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three-dimensional compound structure library  (Chembridge)

 
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    Structured Review

    Chembridge three-dimensional compound structure library
    Three Dimensional Compound Structure Library, supplied by Chembridge, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/three-dimensional+structures/3d+structure+library/pm40333783-2-31-34
    Average 90 stars, based on 1 article reviews
    three-dimensional compound structure library - by Bioz Stars, 2026-09
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    other:

    Article Title: Discovery of Novel Antimicrobial-Active Compounds and Their Analogues by In Silico Small Chemical Screening Targeting Staphylococcus aureus MurB
    Article Snippet: We used a 3D structure library of compounds (154,118 compounds: ChemBridge [ ]) obtained from the Ressource Parisienne en Bioinformatioque Structurale (RPBS) database for the SBDS.

    Article Title: Recent Advances in Epidermal Growth Factor Receptor Inhibitors (EGFRIs) and their Role in the Treatment of Cancer: A Review.
    Article Snippet: Tyrosine kinases are known to play a role in tumour growth and proliferation, and they have become common drug targets.. Tyrosine kinase inhibitors (TKIs) prohibit associated kinases from phosphorylating tyrosine residues in their substrates, preventing downstream signaling pathways from being activated.. Multiple robust and well-tolerated TKIs targeting single or multiple targets, including EGFR, ALK, ROS1, HER2, NTRK, VEGFR, RET, MET, MEK, FGFR, PDGFR, and KIT, have been developed over the last two decades, contributing to our understanding of precision cancer medicine based on a patient's genetic alteration profile.

    Article Title: Discovery of Antibacterial Compounds with Potential Multi-Pharmacology against Staphylococcus Mur ligase Family Members by In Silico Structure-Based Drug Screening
    Article Snippet: The compound structure data library used in this study is the ChemBridge 3D structure library of 154,118 compounds obtained from the RPBS (Ressource Parisienne en Bioinformatioque Structurale) web-based database.

    In Silico:

    Article Title: Identification of Novel Compounds That Bind to the HGF β-Chain In Silico, Verification by Molecular Mechanics and Quantum Mechanics, and Validation of Their HGF Inhibitory Activity In Vitro.
    Article Snippet: .. To identify compounds that bind to the β-chain of HGF and inhibit signaling through HGF and its receptor Met interaction, we performed a hierarchical in silico drug screen using a three-dimensional compound structure library (Chembridge, 154,118 compounds). ..

    Article Title: Identification of Novel Compounds That Bind to the HGF β-Chain In Silico, Verification by Molecular Mechanics and Quantum Mechanics, and Validation of Their HGF Inhibitory Activity In Vitro
    Article Snippet: .. The 3D structure library (Chembridge, 154,118 compounds) used in the in silico SBDS was obtained from the web database of Ressource Parisienne en BioInformatique Structurale (RPBS) [ ]. ..

    Article Title: Identification of Novel Compounds That Bind to the HGF β-Chain In Silico, Verification by Molecular Mechanics and Quantum Mechanics, and Validation of Their HGF Inhibitory Activity In Vitro.
    Article Snippet: .. The 3D structure library (Chembridge, 154,118 compounds) used in the in silico SBDS was obtained from the web database of Ressource Parisienne en BioInformatique Structurale (RPBS) [23]. ..

    Binding Assay:

    Article Title: Discovery of Antibacterial Compounds with Potential Multi-Pharmacology against Staphylococcus Mur ligase Family Members by In Silico Structure-Based Drug Screening
    Article Snippet: .. Docking simulations were performed using Auto Dock Vina 1.1.2 (ADV) [ ] for the substrate binding sites of MurE with the compound 3D structure library (154,118 compounds) from ChemBridge. ..

    Generated:

    Article Title: Identification of Novel Influenza Polymerase PB2 Inhibitors Using a Cascade Docking Virtual Screening Approach
    Article Snippet: .. LibDock was used to perform high-throughput screening of the generated ChemBridge compound 3D conformation library with the fast search model. ..



