Prime software

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Prime software is a computational platform developed by Schrödinger that enables the simulation and modeling of molecular structures and their interactions. It provides a comprehensive suite of tools for drug discovery and material science research.

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Lab products found in correlation

Protein preparation wizard, by Schrödinger (2 mentions) Glide software, by Schrödinger (2 mentions) Sitemap, by Schrödinger (1 mentions) Sitemap tool, by Schrödinger (1 mentions) Maestro program, by Schrödinger (1 mentions) Maestro version 10, by Schrödinger (1 mentions) Ligprep program, by Schrödinger (1 mentions)

7 protocols using prime software

Estimating Ligand-Enzyme Binding Energies

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The difference in free energy of the binding of a ligand to an enzyme and a mutant enzyme was calculated using MM/GBSA^{41 (link)}. In MM-GBSA, free energy is treated as the sum of conformational energy term (i.e., MM) and solvation free energy. The MM, which, as mentioned earlier, stands for molecular mechanics, refers to the type of energy function used to calculate the potential energy of a molecular structure. These functions, usually called force fields, are classical potentials including terms describing covalent bonding, van der Waals interactions, etc. The other part, the solvation term, can be further expressed as the sum of a polar component and a non-polar contribution^{42 (link)}. The latter is usually assumed to depend linearly on the solvent-accessible surface area. The binding energies between ThyA and dUMP and ThyA and MTHF in the pre- and post-MD simulated complex were computed using the MM-GBSA approach via Schrödinger Prime software^{43 (link)}.

Pandey B., Grover S., Kaur J, & Grover A. (2019). Analysis of mutations leading to para-aminosalicylic acid resistance in Mycobacterium tuberculosis. Scientific Reports, 9, 13617.

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Comparative Model Building for Protein

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The comparative model was built using Prime software (Schrödinger Release 2016-4), using the 2D0T crystal structure as a template, chain A (Sugimoto et al., 2006 (link)), the best available structure on commencing this study. The overall goodness of the models was checked by Ramachandran plots, via PROCHECK (Laskowski et al., 1996 (link)), whereby > 97% of the IdoA and IdoB residues fitted in the allowed region of the plot (Figure S2D). A further comparison with other human crystal structures made available while this study was underway was also performed to check for appropriateness of the original template in the light of such new pieces of information (Peng et al., 2016 (link); Tojo et al., 2014 (link)). In terms of secondary structure and spatial arrangement, no critical issues were raised by the analysis of the new structures. The right protonation state at pH 7.4 was assigned using Protein Preparation wizard from Schrödinger. Maps of the binding sites were generated using SiteMap (SiteMap, version 3.0, Schrödinger).

Zelante T., Choera T., Beauvais A., Fallarino F., Paolicelli G., Pieraccini G., Pieroni M., Galosi C., Beato C., De Luca A., Boscaro F., Romoli R., Liu X., Warris A., Verweij P.E., Ballard E., Borghi M., Pariano M., Costantino G., Calvitti M., Vacca C., Oikonomou V., Gargaro M., Wong A.Y., Boon L., den Hartog M., Spáčil Z., Puccetti P., Latgè J.P., Keller N.P, & Romani L. (2021). Aspergillus fumigatus tryptophan metabolic route differently affects host immunity. Cell Reports, 34(4), 108673.

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Homology Modeling of Yeast Sodium-Potassium Pump

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To better understand the KAE609 binding pose, a homology model of ScPma1p
was built with Schrödinger’s Prime software59
using the UniProt60 (link) sequence P05030 and a structure of the highly
homologous Sus scrofa sodium-potassium pump (PDBID: 3N2F, chain C)61 (link). The 3N2F and P05030 amino-acid sequences were first aligned
using ClustalW62 (link). The model was then constructed using
Schrödinger’s knowledge-based method. The structure was further
processed with Schrödinger’s Protein Preparation Wizard63 (link). Hydrogen atoms were added at pH 7.0 using PROPKA64 (link), water molecules were removed, and disulfide bonds were appropriately
modeled. The system was then subjected to a restrained minimization using the
OPLS_2005 forcefield65 66 (link), converging the heavy atoms to an RMSD
of 0.30 Å.

Goldgof G.M., Durrant J.D., Ottilie S., Vigil E., Allen K.E., Gunawan F., Kostylev M., Henderson K.A., Yang J., Schenken J., LaMonte G.M., Manary M.J., Murao A., Nachon M., Murray R., Prescott M., McNamara C.W., Slayman C.W., Amaro R.E., Suzuki Y, & Winzeler E.A. (2016). Comparative chemical genomics reveal that the spiroindolone antimalarial KAE609 (Cipargamin) is a P-type ATPase inhibitor. Scientific Reports, 6, 27806.

