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
European Cooperation in Science and Technology	CM1207

Keywords

Journal Article

Access to Document

10.1021/acs.jcim.6b00686

Persistent URL (handle)

Persistent link

Cite this

@article{34968b166a314fd8b49d152f1c4fc880,

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 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\}, C.",

year = "2017",

month = feb,

day = "27",

doi = "10.1021/acs.jcim.6b00686",

language = "English",

volume = "57",

pages = "115--121",

journal = "Journal of Chemical Information and Modeling",

issn = "1549-9596",

publisher = "American Chemical Society",

number = "2",

}

TY - JOUR

T1 - 3D-e-Chem-VM

T2 - Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine

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

Y1 - 2017/2/27

N2 - 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).

AB - 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).

KW - Journal Article

UR - https://www.scopus.com/pages/publications/85014166934

UR - https://www.scopus.com/inward/citedby.url?scp=85014166934&partnerID=8YFLogxK

U2 - 10.1021/acs.jcim.6b00686

DO - 10.1021/acs.jcim.6b00686

M3 - Article

C2 - 28125221

SN - 1549-9596

VL - 57

SP - 115

EP - 121

JO - Journal of Chemical Information and Modeling

JF - Journal of Chemical Information and Modeling

IS - 2

ER -

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

Abstract

Funding

Keywords

Access to Document

Persistent URL (handle)

Other files and links

Fingerprint

Cite this