5 research outputs found
Two Decades of 4D-QSAR: A Dying Art or Staging a Comeback?
A key question confronting computational chemists concerns the preferable ligand geometry
that fits complementarily into the receptor pocket. Typically, the postulated âbioactiveâ 3D
ligand conformation is constructed as a âsophisticated guessâ (unnecessarily geometry-optimized)
mirroring the pharmacophore hypothesisâsometimes based on an erroneous prerequisite. Hence,
4D-QSAR scheme and its âdialectsâ have been practically implemented as higher level of model
abstraction that allows the examination of the multiple molecular conformation, orientation and
protonation representation, respectively. Nearly a quarter of a century has passed since the eminent
work of Hopfinger appeared on the stage; therefore the natural question occurs whether 4D-QSAR
approach is still appealing to the scientific community? With no intention to be comprehensive, a
review of the current state of art in the field of receptor-independent (RI) and receptor-dependent
(RD) 4D-QSAR methodology is provided with a brief examination of the âmainstreamâ algorithms. In
fact, a myriad of 4D-QSAR methods have been implemented and applied practically for a diverse
range of molecules. It seems that, 4D-QSAR approach has been experiencing a promising renaissance
of interests that might be fuelled by the rising power of the graphics processing unit (GPU) clusters
applied to full-atom MD-based simulations of the protein-ligand complexes
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