Glide software

Manufactured by Schrödinger

Sourced in United States

Glide software is a molecular modeling and simulation tool developed by Schrödinger. It is designed to analyze and manipulate molecular structures and their properties.

Automatically generated - may contain errors

Lab products found in correlation

47 protocols using glide software

Molecular Docking for Drug Discovery

Check if the same lab product or an alternative is used in the 5 most similar protocols

Compounds selected by the SVM model were filtered according to ADME criteria (Table 9).
The filtered compounds were docked using the Glide software (Schrodinger, L.LC) on 5RGW and 6WCO. The retrieved binding mode of the consensus prioritized molecules was analysed.
A maximum of 10 generated conformers was set. The binding site was defined using the co-crystallized ligands coordinates. Finally, 200 selected compounds from the commercial libraries were docked in standard precision mode (SP) and the top ranked poses were analysed [43 (link)].

Mekni N., Coronnello C., Langer T., Rosa M.D, & Perricone U. (2021). Support Vector Machine as a Supervised Learning for the Prioritization of Novel Potential SARS-CoV-2 Main Protease Inhibitors. International Journal of Molecular Sciences, 22(14), 7714.

+ Open protocol

+ Expand

Homology Modeling and Docking of h12/15-LOX

Check if the same lab product or an alternative is used in the 5 most similar protocols

A homology model of human reticulocyte 12/15-lipoxygenase protein (Uniprot ID P16050) was built using the software PRIME Version 3.9 (Schrodinger Inc)²⁹ from the rabbit reticulocyte 15-Lipoxygenase-1 crystal structure (PDB ID 2p0m, chain B). The two LOX isozymes have 90% similarity and 81% identity between the two. Both the co-crystallized ligand and the metal ion were retained during the homology modeling. After the model was built, it was subjected to a protein preparation step using Protein Preparation Wizard (Schrodinger Inc). During this step hydrogen atoms were added, proper bond-orders and atom-types were set and the protein structure was minimized such that heavy-atoms were not allowed to move beyond 0.3Å. Iron was treated as ferric ion (Fe³⁺). The inhibitor, 99089, structure was built using Maestro’s Edit/Build panel. We minimized the structure using LigPrep software (Schrodinger Inc), and enumerated plausible protonation states of the inhibitor by applying the empirical pK_a prediction software Epik (Schrodinger Inc). We docked the inhibitor to h12/15-LOX active site using Glide software with the standard-precision docking scoring function (Schrodinger Inc).

Armstrong M.M., Freedman C.J., Jung J.E., Zheng Y., Kalyanaraman C., Jacobson M.P., Simeonov A., Maloney D.J., van Leyen K., Jadhav A, & Holman T.R. (2016). A POTENT AND SELECTIVE INHIBITOR TARGETING HUMAN AND MURINE 12/15-LOX. Bioorganic & medicinal chemistry, 24(6), 1183-1190.

+ Open protocol

+ Expand

Molecular Docking and Binding Energy Estimation

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

Grid boxes were centered at reported binding sites for each target, outer box edges were set to 10Å, thus resulting in a box volume of 10 × 10 × 10 Å³ for all the enzymes. Molecular docking was performed with the Glide software (Schrödinger, LLC, New York, NY, USA, 2020), using the standard precision (SP) mode, that uses hierarchical filters to find the best ligand poses in the protein binding site. The filters incorporate a systematic search of orientation space, positional and conformational, of the ligands before assessing the energetic interaction with the protein [34 (link)]. All docking were re-scored by binding free energy calculations using the MM-GBSA (molecular mechanics combined with the generalized Born surface area) method. The idea is to estimate more accurate binding free energies for ligand–protein complex and to get a more reliable ranking. The implementation of MM-GBSA was carried out with the Prime module from Schrodinger [32 (link)]. The PLIP server [35 (link)] were used to visualize interactions of ligand–protein complexes, and visualization was carried out with Pymol [36 ].

Mancipe J.C., Vargas-Pinto P., Rodríguez O.E., Borrego-Muñoz P., Castellanos Londoño I., Ramírez D., Piñeros L.G., Mejía M.C, & Pombo L.M. (2023). Anti-Inflammatory Effect of Izalpinin Derived from Chromolaena leivensis: λ-Carrageenan-Induced Paw Edema and In Silico Model. Molecules, 28(9), 3722.

+ Open protocol

+ Expand

All-Around Docking for p38γ Binding Site Prediction

Check if the same lab product or an alternative is used in the 5 most similar protocols

We implemented our in-house All-Around Docking methodology to predict the best binding site and binding pose of F7 on p38γ protein. Based on the Glide software (Schrödinger) for docking, All-Around Docking allows a small molecule to search the whole surface of a target protein for the best docking site with the lowest docking score. The structure of the p38γ protein in complex with the ANP molecule phosphoaminophosphonic acid-adenylate ester was used as the docking target (RCSB protein databank ID: 1cm8), as shown in Figure 3c.

Zhang X.H., Nam S., Wu J., Chen C.H., Liu X., Li H., McKeithan T., Gong Q., Chan W.C., Yin H.H., Yuan Y.C., Pillai R., Querfeld C., Horne D., Chen Y, & Rosen S.T. (2018). Multi-Kinase Inhibitor with Anti-p38γ Activity in Cutaneous T-Cell Lymphoma. The Journal of investigative dermatology, 138(11), 2377-2387.

+ Open protocol

+ Expand

All-Around Docking for p38γ Binding Site Prediction

Check if the same lab product or an alternative is used in the 5 most similar protocols

+ Open protocol

+ Expand

Molecular Docking of Phospholipids

Cited 2 times

Check if the same lab product or an alternative is used in the 5 most similar protocols

Initial complexes of GV sPLA₂ were generated using our model based on a homology model of GV sPLA₂ based on the crystal structure of GIIA sPLA₂ [5 (link)]. Phospholipids were docked in the active site of each enzyme using the Glide software implemented in the Schrödinger suite using a previously published docking protocol [5 (link),24 (link)–26 (link)].

