3D-e-Chem: Structural Cheminformatics Workflows for Computer-Aided Drug Discovery
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3D-e-Chem : Structural Cheminformatics Workflows for Computer-Aided Drug Discovery. / Kooistra, Albert J.; Vass, Márton; McGuire, Ross; Leurs, Rob; de Esch, Iwan J.P.; Vriend, Gert; Verhoeven, Stefan; de Graaf, Chris.
In: ChemMedChem, Vol. 13, No. 6, 20.03.2018, p. 614-626.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - 3D-e-Chem
T2 - Structural Cheminformatics Workflows for Computer-Aided Drug Discovery
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
N2 - 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.
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.
KW - cheminformatics workflows
KW - KNIME
KW - ligand design
KW - ligand repurposing
KW - target prediction
UR - http://www.scopus.com/inward/record.url?scp=85042062175&partnerID=8YFLogxK
U2 - 10.1002/cmdc.201700754
DO - 10.1002/cmdc.201700754
M3 - Journal article
C2 - 29337438
AN - SCOPUS:85042062175
VL - 13
SP - 614
EP - 626
JO - Farmaco
JF - Farmaco
SN - 1860-7179
IS - 6
ER -
ID: 199351335