Jaguar software

Manufactured by Schrödinger

Jaguar software is a molecular modeling and simulation platform developed by Schrödinger. It provides tools for computational chemistry and drug discovery research. The software enables the analysis and prediction of molecular structures and properties.

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Lab products found in correlation

Glide software, by Schrödinger (1 mentions)

3 protocols using jaguar software

Molecular Conformer Sampling and Analysis

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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.

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Computational Analysis of Isomeric Compounds

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Two isomers I and II of compound 1 were optimized using the B3LYP/6-311g(d,p) method in Schrodinger's Jaguar software. The calculations were conducted under DFT theory, considering NMR shielding constants in the gas phase. Then, the DP4 Java code, available from the Goodman lab (http://wwwjmg.ch.cam.ac.uk/tools/nmr/DP4/), was employed to compare the predicted chemical shifts with the experimentally obtained values. The method followed the previous reports [20 (link),21 (link)]. Coordinations of two isomers were shown in Supporting information.

Tran T.M., Aonbangkhen C., Duong T.H., Nguyen T.H., Ho M.T., Chavasiri W., Wongsuwan S., Chatwichien J., Giao Vo T.P., Nguyen N.H., Kiriwan D, & Choowongkomon K. (2024). Diphenyl ethers from the cultured lichen mycobiont of Graphis handelii Zahlbr. Heliyon, 10(4), e25763.

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Quantum Mechanics Computations in Jaguar Software

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All quantum mechanics computations were performed using density functional theory (DFT) with either the PBE0¹⁷ functional (for vibrational spectra) or PBE^{18 (link)} (for energy calculations) functional with Grimme D3 dispersion corrections^{19 (link),20 (link)} when necessary, implemented in the Schrödinger Jaguar Software.^{21 (link)} The basis sets are noted as used, including the 6–311G**++ extended basis set^{22 (link)–25 (link)} (including diffuse and polarization functions), and the Los Alamos effective core potentials LACV3P**++ (based on the 6–311G basis) and LACVP (based on the 6–31G basis) basis sets.²⁶ An implicit solvation model, PBF,^{27 ,28} was used for all vibrational calculations with a dielectric constant mimicking that of water (80.37).

Oppenheim J., Gray M.H., Di Bilio A.J., Brennan B.J., Henling L.M., Lim P., Soll M., Termini J., Virgil S.C., Gross Z, & Gray H.B. (2019). Structures and Spectroscopic Properties of Metallocorrole Nanoparticles. Inorganic chemistry, 58(15), 10287-10294.

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