3D-e-Chem: Structural Cheminformatics Workflows for Computer-Aided Drug Discovery

Albert J. Kooistra; Márton Vass; Ross McGuire; Rob Leurs; Iwan J.P. de Esch; Gert Vriend; Stefan Verhoeven; Chris de Graaf

doi:10.1002/cmdc.201700754

3D-e-Chem: Structural Cheminformatics Workflows for Computer-Aided Drug Discovery

Albert J. Kooistra, Márton Vass, Ross McGuire, Rob Leurs, Iwan J.P. de Esch, Gert Vriend, Stefan Verhoeven^*, Chris de Graaf

^*Corresponding author for this work

9 Citations (Scopus)

Abstract

eScience technologies are needed to process the information available in many heterogeneous types of protein–ligand interaction data and to capture these data into models that enable the design of efficacious and safe medicines. Here we present scientific KNIME tools and workflows that enable the integration of chemical, pharmacological, and structural information for: i) structure-based bioactivity data mapping, ii) structure-based identification of scaffold replacement strategies for ligand design, iii) ligand-based target prediction, iv) protein sequence-based binding site identification and ligand repurposing, and v) structure-based pharmacophore comparison for ligand repurposing across protein families. The modular setup of the workflows and the use of well-established standards allows the re-use of these protocols and facilitates the design of customized computer-aided drug discovery workflows.

Original language	English
Journal	ChemMedChem
Volume	13
Issue number	6
Pages (from-to)	614-626
Number of pages	13
ISSN	1860-7179
DOIs	https://doi.org/10.1002/cmdc.201700754
Publication status	Published - 20 Mar 2018
Externally published	Yes

Keywords

cheminformatics workflows
KNIME
ligand design
ligand repurposing
target prediction

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10.1002/cmdc.201700754Licence: CC BY

cmdc.201700754Final published version, 3.25 MBLicence: CC BY

Cite this

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AU - Kooistra, Albert J.

AU - Vass, Márton

AU - McGuire, Ross

AU - Leurs, Rob

AU - de Esch, Iwan J.P.

AU - Vriend, Gert

AU - Verhoeven, Stefan

AU - de Graaf, Chris

PY - 2018/3/20

Y1 - 2018/3/20

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AB - eScience technologies are needed to process the information available in many heterogeneous types of protein–ligand interaction data and to capture these data into models that enable the design of efficacious and safe medicines. Here we present scientific KNIME tools and workflows that enable the integration of chemical, pharmacological, and structural information for: i) structure-based bioactivity data mapping, ii) structure-based identification of scaffold replacement strategies for ligand design, iii) ligand-based target prediction, iv) protein sequence-based binding site identification and ligand repurposing, and v) structure-based pharmacophore comparison for ligand repurposing across protein families. The modular setup of the workflows and the use of well-established standards allows the re-use of these protocols and facilitates the design of customized computer-aided drug discovery workflows.

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ER -

3D-e-Chem: Structural Cheminformatics Workflows for Computer-Aided Drug Discovery

Abstract

Keywords

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