Journal: Scientific Reports

Article Title: Novel small molecule 11 β -HSD1 inhibitor from the endophytic fungus Penicillium commune

doi: 10.1038/srep26418

Figure Lengend Snippet: ( A ) Compound 3 was observed to occupy the active site with significant scores of ICM docking score and IMC docking mfScore, and adopted a conformation similar to that of known inhibitors. ( B ) Compound 3 had the ability to form key hydrophobic interaction with residues Leu126, Tyr177, Tyr183, and Leu171.

Article Snippet: Using the Molsoft ICM method (ICM-Pro 3.8 molecular docking software), we optimized the geometry of compound 3 and determined the binding site with the lowest-energy and the most favorable orientation of the compound.

Techniques:

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: 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