From heptahelical bundle to hits from the haystack: Structure-based virtual screening for GPCR ligands

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

Standard

From heptahelical bundle to hits from the haystack : Structure-based virtual screening for GPCR ligands. / Kooistra, Albert J.; Roumen, Luc; Leurs, Rob; De Esch, Iwan J.P.; De Graaf, Chris.

G Protein Coupled ReceptorsModeling, Activation, Interactions and Virtual Screening. 2013. p. 279-336 (Methods in Enzymology, Vol. 522).

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

Harvard

Kooistra, AJ, Roumen, L, Leurs, R, De Esch, IJP & De Graaf, C 2013, From heptahelical bundle to hits from the haystack: Structure-based virtual screening for GPCR ligands. in G Protein Coupled ReceptorsModeling, Activation, Interactions and Virtual Screening. Methods in Enzymology, vol. 522, pp. 279-336. https://doi.org/10.1016/B978-0-12-407865-9.00015-7

APA

Kooistra, A. J., Roumen, L., Leurs, R., De Esch, I. J. P., & De Graaf, C. (2013). From heptahelical bundle to hits from the haystack: Structure-based virtual screening for GPCR ligands. In G Protein Coupled ReceptorsModeling, Activation, Interactions and Virtual Screening (pp. 279-336). Methods in Enzymology Vol. 522 https://doi.org/10.1016/B978-0-12-407865-9.00015-7

Vancouver

Kooistra AJ, Roumen L, Leurs R, De Esch IJP, De Graaf C. From heptahelical bundle to hits from the haystack: Structure-based virtual screening for GPCR ligands. In G Protein Coupled ReceptorsModeling, Activation, Interactions and Virtual Screening. 2013. p. 279-336. (Methods in Enzymology, Vol. 522). https://doi.org/10.1016/B978-0-12-407865-9.00015-7

Author

Kooistra, Albert J. ; Roumen, Luc ; Leurs, Rob ; De Esch, Iwan J.P. ; De Graaf, Chris. / From heptahelical bundle to hits from the haystack : Structure-based virtual screening for GPCR ligands. G Protein Coupled ReceptorsModeling, Activation, Interactions and Virtual Screening. 2013. pp. 279-336 (Methods in Enzymology, Vol. 522).

Bibtex

@inbook{f0d786ff83934bf0ad5a1aa0fcf9ed68,
title = "From heptahelical bundle to hits from the haystack: Structure-based virtual screening for GPCR ligands",
abstract = "This review will focus on the construction, refinement, and validation of G-protein-coupled receptor (GPCR) structural models for the purpose of structure-based virtual screening (SBVS) and ligand design. The review will present a comparative analysis of GPCR crystal structures and their implication on GPCR (homology) modeling. The challenges associated with steps along the modeling workflow will be discussed: the use of experimental anchors to steer the modeling procedure, amino acid sequence alignment and template selection, receptor structure refinement, loop modeling, ligand-binding mode prediction, and virtual screening for novel ligands. An overview of several 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.",
keywords = "G Protein-Coupled Receptor (GPCR), ligand discovery, protein homology modeling, structure-based virtual screening",
author = "Kooistra, {Albert J.} and Luc Roumen and Rob Leurs and {De Esch}, {Iwan J.P.} and {De Graaf}, Chris",
year = "2013",
month = feb,
day = "11",
doi = "10.1016/B978-0-12-407865-9.00015-7",
language = "English",
isbn = "9780124078659",
series = "Methods in Enzymology",
publisher = "Academic Press",
pages = "279--336",
booktitle = "G Protein Coupled ReceptorsModeling, Activation, Interactions and Virtual Screening",

}

RIS

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T1 - From heptahelical bundle to hits from the haystack

T2 - Structure-based virtual screening for GPCR ligands

AU - Kooistra, Albert J.

AU - Roumen, Luc

AU - Leurs, Rob

AU - De Esch, Iwan J.P.

AU - De Graaf, Chris

PY - 2013/2/11

Y1 - 2013/2/11

N2 - This review will focus on the construction, refinement, and validation of G-protein-coupled receptor (GPCR) structural models for the purpose of structure-based virtual screening (SBVS) and ligand design. The review will present a comparative analysis of GPCR crystal structures and their implication on GPCR (homology) modeling. The challenges associated with steps along the modeling workflow will be discussed: the use of experimental anchors to steer the modeling procedure, amino acid sequence alignment and template selection, receptor structure refinement, loop modeling, ligand-binding mode prediction, and virtual screening for novel ligands. An overview of several 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.

AB - This review will focus on the construction, refinement, and validation of G-protein-coupled receptor (GPCR) structural models for the purpose of structure-based virtual screening (SBVS) and ligand design. The review will present a comparative analysis of GPCR crystal structures and their implication on GPCR (homology) modeling. The challenges associated with steps along the modeling workflow will be discussed: the use of experimental anchors to steer the modeling procedure, amino acid sequence alignment and template selection, receptor structure refinement, loop modeling, ligand-binding mode prediction, and virtual screening for novel ligands. An overview of several 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.

KW - G Protein-Coupled Receptor (GPCR)

KW - ligand discovery

KW - protein homology modeling

KW - structure-based virtual screening

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U2 - 10.1016/B978-0-12-407865-9.00015-7

DO - 10.1016/B978-0-12-407865-9.00015-7

M3 - Book chapter

C2 - 23374191

AN - SCOPUS:84873344962

SN - 9780124078659

T3 - Methods in Enzymology

SP - 279

EP - 336

BT - G Protein Coupled ReceptorsModeling, Activation, Interactions and Virtual Screening

ER -

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