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Waller, M. P.; Kruse, H.; Muck-Lichtenfeld, C.; Grimme, S. Investigating inclusion complexes using quantum chemical methods. Chem. Soc. Rev., 2012, 41, 3119-3128.

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Article

Docking and Ligand Binding Affinity: Uses and Pitfalls

1Departamento de Química Orgánica I, Facultad de Química, Universidad Complutense, 28040 Madrid, Spain


American Journal of Modeling and Optimization. 2016, Vol. 4 No. 3, 74-114
DOI: 10.12691/ajmo-4-3-2
Copyright © 2016 Science and Education Publishing

Cite this paper:
María J. R. Yunta. Docking and Ligand Binding Affinity: Uses and Pitfalls. American Journal of Modeling and Optimization. 2016; 4(3):74-114. doi: 10.12691/ajmo-4-3-2.

Correspondence to: María  J. R. Yunta, Departamento de Química Orgánica I, Facultad de Química, Universidad Complutense, 28040 Madrid, Spain. Email: mjryun@ucm.es

Abstract

In this review article, we will explore the foundations of different classes of docking and scoring functions, their possible limitations, and their suitable application domains. We also provide assessments of several scoring functions on weakly-interacting protein-ligand complexes, which will be useful information in computational fragment-based drug design or virtual screening.

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