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, Chris
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).
UR - http://www.scopus.com/inward/record.url?scp=85014166934&partnerID=8YFLogxK
U2 - 10.1021/acs.jcim.6b00686
DO - 10.1021/acs.jcim.6b00686
M3 - Journal article
C2 - 28125221
AN - SCOPUS:85014166934
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 -