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docking software openeye fred  (OpenEye Scientific Software Inc)

 
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    OpenEye Scientific Software Inc docking software openeye fred
    Docking Software Openeye Fred, supplied by OpenEye Scientific Software Inc, 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+software+openeye+fred/docking+software+openeye+fred/pm38768836-170-20-20
    Average 90 stars, based on 1 article reviews
    docking software openeye fred - by Bioz Stars, 2026-09
    90/100 stars

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    other:

    Article Title: Identification of ligands binding to MB327-PAM-1, a binding pocket relevant for resensitization of nAChRs.
    Article Snippet: There, we first docked a ZINC20 (Irwin et al., 2020) lead-like library (3,434,621 compounds) into the human muscle-type nAChR using OpenEye FRED (OEDOCKING 4.0.0.0, 2020; McGann, 2012, 2011).

    Article Title: Molecular Simulation of αvβ6 Integrin Inhibitors.
    Article Snippet: Docking was performed using OpenEye FRED.28 Compounds were docked using the high resolution setting with rotational and translational step sizes of 1 Å. Chemgauss4 was used to score the poses.

    Article Title: Alchemical Free Energy Methods Applied to Complexes of the First Bromodomain of BRD4
    Article Snippet: Docking was performed using OpenEye FRED using the high resolution setting with rotational and translational step sizes of 1 Å.

    Software:

    Article Title: Relative assessment of different statistical instruments and measures for the prediction of promising outcomes using docking, virtual screening and ADMET analysis against HIV-RT.
    Article Snippet: Reverse transcriptase is the most therapeutic target for the discovery of novel, potent, and non-toxic new anti-retroviral drugs.. In the present work, various docking software such as Sybyl Surflex-Dock, OpenEye FRED, and Hermes GOLD were evaluated for their efficiency to reproduce known cognate inhibitors’ conformations.. Three metrics were used and compared to assess the performance of the applied scoring functions, i.e. enrichment factor, receiver operating characteristic (ROC) curves, and Bedroc analysis.



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    CID 1067700 docked in the nucleotide binding site of Rab7 in the (a–b) GDP-bound (PDB 1VG9) and (c–d) (GNP)- bound (PDB 1VG8) conformations. <t>Molecular</t> <t>docking</t> carried out using <t>Fred</t> docking <t>software.</t> Both GTP or GDP and CID 1067700 are shown simultaneously docked in the pocket for purposes of comparing their orientations in the pocket. Interaction maps for (e–f) Rab7-GDP vs. CID 1067700 and (g–h) Rab7-GNP vs. CID 1067700 illustrate differences in number and sites of interaction.
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    CID 1067700 docked in the nucleotide binding site of Rab7 in the (a–b) GDP-bound (PDB 1VG9) and (c–d) (GNP)- bound (PDB 1VG8) conformations. Molecular docking carried out using Fred docking software. Both GTP or GDP and CID 1067700 are shown simultaneously docked in the pocket for purposes of comparing their orientations in the pocket. Interaction maps for (e–f) Rab7-GDP vs. CID 1067700 and (g–h) Rab7-GNP vs. CID 1067700 illustrate differences in number and sites of interaction.

    Journal: ACS chemical biology

    Article Title: A Competitive Nucleotide Binding Inhibitor: In vitro Characterization of Rab7 GTPase Inhibition

    doi: 10.1021/cb3001099

    Figure Lengend Snippet: CID 1067700 docked in the nucleotide binding site of Rab7 in the (a–b) GDP-bound (PDB 1VG9) and (c–d) (GNP)- bound (PDB 1VG8) conformations. Molecular docking carried out using Fred docking software. Both GTP or GDP and CID 1067700 are shown simultaneously docked in the pocket for purposes of comparing their orientations in the pocket. Interaction maps for (e–f) Rab7-GDP vs. CID 1067700 and (g–h) Rab7-GNP vs. CID 1067700 illustrate differences in number and sites of interaction.

    Article Snippet: Molecular docking of CID 1067700 on Rab7wt GDP and GTP bound crystal structures shows optimal binding to the nucleotide binding pocket of the GTP-conformer The molecular docking of CID 1067700 to the nucleotide binding site of Rab7 as predicted by the experimental data was examined using molecular docking OpenEye Fred docking software ( ).

    Techniques: Binding Assay, Software