Special Issue "Molecular Docking in Drug Design 2018"
Deadline for manuscript submissions: 31 January 2019
Nowadays, we have tens of various computational docking strategies, with an even wider choice of scoring functions. It is getting difficult, even for the docking-focused expert, to intimately know all the features of all the docking tools. Thus, "docking" grows more and more into a stand-alone discipline of molecular modeling, and its users are increasingly becoming overspecialized. This is unfortunate, since docking is actually at the cross-roads of (quantitative) Structure–Activity Relationships (Q)SAR and physical molecular simulations, such as molecular dynamics. In principle, docking simulations should be able to discover actives with novel site binding modes—molecules that are structurally different (thus, not eligible to be found by similarity searches based on known ligands), and not matching already known binding pharmacophores. In practice, docking is a trained QSAR model, with a limited applicability domain.
In your opinion, where would you situate docking on this scale of empiricism—do you consider it as a simplified physical simulation, or a rather sophisticated 3D-QSAR approach with ligand-site interaction descriptors? What is, in your experience, the key strength of docking over other methods - is it the ability to propose binding modes to inspire medicinal chemists in search for the best substitution patterns? Did you encounter examples of completely novel, "paradigm-breaking" binders discovered in docking-driven virtual screening? Have you encountered situations (benchmarks, prospective predictions) when docking was the only successful method, "seeing" SAR patterns which could not have been captured by 2D-QSAR? On the contrary, did you run time-consuming docking calculations only in order to discover that results highlight an obvious SAR trend which could have been learned by ultrafast 2D-QSAR, or simply by looking at the compound series?
I would thus encourage the members of community to report original work, or review papers that place docking in the wider context of various other chemoinformatics and modeling approaches, in an attempt to pinpoint the "ecological niche" best covered by this approach. In this respect, both docking success and failure stories can be enlightening. Original docking procedures are of course welcome, as their comparison with other methods are necessary for publication.
Dr. Dragos Horvath
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- Docking strategies
- Scoring functions versus force field energies
- Docking versus 2D QSAR
- Molecular Dynamics in Docking