Conformational Searching with Quantum Mechanics.

Clicks: 330
ID: 91402
2020
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Ranked #38 of 139 articles by views in methods in molecular biology (clifton, nj)

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Abstract
Estimating the range of three-dimensional structures (conformations) that are available to a molecule is a key component of computer-aided drug design. Quantum mechanical simulation offers improved accuracy over forcefield methods, but at a high computational cost. The question is whether this increased cost can be justified in a context in which high-throughput analysis of large numbers of molecules is often key. This chapter discusses the application of quantum mechanics to conformational searching, with a focus on three key challenges: (1) the generation of ensembles that include a good approximation to a molecule's bioactive conformation at as prominent a ranking as possible; (2) rational analysis and modification of a pre-established bioactive conformation in terms of its energetics; and (3) approximation of real solution-phase conformational ensembles in tandem with NMR data. The impact of QM on the high-throughput application (1) is debatable, meaning that for the moment its primary application is still lower-throughput applications such as (2) and (3). The optimal choice of QM method is also discussed. Rigorous benchmarking suggests that DFT methods are only acceptable when used with large basis sets, but a trickle of papers continue to obtain useful results with relatively low-cost methods, leading to a dilemma that the literature has yet to fully resolve.
Reference Key
habgood2020conformationalmethods Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Habgood, Matthew;James, Tim;Heifetz, Alexander;
Journal methods in molecular biology (clifton, nj)
Year 2020
DOI
10.1007/978-1-0716-0282-9_14
URL
Keywords
NMR DFT B3LYP bioactive conformation m06-2x solution-phase ensembles

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