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; Chris De Graaf

doi:10.1021/acs.jcim.6b00686

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, Chris De Graaf

^*Corresponding author for this work

18 Citations (Scopus)

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 language	English
Journal	Journal of Chemical Information and Modeling
Volume	57
Issue number	2
Pages (from-to)	115-121
Number of pages	7
ISSN	1549-9596
DOIs	https://doi.org/10.1021/acs.jcim.6b00686
Publication status	Published - 27 Feb 2017
Externally published	Yes

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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).",

author = "Ross McGuire and Stefan Verhoeven and M{\'a}rton 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}, Chris",

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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, Chris

PY - 2017/2/27

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

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