Articles with "ensemble docking" as a keyword



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Prediction of N-Methyl-D-Aspartate Receptor GluN1-Ligand Binding Affinity by a Novel SVM-Pose/SVM-Score Combinatorial Ensemble Docking Scheme

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Published in 2017 at "Scientific Reports"

DOI: 10.1038/srep40053

Abstract: The glycine-binding site of the N-methyl-D-aspartate receptor (NMDAR) subunit GluN1 is a potential pharmacological target for neurodegenerative disorders. A novel combinatorial ensemble docking scheme using ligand and protein conformation ensembles and customized support vector machine… read more here.

Keywords: svm; docking scheme; ensemble docking; scheme ... See more keywords
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Extended-ensemble docking to probe dynamic variation of ligand binding sites during large-scale structural changes of proteins

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Published in 2022 at "Chemical Science"

DOI: 10.1039/d2sc00841f

Abstract: Proteins can sample a broad landscape as they undergo conformational transition between different functional states. At the same time, as key players in almost all cellular processes, proteins are important drug targets. Considering the different… read more here.

Keywords: ensemble docking; extended ensemble; affinity; large scale ... See more keywords
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A selective method for optimizing ensemble docking-based experiments on an InhA Fully-Flexible receptor model

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Published in 2018 at "BMC Bioinformatics"

DOI: 10.1186/s12859-018-2222-2

Abstract: BackgroundIn the rational drug design process, an ensemble of conformations obtained from a molecular dynamics simulation plays a crucial role in docking experiments. Some studies have found that Fully-Flexible Receptor (FFR) models predict realistic binding… read more here.

Keywords: fully flexible; ensemble docking; method; model ... See more keywords
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Identification of Catechins’ Binding Sites in Monomeric Aβ42 through Ensemble Docking and MD Simulations

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Published in 2022 at "International Journal of Molecular Sciences"

DOI: 10.3390/ijms24098161

Abstract: The assembly of the Amyloid-β peptide (Aβ) into toxic oligomers and fibrils is associated with Alzheimer’s disease and dementia. Therefore, disrupting amyloid assembly by direct targeting of the Aβ monomeric form with small molecules or… read more here.

Keywords: ensemble docking; identification catechins; monomeric ensemble; catechins binding ... See more keywords