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On the Effect of the Various Assumptions and Approximations used in Molecular Simulations on the Properties of Bio-Molecular Systems : Overview and Perspective on Issues

W. Gunsteren, X. Daura, P. Fuchs, N. Hansen, B. Horta, P. Hünenberger, A. Mark, M. Pechlaner, S. Riniker, and C. Oostenbrink. ChemPhysChem, 22 (3): 264-282 (2021)
DOI: 10.1002/cphc.202000968

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Reoptimized interaction parameters for the peptide-backbone model compound N-methylacetamide in the GROMOS force field: Influence on the folding properties of two beta-peptides in methanol.B. Horta, Z. Lin, W. Huang, S. Riniker, W. van Gunsteren, and P. Hünenberger. Journal of Computational Chemistry, 33 (24): 1907-1917 (2012)Using Information from Historical High-Throughput Screens to Predict Active Compounds.S. Riniker, Y. Wang, J. Jenkins, and G. Landrum. Journal of Chemical Information and Modeling, 54 (7): 1880-1891 (2014)On the Effect of the Various Assumptions and Approximations used in Molecular Simulations on the Properties of Bio-Molecular Systems : Overview and Perspective on IssuesW. Gunsteren, X. Daura, P. Fuchs, N. Hansen, B. Horta, P. Hünenberger, A. Mark, M. Pechlaner, S. Riniker, and C. Oostenbrink. ChemPhysChem, 22 (3): 264-282 (2021)Comparison of enveloping distribution sampling and thermodynamic integration to calculate binding free energies of phenylethanolamine N-methyltransferase inhibitorsS. Riniker, C. Christ, N. Hansen, A. Mark, P. Nair, and W. van Gunsteren. The Journal of Chemical Physics, 135 (2): 024105 (July 2011)Assessment of enveloping distribution sampling to calculate relative free enthalpies of binding for eight netropsin-DNA duplex complexes in aqueous solution.N. Hansen, J. Dolenc, M. Knecht, S. Riniker, and W. van Gunsteren. Journal of Computational Chemistry, 33 (6): 640-651 (2012)Heterogeneous Classifier Fusion for Ligand-Based Virtual Screening: Or, How Decision Making by Committee Can Be a Good Thing.S. Riniker, N. Fechner, and G. Landrum. Journal of Chemical Information and Modeling, 53 (11): 2829-2836 (2013)Free enthalpies of replacing water molecules in protein binding pockets.S. Riniker, L. Barandun, F. Diederich, O. Krämer, A. Steffen, and W. van Gunsteren. Journal of Computer-Aided Molecular Design, 26 (12): 1293-1309 (2012)Open-source platform to benchmark fingerprints for ligand-based virtual screening.S. Riniker, and G. Landrum. J. Cheminformatics, (2013)Similarity maps - a visualization strategy for molecular fingerprints and machine-learning methods.S. Riniker, and G. Landrum. J. Cheminformatics, (2013)Systematic Optimization of a Fragment-Based Force Field against Experimental Pure-Liquid Properties Considering Large Compound Families: Application to Saturated HaloalkanesM. Oliveira, M. Andrey, S. Rieder, L. Kern, D. Hahn, S. Riniker, B. Horta, and P. Hünenberger. Journal of Chemical Theory and Computation, 16 (12): 7525--7555 (2020)

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