Refine
Document Type
- Article (18) (remove)
Keywords
- AI (1)
- CDK (1)
- Chemical space (1)
- Cheminformatics (1)
- Chemistry Development Kit (1)
- Chemistry Development Kit, CDK, Molecule fragmentation, In silico fragmentation, Scaffolds, Functional groups, Glycosidic moieties, Rich client, Graphical user interface, GUI (1)
- Clustering (1)
- DECIMER (1)
- Deep Learning (1)
- Dissipative particle dynamics, DPD, Surfactant, Bilayer, Lamellar, Simulation, Mesoscopic (1)
- Fragmentation (1)
- Hand-drawn chemical structures (1)
- Natural products (1)
- OCSR (1)
- OCSR, Optical Chemical Structure Recognition (1)
- Scaffold (1)
- Scaffold network (1)
- Scaffold tree (1)
- Transformer (1)
- artificial intelligence (1)
- machine learning (1)
- optical chemical structure recognition (1)
Institute
- Institut für biologische und chemische Informatik (18) (remove)
Description and Analysis of Glycosidic Residues in the Largest Open Natural Products Database
(2021)
Different charge treatment approaches are examined for cyclotide-induced plasma membrane disruption by lipid extraction studied with dissipative particle dynamics. A pure Coulomb approach with truncated forces tuned to avoid individual strong ion pairing still reveals hidden statistical pairing effects that may lead to artificial membrane stabilization or distortion of cyclotide activity depending on the cyclotide’s charge state. While qualitative behavior is not affected in an apparent manner, more sensitive quantitative evaluations can be systematically biased. The findings suggest a charge smearing of point charges by an adequate charge distribution. For large mesoscopic simulation boxes, approximations for the Ewald sum to account for mirror charges due to periodic boundary conditions are of negligible influence.