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 af dette arbejde

18 Citationer (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).

Originalsprog	Engelsk
Tidsskrift	Journal of Chemical Information and Modeling
Vol/bind	57
Udgave nummer	2
Sider (fra-til)	115-121
Antal sider	7
ISSN	1549-9596
DOI	https://doi.org/10.1021/acs.jcim.6b00686
Status	Udgivet - 27 feb. 2017
Udgivet eksternt	Ja

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10.1021/acs.jcim.6b00686Licens: CC BY-NC-ND

http://europepmc.org/articles/pmc5342320?pdf=render

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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).",

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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

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

Abstract

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