3D-e-Chem-VM: Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine

Ross McGuire, Stefan Verhoeven, Márton Vass, Gerrit Vriend, Iwan J P De Esch, Scott J. Lusher, Rob Leurs, Lars Ridder, Albert J. Kooistra, Tina Ritschel, C. de Graaf

Research output: Contribution to journalArticle

Abstract

3D-e-Chem-VM is an open source, freely available Virtual Machine ( http://3d-e-chem.github.io/3D-e-Chem-VM/ ) that integrates cheminformatics and bioinformatics tools for the analysis of protein-ligand interaction data. 3D-e-Chem-VM consists of software libraries, and database and workflow tools that can analyze and combine small molecule and protein structural information in a graphical programming environment. New chemical and biological data analytics tools and workflows have been developed for the efficient exploitation of structural and pharmacological protein-ligand interaction data from proteomewide databases (e.g., ChEMBLdb and PDB), as well as customized information systems focused on, e.g., G protein-coupled receptors (GPCRdb) and protein kinases (KLIFS). The integrated structural cheminformatics research infrastructure compiled in the 3D-e-Chem-VM enables the design of new approaches in virtual ligand screening (Chemdb4VS), ligand-based metabolism prediction (SyGMa), and structure-based protein binding site comparison and bioisosteric replacement for ligand design (KRIPOdb).

LanguageEnglish
Pages115-121
Number of pages7
JournalJournal of Chemical Information and Modeling
Volume57
Issue number2
DOIs
StatePublished - 27 Feb 2017

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Ligands
workflow
infrastructure
Proteins
interaction
G-Protein-Coupled Receptor Kinases
exploitation
information system
programming
Binding sites
Bioinformatics
Metabolism
Protein Kinases
Screening
Information systems
Binding Sites
Virtual machine
Molecules
software

Keywords

  • Journal Article

Cite this

McGuire, Ross ; Verhoeven, Stefan ; Vass, Márton ; Vriend, Gerrit ; De Esch, Iwan J P ; Lusher, Scott J. ; Leurs, Rob ; Ridder, Lars ; Kooistra, Albert J. ; Ritschel, Tina ; de Graaf, C./ 3D-e-Chem-VM : Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine. In: Journal of Chemical Information and Modeling. 2017 ; Vol. 57, No. 2. pp. 115-121
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McGuire, R, Verhoeven, S, Vass, M, Vriend, G, De Esch, IJP, Lusher, SJ, Leurs, R, Ridder, L, Kooistra, AJ, Ritschel, T & de Graaf, C 2017, '3D-e-Chem-VM: Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine' Journal of Chemical Information and Modeling, vol 57, no. 2, pp. 115-121. DOI: 10.1021/acs.jcim.6b00686

3D-e-Chem-VM : Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine. / McGuire, Ross; Verhoeven, Stefan; Vass, Márton; Vriend, Gerrit; De Esch, Iwan J P; Lusher, Scott J.; Leurs, Rob; Ridder, Lars; Kooistra, Albert J.; Ritschel, Tina; de Graaf, C.

In: Journal of Chemical Information and Modeling, Vol. 57, No. 2, 27.02.2017, p. 115-121.

Research output: Contribution to journalArticle

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AU - Ritschel,Tina

AU - de Graaf,C.

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