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AUTODOCK GmbH molecular docking analyses autodock vina
Molecular Docking Analyses Autodock Vina, supplied by AUTODOCK GmbH, 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/docking+analyses/autodock+vina/pmc12213726-99-5-5
Average 90 stars, based on 1 article reviews
molecular docking analyses autodock vina - by Bioz Stars, 2026-10
90/100 stars

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Software:

Article Title: Aged garlic extract major constituent S-1-propenyl-l-cysteine inhibits proinflammatory mRNA expression in bronchial epithelial IB3-1 cells exposed to the BNT162b2 vaccine
Article Snippet: .. A blind docking simulation was performed on the entire TLR4 dimer surface using the AutoDock Vina software (ver. ..

Article Title: A phytotherapeutic approach to hinder the resistance against clindamycin by MRSA: in vitro and in silico studies.
Article Snippet: .. 2D NMR determined the binding residues of the binding site. the x-ray structure of S. aureus agra lyttR domain was downloaded from RcsB Protein Data Bank, rcsb.org (PDB: 4G4K with a resolution of 1.5Å). autodock Vina 1.5.7 software was used to dock trans-cinnamaldehyde to the binding site of agra using default parameters. autodock Vina uses the Broyden-Fletcher-Goldfarb-shanno method, which is a local minimization algorithm, to search for the binding mode. it generates many random conformations for the ligand, and it then uses a genetic algorithm to find a bound conformer with the lowest binding energy using a series of steps. it considers the position and orientation of the ligand, as well as the torsions for the active rotatable bonds in the ligand [79, 80]. the binding site of agra was detected according to the NMR data presented by leonard et al., where the shallow binding site is located between Val232 and lys236 [65]. ..

other:

Article Title: Targeting cholinergic dysfunction in Alzheimer’s disease: Development of next-generation galantamine derivatives
Article Snippet: To elucidate the binding modes and estimate the binding affinities of GNT analogs with the AChE receptor, molecular docking simulations were performed using AutoDock version 1.5.2.4 with AutoDock Tools.

Article Title: A Putative Binding Model of Nitazene Derivatives at the µ -Opioid Receptor
Article Snippet: Both μ OR and fentanyl were prepared using Autodock-Tools.

Article Title: MOF nanozyme mediated bacterial metabolic regulation to intervene MRSA antibiotic tolerance for enhanced antimicrobial efficacy
Article Snippet: The rising prevalence of multidrug-resistant pathogens poses a significant threat to human health, with methicillin-resistant Staphylococcus aureus (MRSA) being particularly concerning.. Although vancomycin has long been the standard treatment for MRSA, its repeated use can lead to antibiotic tolerance and resistance.. The accumulation of bacterial metabolites contributes to this tolerance, suggesting that modulation of bacterial metabolic pathways may provide a novel solution.

Article Title: Ultrasound-activated carrier-free nanoprodrugs enhanced universality and efficiency of solid tumor-targeting chemotherapy
Article Snippet: The binding energy between two molecules (PBSN38 and OS) was calculated through AutoDock 4.2 software [ ].

Article Title: Identification, characterization, and application of an NADPH-dependent carbonyl reductase in Saccharomyces cerevisiae AS2.346 for improving production of (13R,17S)-ethyl secol
Article Snippet: The molecular docking was performed by AutoDock Vina V1.1.2, using the docking conformation with the lowest energy.

Article Title: Sophormodines D−K, matrine-type alkaloids with anti-HBV activity from the Seeds of Tibetan Medicine Sophora moorcroftiana
Article Snippet: Eight previously undescribed matrine-type alkaloids sophormodines D− K (1–8), along with twenty-nine known ones (9–37), were isolated and fully elucidated from the seeds of Tibetan medicine Sophora moorcroftiana.. Their structures with absolute configurations were elucidated by detailed interpretation of NMR spectroscopy, MS, and ECD calculations.. Anti-HBV antigen secretion activities and anti-HBV DNA replication activity were assayed in vitro using HepG2.2.15 cells by ELISA and Q-PCR, respectively.

Nuclear Magnetic Resonance:

Article Title: A phytotherapeutic approach to hinder the resistance against clindamycin by MRSA: in vitro and in silico studies.
Article Snippet: .. 2D NMR determined the binding residues of the binding site. the x-ray structure of S. aureus agra lyttR domain was downloaded from RcsB Protein Data Bank, rcsb.org (PDB: 4G4K with a resolution of 1.5Å). autodock Vina 1.5.7 software was used to dock trans-cinnamaldehyde to the binding site of agra using default parameters. autodock Vina uses the Broyden-Fletcher-Goldfarb-shanno method, which is a local minimization algorithm, to search for the binding mode. it generates many random conformations for the ligand, and it then uses a genetic algorithm to find a bound conformer with the lowest binding energy using a series of steps. it considers the position and orientation of the ligand, as well as the torsions for the active rotatable bonds in the ligand [79, 80]. the binding site of agra was detected according to the NMR data presented by leonard et al., where the shallow binding site is located between Val232 and lys236 [65]. ..

Binding Assay:

Article Title: A phytotherapeutic approach to hinder the resistance against clindamycin by MRSA: in vitro and in silico studies.
Article Snippet: .. 2D NMR determined the binding residues of the binding site. the x-ray structure of S. aureus agra lyttR domain was downloaded from RcsB Protein Data Bank, rcsb.org (PDB: 4G4K with a resolution of 1.5Å). autodock Vina 1.5.7 software was used to dock trans-cinnamaldehyde to the binding site of agra using default parameters. autodock Vina uses the Broyden-Fletcher-Goldfarb-shanno method, which is a local minimization algorithm, to search for the binding mode. it generates many random conformations for the ligand, and it then uses a genetic algorithm to find a bound conformer with the lowest binding energy using a series of steps. it considers the position and orientation of the ligand, as well as the torsions for the active rotatable bonds in the ligand [79, 80]. the binding site of agra was detected according to the NMR data presented by leonard et al., where the shallow binding site is located between Val232 and lys236 [65]. ..



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