A Practical Perspective : The Effect of Ligand Conformers on the Negative Image-Based Screening
Ahinko, M., Kurkinen, S., Niinivehmas, S., Pentikäinen, O., & Postila, P. (2019). A Practical Perspective : The Effect of Ligand Conformers on the Negative Image-Based Screening. International Journal of Molecular Sciences, 20(11), Article 2779. https://doi.org/10.3390/ijms20112779
Julkaistu sarjassa
International Journal of Molecular SciencesPäivämäärä
2019Tekijänoikeudet
© 2019 by the authors.
Negative image-based (NIB) screening is a rigid molecular docking methodology that can
also be employed in docking rescoring. During the NIB screening, a negative image is generated based
on the target protein’s ligand-binding cavity by inverting its shape and electrostatics. The resulting NIB
model is a drug-like entity or pseudo-ligand that is compared directly against ligand 3D conformers,
as is done with a template compound in the ligand-based screening. This cavity-based rigid docking
has been demonstrated to work with genuine drug targets in both benchmark testing and drug
candidate/lead discovery. Firstly, the study explores in-depth the applicability of different ligand 3D
conformer generation software for acquiring the best NIB screening results using cyclooxygenase-2
(COX-2) as the example system. Secondly, the entire NIB workflow from the protein structure
preparation, model build-up, and ligand conformer generation to the similarity comparison is
performed for COX-2. Accordingly, hands-on instructions are provided on how to employ the
NIB methodology from start to finish, both with the rigid docking and docking rescoring using
noncommercial software. The practical aspects of the NIB methodology, especially the effect of ligand
conformers, are discussed thoroughly, thus, making the methodology accessible for new users.
...
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