Molecular Dynamics-Ensemble Docking and Biophysical Studies for Structure-Based Identification of Non-Amino Acidic Ligands of DDAH-1
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DOI: 10.1021/acs.jcim.4c01150
Abstract: Dimethylarginine dimethylaminohydrolase-1 (DDAH-1) accounts for the catabolism of the endogenous inhibitors of nitric oxide (NO) synthases, namely, ADMA (Nω,Nω-dimethyl-l-arginine) and NMMA (Nω-monomethyl-l-arginine). Inhibition of DDAH-1 may prove a therapeutic benefit in diseases associated with elevated… read more here.
Keywords: ensemble docking; amino acidic; ddah; acidic ligands ... See more keywords
Ensemble Docking for Intrinsically Disordered Proteins
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DOI: 10.1021/acs.jcim.5c00370
Abstract: Intrinsically disordered proteins (IDPs) are implicated in many human diseases and are increasingly being pursued as drug targets. Conventional structure-based drug design methods that rely on well-defined binding sites are, however, largely unsuitable for IDPs.… read more here.
Keywords: docking intrinsically; spectroscopy; intrinsically disordered; ensemble docking ... See more keywords
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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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
Extended-ensemble docking to probe dynamic variation of ligand binding sites during large-scale structural changes of proteins
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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
A selective method for optimizing ensemble docking-based experiments on an InhA Fully-Flexible receptor model
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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
Identification of Catechins’ Binding Sites in Monomeric Aβ42 through Ensemble Docking and MD Simulations
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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
An Ensemble Docking Approach for Analyzing and Designing Aptamer Heterodimers Targeting VEGF165
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DOI: 10.3390/ijms25074066
Abstract: Vascular endothelial growth factor 165 (VEGF165) is a prominent isoform of the VEGF-A protein that plays a crucial role in various angiogenesis-related diseases. It is homodimeric, and each of its monomers is composed of two… read more here.
Keywords: docking approach; ensemble docking; aptamer heterodimer; vegf165 ... See more keywords