Induced fit docking

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Induced Fit Docking is a computational modeling tool that simulates the dynamic interaction between a ligand and a protein. It accounts for conformational changes in both the ligand and the protein during the binding process, providing a more accurate representation of the interactions compared to rigid docking methods.

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Lab products found in correlation

Ligprep, by Schrödinger (3 mentions) Protein preparation wizard, by Schrödinger (1 mentions) Protein preparation wizard panel, by Schrödinger (1 mentions)

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Induced Fit Docking module (5 citations) Induced Fit Docking protocol (3 citations) Induced fit docking program (2 citations)

5 protocols using induced fit docking

Computational Modeling of 4HD/XAG Binding

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The computer modeling of 4HD or XAG with BRAFV600E and PI3-K was performed using the Schrödinger Suite 2015 software programs (18 ). The BRAFV600E and PI3-K crystal structures were prepared under the standard procedure of the Protein Preparation Wizard in Schrödinger Suite 2015. Hydrogen atoms were added consistent with a pH of 7 and all water molecules were removed. The ATP binding site-based receptor grid was generated for docking. 4HD or XAG was prepared using the LigPrep program (Schrödinger) and the lowest energy conformations for docking were determined by using default parameters under the extra precision (XP) mode and the program Glide. The protein-ligand docking analysis was conducted using the induced fit docking program of Schrödinger, which can provide ligand binding flexibility with binding pocket residues.

Zhang T., Wang Q., Fredimoses M., Gao G., Wang K., Chen H., Wang T., Oi N., Zykova T.A., Reddy K., Yao K., Ma W., Chang X., Lee M.H., Rathore M.G., Bode A.M., Ashida H, & Dong Z. (2018). The Ashitaba (Angelica keiskei) chalcones 4-hydroxyderricin and xanthoangelol suppress melanomagenesis by targeting BRAF and PI3-K. Cancer prevention research (Philadelphia, Pa.), 11(10), 607-620.

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Homology Modeling and Docking of CDK11A

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A homology model of CDK11A kinase domain from V423 to F723 was built based on a CDK2 cocrystal structure (PDB code: 1GIJ chain A) using Prime (Schrodinger suite 2019–4 Release). Default protocol and parameters were used, and the cocrystal ligand in CDK2 was retained in the model building so that the ATP site is likely compatible with other ligand docking. The initial homology model was subject to Prime loop refinement. InducedFit docking from Schrodinger suite was used to docking inhibitors (e.g. JWD-047 and ZNL-05-044). The binding site was defined by the ligand retained in the homology model and default parameters were applied with the constraint of two hinge hydrogen bonds with the backbone carbonyl and amine of V507. Ligands were prepared by ligprep (Schrodinger suite) prior to docking.

Li Z., Ishida R., Liu Y., Wang J., Li Y., Gao Y., Jiang J., Che J., Sheltzer J.M., Robers M.B., Zhang T., Westover K.D., Nabet B, & Gray N.S. (2022). Synthesis and Structure–Activity Relationships of Cyclin-Dependent Kinase 11 Inhibitors Based on a Diaminothiazole Scaffold. European journal of medicinal chemistry, 238, 114433.

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Structural Analysis of Nur77-3NB Complex

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The crystal structure of the Nur77-3NB complex utilized in this study was sourced from the PDB database and had a resolution of 2.18 Å (PDB ID: 4WHG). The protein structure was prepared using the default parameters of the Protein Preparation Wizard panel of the Schrödinger Suite (version 2021-2). The preparation steps involved adding hydrogen atoms, deleting water molecules, adding charges, removing crystal solvents, completing missing residue side chains and loops utilizing the Prime module (Jacobson et al., 2002 (link); Jacobson et al., 2004 (link)), optimizing hydrogen bond networks, and performing restrained energy minimization of the protein structure utilizing the OPLS4 force field (Lu et al., 2021 (link)). The small molecule ligand was prepared by subjecting it to the LigPrep (LigPrep, Schrödinger, LLC, New York, NY, 2021) tool of Schrödinger with default parameters, thereby converting its 2D structure to a 3D structure. Thereafter, molecular docking was conducted using the Induced Fit Docking panel (Induced Fit Docking, Schrödinger, LLC, New York, NY, 2021) of Schrödinger. The native ligand 3NB served as the docking box center, and default parameters were applied under the standard protocol. The top-ranking docking conformation was selected based on the binding mode and docking score for subsequent MD simulations.

Chang C., He F., Ao M., Chen J., Yu T., Li W., Li B., Fang M, & Yang T. (2023). Inhibition of Nur77 expression and translocation by compound B6 reduces ER stress and alleviates cigarette smoke-induced inflammation and injury in bronchial epithelial cells. Frontiers in Pharmacology, 14, 1200110.

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Modeling and Docking of Rh7 Transmembrane Domains

Cited 1 time

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We modeled the 3D structure of the Rh7 transmembrane domains by GPCR-I-TASSER, a fragment-based method in which fragments are excised from GPCR template structures and reassembled based on threading alignments [36 (link)]. The crystal structures that mostly contributed to the modeling were the human (PDB:4ZWJ), bovine (PDB:1GZM), and squid (PDB:2Z73) rhodopsins. We predicted ligand binding modes of aristolochic acid and piperonyl acetate to Rh7 using Induced Fit Docking (Schrödinger Release 2018–1, Induced Fit Docking protocol; Glide, Schrödinger, LLC, New York, NY, 2018; Prime, Schrödinger, LLC, New York, NY, 2018). The grid box was centroid to the retinal coordinates in bovine rhodopsin. The docking was performed using the Standard Precision (SP) mode of Glide (Table S2).

Leung N.Y., Thakur D.P., Gurav A.S., Kim S.H., Di Pizio A., Niv M.Y, & Montell C. (2020). Functions of opsins in Drosophila taste. Current biology : CB, 30(8), 1367-1379.e6.

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Induced-Fit Docking for Ligand-Receptor Analysis

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The proteins and ligands were prepared in Maestro, as mentioned in the method above, followed by the induced-fit docking (Induced Fit Docking, Schrödinger2018-1, LLC, New York, NY, USA). The prepared ligands file was imported, and the standard protocol was selected, with the OPLS3 as the force field due to its wider parameter range and significant improvements. The native ligand was selected as centroid, to generate a box of automatically generated size. We ignored constraints and, in the Ligand options, we ticked “Sample ring conformations”, with 2.5 kcal/mol as the energy window. In Prime Refinement, we refined residues within 5.0 Å of ligand poses; with Optimize, “Side chains” was ticked; and in Glide Redocking, we choose “SP docking” for the precision. We redocked the structures within 30.0 kcal/mol of the best structure, and within the top 20 structures overal1. Other parameters were maintained at the default. The docking results were displayed in Maestro (Maestro v128117, Schrödinger 2018-1, New York, NY, USA), and their ligand-receptor interaction was analyzed, including hydrogen bonds (within 3.5 Å), halogen bonds (within 3.5 Å), salt bridges (within 5.0 Å), pi-pi stacking (within 5.5 Å), and pi-action (within 6.6 Å).

Liu N., Yang Z., Liu Y., Dang X., Zhang Q., Wang J., Liu X., Zhang J, & Pan X. (2023). Identification of a Putative SARS-CoV-2 Main Protease Inhibitor through In Silico Screening of Self-Designed Molecular Library. International Journal of Molecular Sciences, 24(14), 11390.

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