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Curr Opin Struct Biol. 2018 Apr;49:1-10. doi: 10.1016/j.sbi.2017.10.001. Epub 2017 Nov 11.

New approaches for computing ligand-receptor binding kinetics.

Author information

1
Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.
2
Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany; Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany.
3
Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany; Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany; Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany. Electronic address: Rebecca.wade@h-its.org.

Abstract

The recent and growing evidence that the efficacy of a drug can be correlated to target binding kinetics has seeded the development of a multitude of novel methods aimed at computing rate constants for receptor-ligand binding processes, as well as gaining an understanding of the binding and unbinding pathways and the determinants of structure-kinetic relationships. These new approaches include various types of enhanced sampling molecular dynamics simulations and the combination of energy-based models with chemometric analysis. We assess these approaches in the light of the varying levels of complexity of protein-ligand binding processes.

PMID:
29132080
DOI:
10.1016/j.sbi.2017.10.001

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