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).
authors.affiliation: Centre for Molecular and Biomolecular Informatics (CMBI), Radboudumc , 6525 GA Nijmegen, The Netherlands.|BioAxis Research , Pivot Park, 5349 AE Oss, The Netherlands.
authors.forename: Ross
authors.identifier: 0000-0003-3404-6456
authors.initials: R
authors.lastname: McGuire
authors.affiliation: Netherlands eScience Center , 1098 XG Amsterdam, The Netherlands.
authors.forename: Stefan
authors.identifier: 0000-0002-5821-2060
authors.initials: S
authors.lastname: Verhoeven
authors.affiliation: Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam , 1081 HZ Amsterdam, The Netherlands.
authors.forename: Márton
authors.identifier: 0000-0003-1486-0063
authors.initials: M
authors.lastname: Vass
authors.affiliation: Centre for Molecular and Biomolecular Informatics (CMBI), Radboudumc , 6525 GA Nijmegen, The Netherlands.
authors.forename: Gerrit
authors.initials: G
authors.lastname: Vriend
authors.affiliation: Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam , 1081 HZ Amsterdam, The Netherlands.
authors.forename: Iwan J P
authors.initials: IJ
authors.lastname: de Esch
authors.affiliation: Centre for Molecular and Biomolecular Informatics (CMBI), Radboudumc , 6525 GA Nijmegen, The Netherlands.|Netherlands eScience Center , 1098 XG Amsterdam, The Netherlands.
authors.forename: Scott J
authors.initials: SJ
authors.lastname: Lusher
authors.affiliation: Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam , 1081 HZ Amsterdam, The Netherlands.
authors.forename: Rob
authors.initials: R
authors.lastname: Leurs
authors.affiliation: Netherlands eScience Center , 1098 XG Amsterdam, The Netherlands.
authors.forename: Lars
authors.initials: L
authors.lastname: Ridder
authors.affiliation: Centre for Molecular and Biomolecular Informatics (CMBI), Radboudumc , 6525 GA Nijmegen, The Netherlands.|Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam , 1081 HZ Amsterdam, The Netherlands.
authors.forename: Albert J
authors.identifier: 0000-0001-5514-6021
authors.initials: AJ
authors.lastname: Kooistra
authors.affiliation: Centre for Molecular and Biomolecular Informatics (CMBI), Radboudumc , 6525 GA Nijmegen, The Netherlands.
authors.forename: Tina
authors.initials: T
authors.lastname: Ritschel
authors.affiliation: Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam , 1081 HZ Amsterdam, The Netherlands.
authors.forename: Chris
authors.identifier: 0000-0002-1226-2150
authors.initials: C
authors.lastname: de Graaf
mesh_terms: D015195:Drug Design; D048088:Informatics / Q000379:methods*; D008024:Ligands; D011494:Protein Kinases / Q000378:metabolism; D043562:Receptors, G-Protein-Coupled / Q000378:metabolism; D012984:Software; D014584:User-Computer Interface
chemical_list: D008024:Ligands; D043562:Receptors, G-Protein-Coupled; D011494:Protein Kinases