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Structure and Ligand Based Virtual Screening and MPO Topological Analysis of Triazolo Thiadiazepine-fused Coumarin Derivatives as Anti-Parkinson Drug Candidates
Parkinson’s disease (PD) is a debilitating condition that can cause locomotor problems in affected patients, such as tremors and body rigidity. PD...
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On the relevance of query definition in the performance of 3D ligand-based virtual screening
Ligand-based virtual screening (LBVS) methods are widely used to explore the vast chemical space in the search of novel compounds resorting to a...
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Cu(I)-thioether coordination complexes based on a chiral cyclic β-amino acid ligand
Coordination complexes, particularly metalloproteins, highlight the significance of metal-sulfur bonds in biological processes. Their unique...
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Orientation of ruthenium dipyridophenazine complexes in liposome membranes sensitively controlled by ligand substituents
Liposomes can be deformed to ellipsoidal shapes in a shear flow, and the orientation of chromophores in the lipid bilayers can then be examined with...
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Nanometre-resolved observation of electrochemical microenvironment formation at the nanoparticle–ligand interface
The dynamic response of surface ligands on nanoparticles (NPs) to external stimuli critically determines the functionality of NP–ligand systems. For...
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Complex peptide macrocycle optimization: combining NMR restraints with conformational analysis to guide structure-based and ligand-based design
Systematic optimization of large macrocyclic peptide ligands is a serious challenge. Here, we describe an approach for lead-optimization using the...
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PSnpBind-ML: predicting the effect of binding site mutations on protein-ligand binding affinity
Protein mutations, especially those which occur in the binding site, play an important role in inter-individual drug response and may alter binding...
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User-centric design of a 3D search interface for protein-ligand complexes
In this work, we present the frontend of GeoMine and showcase its application, focusing on the new features of its latest version. GeoMine is a...
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VSFlow: an open-source ligand-based virtual screening tool
Ligand-based virtual screening is a widespread method in modern drug design. It allows for a rapid screening of large compound databases in order to...
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Nanocluster superstructures assembled via surface ligand switching at high temperature
Superstructures with nanoscale building blocks, when coupled with precise control of the constituent units, open opportunities in rationally...
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Discovery of Aptamers Against Cell Surface Markers Using Ligand-Guided Selection
Oligonucleotide ligands (DNA, RNA, or XNA), also known as aptamers, are selected against various target molecules using an iterative, evolutionary...
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The Structural Features of MlaD Illuminate its Unique Ligand-Transporting Mechanism and Ancestry
The membrane-associated solute-binding protein (SBP) MlaD of the maintenance of lipid asymmetry (Mla) system has been reported to help the transport...
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One class classification for the detection of β2 adrenergic receptor agonists using single-ligand dynamic interaction data
G protein-coupled receptors are involved in many biological processes, relaying the extracellular signal inside the cell. Signaling is regulated by...
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Ligand-based 3D pharmacophore modeling, virtual screening, and molecular dynamic simulation of potential smoothened inhibitors
ContextThe Hedgehog (Hh) signaling pathway is a crucial regulator of various cellular processes. Dysregulated activation of the Smoothened (SMO)...
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Structures of the ADGRG2–Gs complex in apo and ligand-bound forms
Adhesion G protein-coupled receptors are elusive in terms of their structural information and ligands. Here, we solved the cryogenic-electron...
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Identifying and characterising promising small molecule inhibitors of kinesin spindle protein using ligand-based virtual screening, molecular docking, molecular dynamics and MM‑GBSA calculations
The kinesin spindle protein (Eg5) is a mitotic protein that plays an essential role in the formation of the bipolar spindles during the mitotic...
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Exploring the dual capabilities of BNQDs: a comprehensive study on enhancing photoelectric performance and photoluminescence via ligand functionalization
ContextBoron nitride quantum dots (BNQDs) are emerging as promising multifunctional nanomaterials for renewable energy and optoelectronics owing to...
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Ligand-based and structure-based studies to develop predictive models for SARS-CoV-2 main protease inhibitors through the 3d-qsar.com portal
The main protease (M pro ) of SARS-Cov-2 is the essential enzyme for maturation of functional proteins implicated in viral replication and...
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In situ vertical alignment of 2D MoS2 layers on GO film: enhanced electrochemical properties for PD-L1 sensing
There is an urgent need for a flexible and simple programmed cell death ligand 1 (PD-L1) dynamic measurement method enabling real-time monitoring of...
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Structural basis of efficacy-driven ligand selectivity at GPCRs
A drug’s selectivity for target receptors is essential to its therapeutic utility, but achieving selectivity between similar receptors is...
