A combined protocol in which residual dipolar couplings are first introduced as intervector projection angle restraints and at a later stage as direct restraints is shown here to give the best performance.
The interface prediction program WHISCY is presented, which combines surface conservation and structural information to predict protein–protein interfaces and demonstrates the potential of using interface predictions to drive protein–protein docking.
S. D. de Vries, A. V. van Dijk, A. M. J. J. Bonvin· 0 citations
A novel and simple hydrophobicity scale derived from the Kyte-Doolittle hydrophobicity scale leads to a performance improvement of around 10% in ranking, cluster quality and water recovery at the interface compared with the statistics-based original solvated docking protocol.
P. Kastritis, K. Visscher, A. V. van Dijk et al.· 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
An extension of the TAiBP approach for providing a relevant description of the conformational landscapes of IDRs in the cases where residual dipolar couplings (RDC) have been measured, and comparing the descriptions of the conformational space obtained using TAiBP and classical approaches in the literature are compared...
Marina Botnari, Nathalie Sibille, Jung-Hsin Lin et al.· Journal of Physical Chemistr...· 0 citations
A practical overview of classical atomistic MD methodologies commonly used in medicinal chemistry, including force-field-based simulations, enhanced sampling techniques, and free-energy calculation methods such as alchemical and end-point approaches are provided.
S. S. Çınaroğlu· Mini-Reviews in Medical Chem...· 1 citation
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
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