Blar i Department of Chemistry på tidsskrift "Journal of Chemical Information and Modeling"
Viser treff 1-7 av 7
-
Conformator: A Novel Method for the Generation of Conformer Ensembles
(Journal article; Peer reviewed, 2019)Computer-aided drug design methods such as docking, pharmacophore searching, 3D database searching, and the creation of 3D-QSAR models need conformational ensembles to handle the flexibility of small molecules. Here, we ... -
DENOPTIM: Software for Computational de Novo Design of Organic and Inorganic Molecules
(Journal article; Peer reviewed, 2019)A general-purpose software package, termed DE Novo OPTimization of In/organic Molecules (DENOPTIM), for de novo design and virtual screening of functional molecules is described. Molecules of any element and kind, including ... -
FAME 3: Predicting the sites of metabolism in synthetic compounds and natural products for phase 1 and phase 2 metabolic enzymes
(Journal article; Peer reviewed, 2019)In this work we present the third generation of FAst MEtabolizer (FAME 3), a collection of extra trees classifiers for the prediction of sites of metabolism (SoMs) in small molecules such as drugs, druglike compounds, ... -
Hit Dexter 2.0: Machine-Learning Models for the Prediction of Frequent Hitters
(Journal article; Peer reviewed, 2019)Assay interference caused by small molecules continues to pose a significant challenge for early drug discovery. A number of rule-based and similarity-based approaches have been derived that allow the flagging of potentially ... -
Investigating Polypharmacology through Targeting Known Human Neutrophil Elastase Inhibitors to Proteinase 3
(Journal article; Peer reviewed, 2024)Using a combination of multisite λ−dynamics (MSλD) together with in vitro IC50 assays, we evaluated the polypharmacological potential of a scaffold currently in clinical trials for inhibition of human neutrophil elastase ... -
Scope of 3D shape-based approaches in predicting the macromolecular targets of structurally complex small molecules including natural products and macrocyclic ligands
(Journal article; Peer reviewed, 2020)A plethora of similarity-based, network-based, machine learning, docking and hybrid approaches for predicting the macromolecular targets of small molecules are available today and recognized as valuable tools for providing ... -
Structure of POPC Lipid Bilayers in OPLS3e Force Field
(Journal article; Peer reviewed, 2022)It is crucial for molecular dynamics simulations of biomembranes that the force field parameters give a realistic model of the membrane behavior. In this study, we examined the OPLS3e force field for the carbon−hydrogen ...