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: Scientific - peer-reviewArticle

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).

Original languageEnglish
Pages (from-to)115-121
Number of pages7
JournalJournal of Chemical Information and Modeling
Volume57
Issue number2
DOIs
StatePublished - 27 Feb 2017

Cite this

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title = "3D-e-Chem-VM: Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine",
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).",
keywords = "Journal Article",
author = "Ross McGuire and Stefan Verhoeven and Márton Vass and Gerrit Vriend and {De Esch}, {Iwan J P} and Lusher, {Scott J.} and Rob Leurs and Lars Ridder and Kooistra, {Albert J.} and Tina Ritschel and {de Graaf}, C.",
year = "2017",
month = "2",
doi = "10.1021/acs.jcim.6b00686",
volume = "57",
pages = "115--121",
journal = "Journal of Chemical Information and Modeling",
issn = "1549-9596",
publisher = "American Chemical Society",
number = "2",

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AU - McGuire,Ross

AU - Verhoeven,Stefan

AU - Vass,Márton

AU - Vriend,Gerrit

AU - De Esch,Iwan J P

AU - Lusher,Scott J.

AU - Leurs,Rob

AU - Ridder,Lars

AU - Kooistra,Albert J.

AU - Ritschel,Tina

AU - de Graaf,C.

PY - 2017/2/27

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