S., Boomsma, W., and Hamelryck, T.
      Physical Chemistry Chemical Physics 2016
    4. The Exact NOE as an Alternative in Ensemble Structure Determination
      Vögeli, Beat, Olsson, Simon, Güntert, Peter, and Riek, Roland
      Biophysical Journal 2016

    2015

    1. Molecular Determinants for Unphosphorylated STAT3 Dimerization Determined by Integrative Modeling
      Sgrignani, Jacopo, Olsson, Simon, Ekonomiuk, Dariusz, Genini, Davide, Krause, Rolf, Catapano, Carlo V., and Cavalli, Andrea
      Biochemistry 2015
    2. Quantification of Entropy-Loss in Replica-Averaged Modeling
      Olsson, Simon, and Cavalli, Andrea
      Journal of Chemical Theory and Computation 2015
    3. Compiled data set of exact NOE distance limits, residual dipolar couplings and scalar couplings for the protein GB3
      Vögeli, Beat, Olsson, Simon, Riek, Roland, and Güntert, Peter
      Data in Brief 2015
    4. Complementarity and congruence between exact NOEs and traditional NMR probes for spatial decoding of protein dynamics
      Vögeli, Beat, Olsson, Simon, Riek, Roland, and Güntert, Peter
      Journal of Structural Biology 2015
    5. Molecular Dynamics of Biomolecules through Direct Analysis of Dipolar Couplings
      Olsson, Simon, Ekonomiuk, Dariusz, Sgrignani, Jacopo, and Cavalli, Andrea
      Journal of the American Chemical Society 2015

    2014

    1. Probabilistic Determination of Native State Ensembles of Proteins
      Olsson, Simon, Vögeli, Beat Rolf, Cavalli, Andrea, Boomsma, Wouter, Ferkinghoff-Borg, Jesper, Lindorff-Larsen, Kresten, and Hamelryck, Thomas
      Journal of Chemical Theory and Computation 2014

    2013

    1. Inference of Structure Ensembles of Flexible Biomolecules from Sparse, Averaged Data
      Olsson, Simon, Frellsen, Jes, Boomsma, Wouter, Mardia, Kanti V., and Hamelryck, Thomas
      PLoS ONE 2013
    2. PHAISTOS: A framework for Markov chain Monte Carlo simulation and inference of protein structure
      Boomsma, Wouter, Frellsen, Jes, Harder, Tim, Bottaro, Sandro, Johansson, Kristoffer E., Tian, Pengfei, Stovgaard, Kasper, Andreetta, Christian, Olsson, Simon, Valentin, Jan B., Antonov, Lubomir D., Christensen, Anders S., Borg, Mikael, Jensen, Jan H., Lindorff-Larsen, Kresten, Ferkinghoff-Borg, Jesper, and Hamelryck, Thomas
      Journal of Computational Chemistry 2013

    2012

    1. An Efficient Null Model for Conformational Fluctuations in Proteins
      Harder, Tim, Borg, Mikael, Bottaro, Sandro, Boomsma, Wouter, Olsson, Simon, Ferkinghoff-Borg, Jesper, and Hamelryck, Thomas
      Structure 2012

    2011

    1. Generative probabilistic models extend the scope of inferential structure determination
      Olsson, Simon, Boomsma, Wouter, Frellsen, Jes, Bottaro, Sandro, Harder, Tim, Ferkinghoff-Borg, Jesper, and Hamelryck, Thomas
      Journal of Magnetic Resonance 2011