Browsing by Author "Doerr, Stefan, 1987-"

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  • Doerr, Stefan, 1987- (Universitat Pompeu Fabra, 2016-09-16)
    Molecular dynamics has established itself over the last years as a strong tool for structure-based molecular investigation in biology. Stefan Doerr's thesis concerns the application of machine learning methods to molecular ...
  • Ferruz Capapey, Noelia, 1988-; Doerr, Stefan, 1987-; Vanase Frawley, Michelle A.; Zou, Yaozhong; Chen, Xiaomin; Marr, Eric S.; Nelson, Robin T.; Kormos, Bethany L.; Wager, Travis T.; Hou, Xinjun J.; Villalobos, Anabella; Sciabola, Simone; De Fabritiis, Gianni (Nature Publishing Group, 2018)
    The recent increase in the number of X-ray crystal structures of G-protein coupled receptors (GPCRs) has been enabling for structure-based drug design (SBDD) efforts. These structures have revealed that GPCRs are highly ...
  • Varela-Rial, Alejandro; Maryanow, Iain; Majewski, Maciej; Doerr, Stefan, 1987-; Schapin, Nikolai; Jiménez Luna, José, 1993-; De Fabritiis, Gianni (American Chemical Society (ACS), 2022)
    Deep learning has been successfully applied to structure-based protein-ligand affinity prediction, yet the black box nature of these models raises some questions. In a previous study, we presented KDEEP, a convolutional ...
  • Doerr, Stefan, 1987-; Majewski, Maciej; Pérez, Adrià; Krämer, Andreas; Clementi, Cecilia; Noé, Frank; Giorgino, Toni; De Fabritiis, Gianni (American Chemical Society (ACS), 2021)
    Molecular dynamics simulations provide a mechanistic description of molecules by relying on empirical potentials. The quality and transferability of such potentials can be improved leveraging data-driven models derived ...