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Computational Modeling of SARS-CoV-2 Spike Protein

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A homology model of SPIKE protein was built using the Schrodinger Prime software based on the Cryo-EM structures of the human (PDB ID: 7DF4) and Pangolin coronavirus (PDB ID: 7CN8) SPIKE proteins. Each chain of SPIKE protein was modeled individually. Then, the individual chains were superimposed with the 7DF4 SPIKE structure to form the SPIKE trimer. The energy of the resulting model was minimized using the Schrodinger MacroModel program with the Polak–Ribier conjugate gradient minimization method, the OPLS4 force field, and the coverage threshold of 0.05. The unconstrained protein–protein docking was conducted between SPIKE as a receptor and TMPRSS2 (PDB ID: 7MEQ) as a ligand. A total of 70000 ligand rotations were probed. The small molecule binding sites at SPIKE proteins were identified using the Schrodinger SiteMap tool (Shin et al., 2020 (link)). Small molecule docking was performed using the Schrodinger Glide software (Friesner et al., 2006 (link)) in the standard precision mode with the default settings.

Cicka D., Niu Q., Qui M., Qian K., Miller E., Fan D., Mo X., Ivanov A.A., Sarafianos S.G., Du Y, & Fu H. (2023). TMPRSS2 and SARS-CoV-2 SPIKE interaction assay for uHTS. Journal of Molecular Cell Biology, 15(3), mjad017.

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Virtual Screening for Sortilin Ligands

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Schrödinger’s Maestro program (version 9.3.5) was used as the primary graphical user interface and Maestro version 10.2 (Schrödinger, LLC, New York, NY) was used for ligand interaction diagramming. Virtual screening was performed on compounds contained in ChemBridge libraries (www.chembridge.com) that were prepared with Schrödinger’s LigPrep program [14 ]. The virtual screening method was performed using Schrödinger’s GLIDE software [15 (link)] on the hsortilin crystal structure PDB ID: 4PO7 [16 (link)]. Compounds were docked using GLIDE at the site where the N-terminal fragment of NT is found in the crystal structure and cpd984 was chosen for biological screening based on its docking score. Schrödinger’s PRIME software was used to generate missing side chains and loops of this crystal structure predicting the NT peptide spanning the cavity of hsortilin [17 (link)]. LigPrep was used on the N-terminal peptide XLYEN-OH from this crystal structure and it was then docked back into its respective site on the crystal structure. This self-docking task was able to reproduce the X-ray pose for this ligand.

Sparks R.P., Guida W.C., Sowden M.P., Jenkins J.L., Starr M.L., Fratti R.A., Sparks C.E, & Sparks J.D. (2016). Sortilin facilitates VLDL-B100 secretion by insulin sensitive McArdle RH7777 cells. Biochemical and biophysical research communications, 478(2), 546-552.

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Ligand-Receptor Binding Energy Evaluation

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MM-GBSA (Generalized-Born/Surface Area) was used to calculate the binding free energy for all ligand-receptor complexes to select the correct poses between possible binding modes. The binding free energy was calculated using ligand charges obtained via the QM/MM calculations using Prime software from Schrodinger. To assess the influence of a given substituent on the binding, the ΔΔG was calculated as a difference between binding free energy (ΔG) of unsubstituted (1w) and substituted analogues.

Hogendorf A.S., Hogendorf A., Kurczab R., Satała G., Lenda T., Walczak M., Latacz G., Handzlik J., Kieć-Kononowicz K., Wierońska J.M., Woźniak M., Cieślik P., Bugno R., Staroń J, & Bojarski A.J. (2017). Low-basicity 5-HT7 Receptor Agonists Synthesized Using the van Leusen Multicomponent Protocol. Scientific Reports, 7, 1444.

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Molecular Docking of Aminononane Isomers

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Homology models were developed using Prime software from Schrödinger. Prime uses BLAST (with the BLOSUM62 matrix) for homology search and alignment and refines the results using the Pfam database and pairwise alignment with ClustalW. Docking simulations of (S)-(+)-2-aminononane and (R)-(−)-2-aminononane with the structural models created for each of the class III ω-TAs were carried out using the Protein Energy Landscape Exploration software, which offers one of the best modeling alternatives to map protein-ligand dynamics and induced fit, as described previously (48 (link)). The substrate was initially positioned in the active site with the nitrogen atom of the substrate toward the Lys catalytic base. The substrate conformation was set to be fully flexible in the docking simulations, whereas the protein conformation was not allowed to change.

Coscolín C., Katzke N., García-Moyano A., Navarro-Fernández J., Almendral D., Martínez-Martínez M., Bollinger A., Bargiela R., Gertler C., Chernikova T.N., Rojo D., Barbas C., Tran H., Golyshina O.V., Koch R., Yakimov M.M., Bjerga G.E., Golyshin P.N., Jaeger K.E, & Ferrer M. (2019). Bioprospecting Reveals Class III ω-Transaminases Converting Bulky Ketones and Environmentally Relevant Polyamines. Applied and Environmental Microbiology, 85(2), e02404-18.

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