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

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
, C. de Graaf

^*Corresponding author for this work

Research output: Contribution to Journal › Article › Academic › peer-review

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

Funding

Netherlands eScience Center/NWO (3D-e-Chem, grant 027.014.201). M.V., R.L., G.V., I.J.P.d.E., A.J.K., and C.d.G. participate in the COST Action CM1207 (GLISTEN). M.V., I.J.P.d.E, R.L., and C.d.G. participate in the GPCR Consortium (gpcrconsortium.org).

Funders	Funder number
???publication-publication-funding-organisation-not-added???	027.014.201
European Cooperation in Science and Technology	CM1207

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10.1021/acs.jcim.6b00686

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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).",

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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.

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

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