The tortoise beetle genus Ogdoecosta Spaeth 1909 is revised and an illustrated key to 12 species is provided, based on a morphological analysis of all species. All the known species are redescribed and one new species, Ogdoecosta paraflavomaculata López-Pérez sp. nov., is described from Belize and México. Lectotypes are designated for O. omissa Dohrn 1880, O. epilachnoides (Champion 1893), O. fasciata (Boheman 1856), O. flavomaculata (Champion 1893), O. mexicana (Champion 1893 and O. obliterata (Champion 1893). The distribution ranges for O. biannularis (Boheman 1854), O. catenulata (Boheman 1854), O. decemstillata (Boheman 1856), O. epilachnoides, O. fasciata, O. guttifera, O. juvenca, and O. obliterata are extended within México. Ogdoecosta guttifera (Boheman) is a new record for Venezuela.
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http://dx.doi.org/10.11646/zootaxa.4179.3.4 | DOI Listing |
J Chem Theory Comput
May 2024
Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland.
The majority of drug-like molecules contain at least one ionizable group, and many common drug scaffolds are subject to tautomeric equilibria. Thus, these compounds are found in a mixture of protonation and/or tautomeric states at physiological pH. Intrinsically, standard classical molecular dynamics (MD) simulations cannot describe such equilibria between states, which negatively impacts the prediction of key molecular properties .
View Article and Find Full Text PDFJ Chem Phys
March 2024
Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland.
Nuclear magnetic resonance (NMR) relaxation experiments shine light onto the dynamics of molecular systems in the picosecond to millisecond timescales. As these methods cannot provide an atomically resolved view of the motion of atoms, functional groups, or domains giving rise to such signals, relaxation techniques have been combined with molecular dynamics (MD) simulations to obtain mechanistic descriptions and gain insights into the functional role of side chain or domain motion. In this work, we present a comparison of five computational methods that permit the joint analysis of MD simulations and NMR relaxation experiments.
View Article and Find Full Text PDFJ Chem Inf Model
November 2023
Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland.
Alchemical free-energy methods based on molecular dynamics (MD) simulations have become important tools to identify modifications of small organic molecules that improve their protein binding affinity during lead optimization. The routine application of pairwise free-energy methods to rank potential binders from best to worst is impacted by the combinatorial increase in calculations to perform when the number of molecules to assess grows. To address this fundamental limitation, our group has developed replica-exchange enveloping distribution sampling (RE-EDS), a pathway-independent multistate method, enabling the calculation of alchemical free-energy differences between multiple ligands ( > 2) from a single MD simulation.
View Article and Find Full Text PDFZookeys
July 2023
Biodiversity Knowledge Integration Center, Arizona State University, Tempe, Arizona, USA.
The tribes Goniaderini Lacordaire, 1859 and Lupropini Lesne, 1926 within the tenebrionid subfamily Lagriinae Latreille, 1825 have previously been shown to be non-monophyletic by molecular phylogenetic analyses. The tribes and constituent genera are here reviewed and redefined morphologically. As part of tribal redefinitions, we establish Prateini with type genus LeConte, 1862.
View Article and Find Full Text PDFJ Chem Inf Model
March 2023
Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland.
Macromolecular recognition and ligand binding are at the core of biological function and drug discovery efforts. Water molecules play a significant role in mediating the protein-ligand interaction, acting as more than just the surrounding medium by affecting the thermodynamics and thus the outcome of the binding process. As individual water contributions are impossible to measure experimentally, a range of computational methods have emerged to identify hydration sites in protein pockets and characterize their energetic contributions for drug discovery applications.
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