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    Prediction of protein stability at the alteration site through interaction formation. ( a ) Visualization performed <t>using</t> <t>BIOVIA</t> Discovery Studio Visualizer (Version 21.1.0.20298). ( b ) Conservation of amino acids around position 86 in <t>PIGT</t> across different species. An asterisk ( * ) indicates p.86 of the PIGT protein in each species. ( c , d ) Comparison of intramolecular bonds at the alteration site in wild-type (wt) and mutant (mt) proteins, computed and visualized via DDMut.
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    Image Search Results


    Coumarin derivatives can selectively bind to RNA G 1 × 0 bulges: ( A ) RNA structures of the 1 × 0 RNA bulges used for in vitro binding profiling using the FP assay. N = G , A , U , or C (RNA1-4). ( B ) Heatmap profile of the ΔmP = (FP RNA-ligand – FP ligand ) × 1000 for RNA binders in the presence of [RNA] = 5 or 1 μM (red = high polarization, blue = low polarization). ( C ) ΔmP of RNA-ligand complex for RNA ligands at 5 μM. Each data point represents a measurement of a ligand in the 69-compound collection. **** indicates P < .0001. ( D ) Dose-response curves for compounds (SMSM6, C30) selectively binding to the bulged G RNA (RNA1) compared to an 11-nucleotide GA-rich sequence that would form a double loop-like RNA structure measured by the FP assay.

    Journal: Nucleic Acids Research

    Article Title: Mechanistic studies of small molecule ligands selective to RNA single G bulges

    doi: 10.1093/nar/gkaf559

    Figure Lengend Snippet: Coumarin derivatives can selectively bind to RNA G 1 × 0 bulges: ( A ) RNA structures of the 1 × 0 RNA bulges used for in vitro binding profiling using the FP assay. N = G , A , U , or C (RNA1-4). ( B ) Heatmap profile of the ΔmP = (FP RNA-ligand – FP ligand ) × 1000 for RNA binders in the presence of [RNA] = 5 or 1 μM (red = high polarization, blue = low polarization). ( C ) ΔmP of RNA-ligand complex for RNA ligands at 5 μM. Each data point represents a measurement of a ligand in the 69-compound collection. **** indicates P < .0001. ( D ) Dose-response curves for compounds (SMSM6, C30) selectively binding to the bulged G RNA (RNA1) compared to an 11-nucleotide GA-rich sequence that would form a double loop-like RNA structure measured by the FP assay.

    Article Snippet: 3-Dimensional (3D) structures of three coumarin derivatives (C30, C30-Me, and SMSM64) were prepared using ChemBio Tool.

    Techniques: In Vitro, Binding Assay, FP Assay, Sequencing

    Protonation state of the ligands contributes to the RNA binding. ( A ) Equilibria for the protonation reactions of four coumarin derivatives. ( B ) Protonation energy (relative to C29) was calculated using DFT with B3LYP 6–31G(d) basis set. ( C ) Observed binding affinity of the four compounds.

    Journal: Nucleic Acids Research

    Article Title: Mechanistic studies of small molecule ligands selective to RNA single G bulges

    doi: 10.1093/nar/gkaf559

    Figure Lengend Snippet: Protonation state of the ligands contributes to the RNA binding. ( A ) Equilibria for the protonation reactions of four coumarin derivatives. ( B ) Protonation energy (relative to C29) was calculated using DFT with B3LYP 6–31G(d) basis set. ( C ) Observed binding affinity of the four compounds.

    Article Snippet: 3-Dimensional (3D) structures of three coumarin derivatives (C30, C30-Me, and SMSM64) were prepared using ChemBio Tool.

    Techniques: RNA Binding Assay, Binding Assay

    Prediction of protein stability at the alteration site through interaction formation. ( a ) Visualization performed using BIOVIA Discovery Studio Visualizer (Version 21.1.0.20298). ( b ) Conservation of amino acids around position 86 in PIGT across different species. An asterisk ( * ) indicates p.86 of the PIGT protein in each species. ( c , d ) Comparison of intramolecular bonds at the alteration site in wild-type (wt) and mutant (mt) proteins, computed and visualized via DDMut.

    Journal: International Journal of Molecular Sciences

    Article Title: A Novel Homozygous Missense Variant of PIGT Related to Multiple Congenital Anomalies-Hypotonia Seizures Syndrome 3 with Elevated of Serum ALP Level in a Thai Newborn Patient

    doi: 10.3390/ijms26062790

    Figure Lengend Snippet: Prediction of protein stability at the alteration site through interaction formation. ( a ) Visualization performed using BIOVIA Discovery Studio Visualizer (Version 21.1.0.20298). ( b ) Conservation of amino acids around position 86 in PIGT across different species. An asterisk ( * ) indicates p.86 of the PIGT protein in each species. ( c , d ) Comparison of intramolecular bonds at the alteration site in wild-type (wt) and mutant (mt) proteins, computed and visualized via DDMut.

    Article Snippet: The three-dimensional structures of both the wild-type and mutant PIGT (PDB: 7wld) were visualized using BIOVIA software [ ].

    Techniques: Comparison, Mutagenesis