From three-dimensional GPCR structure to rational ligand discovery

Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review

Standard

From three-dimensional GPCR structure to rational ligand discovery. / Kooistra, Albert J.; Leurs, Rob; De Esch, Iwan J.P.; Graaf, Chris De.

G Protein-Coupled Receptors - Modeling and Simulation. Springer New York LLC, 2014. p. 129-157 (Advances in Experimental Medicine and Biology, Vol. 796).

Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review

Harvard

Kooistra, AJ, Leurs, R, De Esch, IJP & Graaf, CD 2014, From three-dimensional GPCR structure to rational ligand discovery. in G Protein-Coupled Receptors - Modeling and Simulation. Springer New York LLC, Advances in Experimental Medicine and Biology, vol. 796, pp. 129-157. https://doi.org/10.1007/978-94-007-7423-0_7

APA

Kooistra, A. J., Leurs, R., De Esch, I. J. P., & Graaf, C. D. (2014). From three-dimensional GPCR structure to rational ligand discovery. In G Protein-Coupled Receptors - Modeling and Simulation (pp. 129-157). Springer New York LLC. Advances in Experimental Medicine and Biology Vol. 796 https://doi.org/10.1007/978-94-007-7423-0_7

Vancouver

Kooistra AJ, Leurs R, De Esch IJP, Graaf CD. From three-dimensional GPCR structure to rational ligand discovery. In G Protein-Coupled Receptors - Modeling and Simulation. Springer New York LLC. 2014. p. 129-157. (Advances in Experimental Medicine and Biology, Vol. 796). https://doi.org/10.1007/978-94-007-7423-0_7

Author

Kooistra, Albert J. ; Leurs, Rob ; De Esch, Iwan J.P. ; Graaf, Chris De. / From three-dimensional GPCR structure to rational ligand discovery. G Protein-Coupled Receptors - Modeling and Simulation. Springer New York LLC, 2014. pp. 129-157 (Advances in Experimental Medicine and Biology, Vol. 796).

Bibtex

@inbook{c6bfe2b483b24093af86962a9ec2dedf,
title = "From three-dimensional GPCR structure to rational ligand discovery",
abstract = "This chapter will focus on G protein-coupled receptor structure-based virtual screening and ligand design. A generic virtual screening workflow and its individual elements will be introduced, covering amongst others the use of experimental data to steer the virtual screening process, ligand binding mode prediction, virtual screening for novel ligands, and rational structure-based virtual screening hit optimization. An overview of recent successful structure-based ligand discovery and design studies shows that receptor models, despite structural inaccuracies, can be efficiently used to find novel ligands for GPCRs. Moreover, the recently solved GPCR crystal structures have further increased the opportunities in structure-based ligand discovery for this pharmaceutically important protein family. The current chapter will discuss several challenges in rational ligand discovery based on GPCR structures including: (i) structure-based identification of ligands with specific effects on GPCR mediated signaling pathways, and (ii) virtual screening and structure-based optimization of fragment-like molecules.",
keywords = "Crystal structures, Docking, Drug design, In silico methods, Virtual screening",
author = "Kooistra, {Albert J.} and Rob Leurs and {De Esch}, {Iwan J.P.} and Graaf, {Chris De}",
year = "2014",
month = jan,
day = "1",
doi = "10.1007/978-94-007-7423-0_7",
language = "English",
isbn = "9789400774223",
series = "Advances in Experimental Medicine and Biology",
publisher = "Springer New York LLC",
pages = "129--157",
booktitle = "G Protein-Coupled Receptors - Modeling and Simulation",

}

RIS

TY - CHAP

T1 - From three-dimensional GPCR structure to rational ligand discovery

AU - Kooistra, Albert J.

AU - Leurs, Rob

AU - De Esch, Iwan J.P.

AU - Graaf, Chris De

PY - 2014/1/1

Y1 - 2014/1/1

N2 - This chapter will focus on G protein-coupled receptor structure-based virtual screening and ligand design. A generic virtual screening workflow and its individual elements will be introduced, covering amongst others the use of experimental data to steer the virtual screening process, ligand binding mode prediction, virtual screening for novel ligands, and rational structure-based virtual screening hit optimization. An overview of recent successful structure-based ligand discovery and design studies shows that receptor models, despite structural inaccuracies, can be efficiently used to find novel ligands for GPCRs. Moreover, the recently solved GPCR crystal structures have further increased the opportunities in structure-based ligand discovery for this pharmaceutically important protein family. The current chapter will discuss several challenges in rational ligand discovery based on GPCR structures including: (i) structure-based identification of ligands with specific effects on GPCR mediated signaling pathways, and (ii) virtual screening and structure-based optimization of fragment-like molecules.

AB - This chapter will focus on G protein-coupled receptor structure-based virtual screening and ligand design. A generic virtual screening workflow and its individual elements will be introduced, covering amongst others the use of experimental data to steer the virtual screening process, ligand binding mode prediction, virtual screening for novel ligands, and rational structure-based virtual screening hit optimization. An overview of recent successful structure-based ligand discovery and design studies shows that receptor models, despite structural inaccuracies, can be efficiently used to find novel ligands for GPCRs. Moreover, the recently solved GPCR crystal structures have further increased the opportunities in structure-based ligand discovery for this pharmaceutically important protein family. The current chapter will discuss several challenges in rational ligand discovery based on GPCR structures including: (i) structure-based identification of ligands with specific effects on GPCR mediated signaling pathways, and (ii) virtual screening and structure-based optimization of fragment-like molecules.

KW - Crystal structures

KW - Docking

KW - Drug design

KW - In silico methods

KW - Virtual screening

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U2 - 10.1007/978-94-007-7423-0_7

DO - 10.1007/978-94-007-7423-0_7

M3 - Book chapter

C2 - 24158804

SN - 9789400774223

T3 - Advances in Experimental Medicine and Biology

SP - 129

EP - 157

BT - G Protein-Coupled Receptors - Modeling and Simulation

PB - Springer New York LLC

ER -

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