Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors.

By Holger Gohlke, Gerhard Klebe. Angewandte Chemie, 2002

687 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Physical and Theoretical Chemistry, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/8a4553f6627bade302a696027d8f0d9d1d0031ea

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In Computational Theory and Mathematics

In Physical and Theoretical Chemistry

In Spectroscopy

Citations in the corpus

Protein-ligand docking in the new millennium--a retrospective of 10 years in the field. (2013, background): “Historically, most of these comparisons have been made in terms of their ability to reproduce the X-ray pose of selected ligands [8, 18, 21, 32-50], their capability to predict binding free energies from the best-scored pose [16, 21, 24, 27, 28, 35, 51-56], or their ability to identify known binders”
Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go (2008, background): “However, commonly used SFs are known to have limitations as the protein–ligand complex formation often includes subtleties not captured by SFs (Gohlke and Klebe, 2002).”
Binding of Small-Molecule Ligands to Proteins: “What You See” Is Not Always “What You Get” (2009, neutral): “For example, protonation states can change on binding (Czodrowski et al., 2007; Dullweber et al., 2001; Gohlke and Klebe, 2002; Steuber et al., 2007), as can tautomeric states (Pospisil et al., 2003) and other factors.”
In silico pharmacology for drug discovery: methods for virtual ligand screening and profiling (2007, background): “In a different field, databases of ligand–protein complexes are being exploited to derive knowledge-based potentials as a means to estimate the free energies of molecular interactions when docking ligands into protein cavities (Gohlke and Klebe, 2002).”
The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities (2015, methodology): “This is alarming, as this term should model the hydrophobic effect, which normally is assumed to be among the most important terms for ligand binding [1].”