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AUTODOCK GmbH tools 4.2 open source software
Tools 4.2 Open Source Software, 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/open+source+software+tool/tools+4+2+software/pm37421789-67-23-22
Average 90 stars, based on 1 article reviews
tools 4.2 open source software - by Bioz Stars, 2026-11
90/100 stars

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Article Title: Renalase rs2296545 variant improve hypertension susceptibility by modifying binding affinity to catecholamines in obstructive sleep apnea.
Article Snippet: AutoDock free open-source software was run using the AlphaFold predictions of renalase (Glu37) (PDB ID: 3QJ4, homo sapiens) and renalase (Asp37, the substitution of Glu37 with Asp) from UniProt (http://www.uniprot.org), and a chemical table file (Adrenaline, CID: 5816; Norepinephrine, CID: 439260; Isoproterenol, CID: 3779; Dopamine, CID: 681; Dobutamine, CID: 36811) from PubChem (NCBI), with the following parameters: Lamarckian genetic algorithm runs, 300; the maximum number of energy evaluations, 30 million; and grid map setting points and spacing, 126 × 126 × 126 and 1 Å, respectively, in all dimensions [22].

Article Title: Exploring the antibacterial potential of Clidemia hirta leaf extract against the pathogenicity of Pseudomonas aeruginosa: in vitro and in silico approaches
Article Snippet: The binding affinity during the target protein and ligand interactions with a minimum free binding energy was determined using the software Autodock Vina 4.2 (offline open-source software).

Article Title: Isolation of the Antifungal Compound Alliodorin from the Heartwood of Cordia elaeagnoides A. DC. and the In Silico Analysis of the Laccase
Article Snippet: Molecular docking was performed using the open-source AutoDock 4.2 software [ ].

Article Title: Methionine aminopeptidases: Potential therapeutic target for microsporidia and other microbes.
Article Snippet: THE unique therapeutic activity of methionine aminopeptidases (MetAPs) has been exploited for the development of new drug motifs over the past three decades (Burkey et al., 2018; Cheruvallath et al., 2016; Grocin et al., 2021; Heinrich et al., 2017; Ingber et al., 1990; Kusaka et al., 1991; McBride et al., 2016).. MetAP is a dinuclear metalloprotease that removes an Nterminal methionine residue from nascent proteins and facilitates posttranslational modifications that are essential for the translocation, activation, regulation, and degradation of proteins in eukaryotic cells (Han & Weiss, 2018; Helgren et al., 2016).. MetAP has emerged as an influential drug target, leading to the synthesis of new compounds containing different functional groups for active drug design.

Article Title: Exploring the effective components of honey-processed licorice (Glycyrrhiza uralensis Fisch.) in attenuating Doxorubicin-induced myocardial cytotoxicity by combining network pharmacology and in vitro experiments.
Article Snippet: Ethnopharmacological relevance: Licorice is widely used clinically as one of the most famous traditional Chinese herbs.. Its herb roasted with honey is called honey-processed licorice (HPL).. Modern studies have shown that HPL has a stronger cardioprotective ability compared to raw licorice (RL), however the material basis and mechanism of action of the potential cardioprotection have not been fully elucidated.

Software:

Article Title: Multiomics reveals gut dysbiosis contributes to fatty acid dysmetabolism in early phase of acute myocardial infarction
Article Snippet: .. The molecular docking studies were performed using the open-source software AutoDock Vina (version 1.1.2) ( ) investigate the interactions between AMI-associated long-chain fatty acids (LCFAs) and selected receptors involved in platelet aggregation. .. Adjustments to the grid box allowed the AutoDock algorithm to predict ligand conformations within the receptor binding sites and evaluate them using scoring functions , with the grid spacing set at 1 Å.

Article Title: Probable targets and mechanism of ginsenoside Rg1 for non-alcoholic fatty liver disease: a study integrating network pharmacology, molecular docking, and molecular dynamics simulation.
Article Snippet: Ginsenoside Rg1 (GRg1), a key bioactive component of medicinal herbs, has shown beneficial effects on non-alcoholic fatty liver disease (NAFLD) and numerous other conditions.. Nevertheless, the specific targets that are actively involved and the potential mechanisms underlying NAFLD treatment remain unclear.. This study aimed to elucidate the therapeutic effects and mechanism of GRg1 in alleviating NAFLD using a combined approach of network pharmacology and molecular biology validation.

Article Title: Hybrid Lanthanide Metal–Organic Compounds with Flavonoids: Magneto-Optical Properties and Biological Activity Profiles
Article Snippet: .. Docking simulations were performed using the AutoDock Vina open-source software (version 1.2.5) [ ], through which compound–protein complexes were evaluated based on their energy scores and binding conformations. ..

Binding Assay:

Article Title: Probable targets and mechanism of ginsenoside Rg1 for non-alcoholic fatty liver disease: a study integrating network pharmacology, molecular docking, and molecular dynamics simulation.
Article Snippet: Ginsenoside Rg1 (GRg1), a key bioactive component of medicinal herbs, has shown beneficial effects on non-alcoholic fatty liver disease (NAFLD) and numerous other conditions.. Nevertheless, the specific targets that are actively involved and the potential mechanisms underlying NAFLD treatment remain unclear.. This study aimed to elucidate the therapeutic effects and mechanism of GRg1 in alleviating NAFLD using a combined approach of network pharmacology and molecular biology validation.

Article Title: Hybrid Lanthanide Metal–Organic Compounds with Flavonoids: Magneto-Optical Properties and Biological Activity Profiles
Article Snippet: .. Docking simulations were performed using the AutoDock Vina open-source software (version 1.2.5) [ ], through which compound–protein complexes were evaluated based on their energy scores and binding conformations. ..



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