Hayashi D., Mouchlis V.D, & Dennis E.A. (2021). Each Phospholipase A2 Type Exhibits Distinct Selectivity Toward sn-1 Ester, Alkyl Ether, and Vinyl Ether Phospholipids. Biochimica et biophysica acta. Molecular and cell biology of lipids, 1867(1), 159067.

+ Open protocol

+ Expand

Rigid Receptor Docking with Glide

Check if the same lab product or an alternative is used in the 5 most similar protocols

The rigid receptor docking (RRD) was performed with standard precision (SP) using Glide software (Schrödinger LLC). The van der Waals (vdW) radii of receptor was softened by 1.0 scaling factor with partial charge cut-off value of 0.25 and receptor grid was generated at the centroid of co-crystalized ligand for docking protocol. The vdW radii of ligands were softened to 0.80 scaling factor with partial charge cut-off value of 0.15. Ligands were flexibly sampled and post-docking minimization was performed to produce, at most, 20 poses for each ligand and ranked per Glide score (Kcal/mol). The cognate re-docking was performed to validate the docking protocol and RMSD value of co-crystalized ligand was calculated.

Ahmad H., Rauf K., Zada W., McCarthy M., Abbas G., Anwar F, & Shah A.J. (2020). Kaempferol Facilitated Extinction Learning in Contextual Fear Conditioned Rats via Inhibition of Fatty-Acid Amide Hydrolase. Molecules, 25(20), 4683.

+ Open protocol

+ Expand

Molecular Docking of CDK1 Inhibitors

Cited 3 times

Check if the same lab product or an alternative is used in the 5 most similar protocols

The binding modes of each compound into the active site of CDK1 were determined using ligand-receptor molecular docking; Glide software from Schrödinger suite was used [25 (link)]. This software has many successful aplications and is widely used for drug discovery [26 (link),27 (link)], structure-activity relationship analysis [28 (link)–30 (link)], virtual screening [31 (link),32 (link)], pharmacophore modeling [33 (link)–35 (link)], evaluation of enzymatic reaction pathways [36 (link),37 (link)], and other studies.
Protein coordinates were extracted from the crystal structure of the complex CDK1-Cyclin bound to an ATP-competitive inhibitor (code 4Y72 in Protein Data Bank) [38 ]. Water molecules inside the active site were deleted before docking experiments to allow each compound to freely find its best pose inside the protein. A grid box of 28Å x 28Å x 28Å was centered on the center of mass of the inhibitor in this crystal structure covering the ATP-binding site of CDK1. To assign ionization states, ring conformations and stereochemistry of the compounds, the module LigPrep was used (LigPrep 3.0, Maestro 10.2.011, Schrödinger LLC). Docking parameters were used as in previous works [28 (link)–30 (link)]. Glide standard (SP) and extra-precision (XP) modes were used. From the found poses, the ones that showed the lower total docking energy (i.e. more favorable pose) were chosen.

Navarro-Retamal C, & Caballero J. (2016). Flavonoids as CDK1 Inhibitors: Insights in Their Binding Orientations and Structure-Activity Relationship. PLoS ONE, 11(8), e0161111.

+ Open protocol

+ Expand

Molecular Conformer Sampling and Analysis

Check if the same lab product or an alternative is used in the 5 most similar protocols

Inhibitor docking simulations used Glide software (Schrödinger) in Standard Precision mode. Possible conformers of repotrectinib and selitrectinib were generated using Schrödinger's Prime Macrocycle Sampling process (Schrödinger Inc) sampling 1,000 conformations for each molecule; 17 conformations of repotrectinib and 18 conformations of selitrectinib were generated. DFT Ab initio analysis with Jaguar software (Schrödinger Inc.) using B3LYP-D3 theory, and the 6-31G** basis set with geometry optimization was used to predict low-energy conformers of repotrectinib and selitrectinib.

Murray B.W., Rogers E., Zhai D., Deng W., Chen X., Sprengeler P.A., Zhang X., Graber A., Reich S.H., Stopatschinskaja S., Solomon B., Besse B, & Drilon A. (2021). Molecular Characteristics of Repotrectinib That Enable Potent Inhibition of TRK Fusion Proteins and Resistant Mutations. Molecular Cancer Therapeutics, 20(12), 2446-2456.

+ Open protocol

+ Expand

Docking and Binding Affinity Estimation

Check if the same lab product or an alternative is used in the 5 most similar protocols

The ligands underwent docking procedures employing the extra precision mode (XP) without any constraints, and specific parameters included a van der Waals (vdw) radius scaling factor of 0.80 and a partial charge cut-off of 0.15. To estimate binding affinity and rank ligands, GlideScore, implemented in the Glide software (Maestro, version 11.8. (2018) Schrödinger, LLC, New York), was employed. The XP Pose Rank was used to identify and select the best-docked pose for each ligand. Subsequently, the final list of compounds was subjected to in-depth analysis by considering binding scores and conducting a comprehensive examination of all binding interactions.

Gomaa M., Gad W., Hussein D., Pottoo F.H., Tawfeeq N., Alturki M., Alfahad D., Alanazi R., Salama I., Aziz M., Zahra A, & Hanafy A. (2024). Sulfadiazine Exerts Potential Anticancer Effect in HepG2 and MCF7 Cells by Inhibiting TNFα, IL1b, COX-1, COX-2, 5-LOX Gene Expression: Evidence from In Vitro and Computational Studies. Pharmaceuticals, 17(2), 189.

+ Open protocol

+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!