SHOP: receptor-based scaffold hopping by GRID-based similarity searches

Research output: Contribution to journalJournal articlepeer-review

Standard

SHOP: receptor-based scaffold hopping by GRID-based similarity searches. / Bergmann, Rikke; Liljefors, Tommy; Sørensen, Morten D; Zamora, Ismael.

In: Journal of Chemical Information and Modeling, Vol. 49, No. 3, 2009, p. 658-669.

Research output: Contribution to journalJournal articlepeer-review

Harvard

Bergmann, R, Liljefors, T, Sørensen, MD & Zamora, I 2009, 'SHOP: receptor-based scaffold hopping by GRID-based similarity searches', Journal of Chemical Information and Modeling, vol. 49, no. 3, pp. 658-669. https://doi.org/10.1021/ci800391v

APA

Bergmann, R., Liljefors, T., Sørensen, M. D., & Zamora, I. (2009). SHOP: receptor-based scaffold hopping by GRID-based similarity searches. Journal of Chemical Information and Modeling, 49(3), 658-669. https://doi.org/10.1021/ci800391v

Vancouver

Bergmann R, Liljefors T, Sørensen MD, Zamora I. SHOP: receptor-based scaffold hopping by GRID-based similarity searches. Journal of Chemical Information and Modeling. 2009;49(3):658-669. https://doi.org/10.1021/ci800391v

Author

Bergmann, Rikke ; Liljefors, Tommy ; Sørensen, Morten D ; Zamora, Ismael. / SHOP: receptor-based scaffold hopping by GRID-based similarity searches. In: Journal of Chemical Information and Modeling. 2009 ; Vol. 49, No. 3. pp. 658-669.

Bibtex

@article{79d732900caf11de8478000ea68e967b,
title = "SHOP: receptor-based scaffold hopping by GRID-based similarity searches",
abstract = "A new field-derived 3D method for receptor-based scaffold hopping, implemented in the software SHOP, is presented. Information from a protein-ligand complex is utilized to substitute a fragment of the ligand with another fragment from a database of synthetically accessible scaffolds. A GRID-based interaction profile of the receptor and geometrical descriptions of a ligand scaffold are used to obtain new scaffolds with different structural features and are able to replace the original scaffold in the protein-ligand complex. An enrichment study was successfully performed verifying the ability of SHOP to find known active CDK2 scaffolds in a database. Additionally, SHOP was used for suggesting new inhibitors of p38 MAP kinase. Four p38 complexes were used to perform six scaffold searches. Several new scaffolds were suggested, and the resulting compounds were successfully docked into the query proteins.",
keywords = "Former Faculty of Pharmaceutical Sciences",
author = "Rikke Bergmann and Tommy Liljefors and S{\o}rensen, {Morten D} and Ismael Zamora",
year = "2009",
doi = "10.1021/ci800391v",
language = "English",
volume = "49",
pages = "658--669",
journal = "Journal of Chemical Information and Modeling",
issn = "1549-9596",
publisher = "American Chemical Society",
number = "3",

}

RIS

TY - JOUR

T1 - SHOP: receptor-based scaffold hopping by GRID-based similarity searches

AU - Bergmann, Rikke

AU - Liljefors, Tommy

AU - Sørensen, Morten D

AU - Zamora, Ismael

PY - 2009

Y1 - 2009

N2 - A new field-derived 3D method for receptor-based scaffold hopping, implemented in the software SHOP, is presented. Information from a protein-ligand complex is utilized to substitute a fragment of the ligand with another fragment from a database of synthetically accessible scaffolds. A GRID-based interaction profile of the receptor and geometrical descriptions of a ligand scaffold are used to obtain new scaffolds with different structural features and are able to replace the original scaffold in the protein-ligand complex. An enrichment study was successfully performed verifying the ability of SHOP to find known active CDK2 scaffolds in a database. Additionally, SHOP was used for suggesting new inhibitors of p38 MAP kinase. Four p38 complexes were used to perform six scaffold searches. Several new scaffolds were suggested, and the resulting compounds were successfully docked into the query proteins.

AB - A new field-derived 3D method for receptor-based scaffold hopping, implemented in the software SHOP, is presented. Information from a protein-ligand complex is utilized to substitute a fragment of the ligand with another fragment from a database of synthetically accessible scaffolds. A GRID-based interaction profile of the receptor and geometrical descriptions of a ligand scaffold are used to obtain new scaffolds with different structural features and are able to replace the original scaffold in the protein-ligand complex. An enrichment study was successfully performed verifying the ability of SHOP to find known active CDK2 scaffolds in a database. Additionally, SHOP was used for suggesting new inhibitors of p38 MAP kinase. Four p38 complexes were used to perform six scaffold searches. Several new scaffolds were suggested, and the resulting compounds were successfully docked into the query proteins.

KW - Former Faculty of Pharmaceutical Sciences

U2 - 10.1021/ci800391v

DO - 10.1021/ci800391v

M3 - Journal article

C2 - 19265417

VL - 49

SP - 658

EP - 669

JO - Journal of Chemical Information and Modeling

JF - Journal of Chemical Information and Modeling

SN - 1549-9596

IS - 3

ER -

ID: 11175353