Zobrazeno 1 - 10
of 527
pro vyhledávání: '"Riniker, Sereina"'
Autor:
Thürlemann, Moritz, Riniker, Sereina
Publikováno v:
Chem. Sci. 14, 12661 (2023)
Electronic structure methods offer in principle accurate predictions of molecular properties, however, their applicability is limited by computational costs. Empirical methods are cheaper, but come with inherent approximations and are dependent on th
Externí odkaz:
http://arxiv.org/abs/2308.08984
Autor:
Lehner, Marc T., Katzberger, Paul, Maeder, Niels, Schiebroek, Carl C. G., Teetz, Jakob, Landrum, Gregory A., Riniker, Sereina
Publikováno v:
J. Chem. Inf. Model. 63, 6014 (2023)
We present a robust and computationally efficient approach for assigning partial charges of atoms in molecules. The method is based on a hierarchical tree constructed from attention values extracted from a graph neural network (GNN), which was traine
Externí odkaz:
http://arxiv.org/abs/2305.15981
Autor:
Thürlemann, Moritz, Riniker, Sereina
Publikováno v:
J. Chem. Phys., 159, 024105 (2023)
Clustering has become an indispensable tool in the presence of increasingly large and complex data sets. Most clustering algorithms depend, either explicitly or implicitly, on the sampled density. However, estimated densities are fragile due to the c
Externí odkaz:
http://arxiv.org/abs/2303.01104
Autor:
Katzberger, Paul, Riniker, Sereina
Publikováno v:
J. Chem. Phys., 158, 204101 (2023)
Molecular dynamics (MD) simulations enable the study of the motion of small and large (bio)molecules and the estimation of their conformational ensembles. The description of the environment (solvent) has thereby a large impact. Implicit solvent repre
Externí odkaz:
http://arxiv.org/abs/2302.09321
Publikováno v:
Phys. Chem. Chem. Phys, 24, 22497-22512 (2022)
To accurately study chemical reactions in the condensed phase or within enzymes, both a quantum-mechanical description and sufficient configurational sampling is required to reach converged estimates. Here, quantum mechanics/molecular mechanics (QM/M
Externí odkaz:
http://arxiv.org/abs/2206.14422
Simulations with an explicit description of intermolecular forces using electronic structure methods are still not feasible for many systems of interest. As a result, empirical methods such as force fields (FF) have become an established tool for the
Externí odkaz:
http://arxiv.org/abs/2206.00355
Autor:
Rieder, Salome R., Ries, Benjamin, Schaller, Kay, Champion, Candide, Barros, Emilia P., Huenenberger, Philippe H., Riniker, Sereina
Publikováno v:
J. Chem. Inf. Mol. (2022), 62, 3043-3056
Free-energy differences between pairs of end-states can be estimated based on molecular dynamics (MD) simulations using standard pathway-dependent methods such as thermodynamic integration (TI), free-energy perturbation, or Bennett's acceptance ratio
Externí odkaz:
http://arxiv.org/abs/2204.01396
Publikováno v:
Journal of Chemical Physics; 8/21/2024, Vol. 161 Issue 7, p1-7, 7p
Publikováno v:
J. Chem. Theory Comput. 18, 1701 (2022)
The accurate description of electrostatic interactions remains a challenging problem for fitted potential-energy functions. The commonly used fixed partial-charge approximation fails to reproduce the electrostatic potential at short range due to its
Externí odkaz:
http://arxiv.org/abs/2110.05417
Autor:
Champion, Candide, Lehner, Marc, Smith, Albert A., Ferrage, Fabien, Bolik-Coulon, Nicolas, Riniker, Sereina
Publikováno v:
Journal of Chemical Physics; 3/14/2024, Vol. 160 Issue 10, p1-16, 16p