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Negative Image-Based Screening: Rigid Docking Using Cavity Information




TekijätPostila Pekka A., Kurkinen Sami T., Pentikäinen Olli T.

ToimittajaFlavio Ballante

KustantajaHumana Press Inc.

Julkaisuvuosi2021

Kokoomateoksen nimiProtein-Ligand Interactions and Drug Design

Tietokannassa oleva lehden nimiMethods in Molecular Biology

Sarjan nimiMethods in Molecular Biology

Vuosikerta2266

Aloitussivu125

Lopetussivu140

ISBN978-1-0716-1208-8

eISBN978-1-0716-1209-5

DOIhttps://doi.org/10.1007/978-1-0716-1209-5_7


Tiivistelmä

Rational drug discovery relies heavily on molecular docking-based virtual screening, which samples flexibly the ligand binding poses against the target protein’s structure. The upside of flexible docking is that the geometries of the generated docking poses are adjusted to match the residue alignment inside the target protein’s ligand-binding pocket. The downside is that the flexible docking requires plenty of computing resources and, regardless, acquiring a decent level of enrichment typically demands further rescoring or post-processing. Negative image-based screening is a rigid docking technique that is ultrafast and computationally light but also effective as proven by vast benchmarking and screening experiments. In the NIB screening, the target protein cavity’s shape/electrostatics is aligned and compared against ab initio-generated ligand 3D conformers. In this chapter, the NIB methodology is explained at the practical level and both its weaknesses and strengths are discussed candidly.



Last updated on 2024-26-11 at 13:15