publications

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