2026· Methods in molecular biology· Vol 3061, pp.
187-221
· 0 citations
Medicine
TL;DR
This chapter provides an overview, with literature examples, of underexplored interactions that contribute to molecular binding, including weak hydrogen bonding; anion-π and cation-π interactions; Bürgi-Dunitz and tetrel interactions; halogen and chalcogen bonding; and S···π, C···π, O···π, N···π, and amide···π interactions.
Sulfur-containing heterocycles such as thiophene, thiazole, and thiadiazole frequently appear in biologically active molecules, although the intrinsic nature of their S···O chalcogen-bonding (ChB) interactions in protein–ligand complexes is yet to be completely understood. In this work, a comprehensive survey of the...
Heena Charaya, Anamika Ghosh, Riya Saha et al.· Journal of Physical Chemistr...· 0 citations
ChalcoVina is presented, an augmented molecular docking program based on AutoDock Vina that simultaneously evaluates intermolecular and intramolecular ChBs for the first time and can be a blueprint for other σ-hole-mediated interactions, facilitating the inclusion of more nonclassical interactions in SBDD.
Wen-Hao Cai, Zi-Yue Li, Yi-Jie Wang et al.· Journal of Chemical Informat...· 0 citations
Theoceptor method can be applied to X-ray crystallography- or cryo-electron microscopy-derived structures, can be applied equally to covalent and noncovalent binders, and can provide excellent predictions for the changes in activity between matched molecular pairs.
Nikeel Cull, Yixin He, Sylvia C. Kaempf et al.· Methods in molecular biology· 0 citations
Halogen bonding (XB) is often analyzed in terms of isolated dimers, yet under realistic solution conditions, it coexists with a dense, rapidly fluctuating network of weaker contacts whose net effect on bond strength is difficult to quantify. Here, we combine gas-phase quantum-chemical calculations with explicit-solvent...
D. V. Krutin, A. A. Titova, M. Kaplanskiy et al.· Journal of Physical Chemistr...· 0 citations
In this study, a pyridinone-based compound was structurally characterized and computationally analyzed using integrated experimental and theoretical methods. The single-crystal X-ray diffraction (SC-XRD) results confirmed that the molecule adopts a non-planar conformation stabilized by strong N–H···O hydrogen bonds and...
G. Karakaya, Erdal Kurt, G. Yakalı et al.· Süleyman Demirel Üniversites...· 0 citations
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