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

Research output: Contribution to journalJournal articleResearchpeer-review

  • Ross McGuire
  • Stefan Verhoeven
  • Márton Vass
  • Gerrit Vriend
  • Iwan J.P. De Esch
  • Scott J. Lusher
  • Rob Leurs
  • Lars Ridder
  • Kooistra, Albert Jelke
  • Tina Ritschel
  • Chris De Graaf

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 languageEnglish
JournalJournal of Chemical Information and Modeling
Issue number2
Pages (from-to)115-121
Number of pages7
Publication statusPublished - 27 Feb 2017
Externally publishedYes

ID: 199352966