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The Schrödinger software suite is a comprehensive collection of computational tools designed for molecular modeling and simulation. It provides a range of functionalities for predicting the properties and behavior of molecules and materials at the atomic and molecular scale.

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Lab products found in correlation

Protein preparation tool, by Schrödinger (1 mentions) Pymol molecular graphics system, by Schrödinger (1 mentions) Maestro, by Schrödinger (1 mentions) Maestro tool, by Schrödinger (1 mentions) Prime mm gbsa module, by Schrödinger (1 mentions) Qikprop, by Schrödinger (1 mentions) Ligprep module, by Schrödinger (1 mentions) Spss 20, by IBM (1 mentions)

27 protocols using software suite

Molecular Docking of CYP121 Ligands

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Lead
compound 2, retrofragments 5 and 6, and all
Ar1, Ar2, and Ar3 analogues were prepared using the LigPrep v3.2 and
Epik v3.0 functions of Schrödinger suite software (Schrödinger
LLC, NY), selecting to include metal binding states when generating
ligand ionization states. Ligands were docking into the crystal structure
of CYP121 bound to lead 2 (PDB 4KTL) or the previously
reported ligand 4-(1H-1,2,4-triazol-1-yl)quinolin-6-amine
(PDB 4G1X).
Proteins were prepared using the internal Protein Preparation function
of the Schrödinger suite software. Ionization states were generated
to be compatible with metal-binding interactions, and the heme-iron
was manually adjusted to the ferric (+3) oxidation state. All water
molecules were removed from the structure PDB 4G1X. Duplicate energy
minimized (OPLS 2005) structures of PDB 4KTL were prepared either with all water molecules
removed or retaining the axial heme–water ligand only. Ar1
and Ar3 analogues were docked using core constraints to replicate
the position of the aminopyrazole ring of lead 2. Ar2
analogues were docked using core constraints to replicate the heme
binding interactions of the 4-(1H-1,2,4-triazol-1-yl)quinolin-6-amine
ligand in PDB 4G1X. Images were generated using the PyMOL Molecular Graphics System,
version 1.3, 2010 (Schrödinger, LLC).

Kavanagh M.E., Coyne A.G., McLean K.J., James G.G., Levy C.W., Marino L.B., de Carvalho L.P., Chan D.S., Hudson S.A., Surade S., Leys D., Munro A.W, & Abell C. (2016). Fragment-Based Approaches to the Development of Mycobacterium tuberculosis CYP121 Inhibitors. Journal of Medicinal Chemistry, 59(7), 3272-3302.

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Antioxidants Targeting SHLP Proteins

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Study of SHLP protein and its variants was carried out using UniProtKB database (http://www.uniprot.org/). Homology modeling was performed using Schrödinger software suite (version 10.4.018; Schrödinger Software, New York, NY),[24 ] and the modeled structure was verified using Ramachandran plot.
Ten antioxidants were selected from PubChem database (https://pubchem.ncbi.nlm.nih.gov/) for interaction analysis with the SHLP proteins. All modeled proteins were docked with the 10 ligands using Glide Dock program[25 (link)] of Schrödinger software suite. Docking results were analyzed and protein–ligand interaction map was studied to identify the best antioxidant against SHLP protein.

Singh S, & Yadav R. (2019). Homology Modeling and Docking Study of Shewanella-like Protein Phosphatase Involved in the Development of Ookinetes in Plasmodium. Journal of Pharmacy & Bioallied Sciences, 11(3), 223-231.

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Ligand Preparation for Computational Studies

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All the ligands used in this work were first prepared using the LigPrep module of Schrödinger Software Suite, Schrodinger LLC [37 (link),38 (link)]. This process assigns the ionization state(s) of the ligands at the physiological condition (pH = 7.4) and generates 3D conformations of the possible tautomeric states and stereoisomers of the ligands. The prepared ligand was used for various calculations within the Schrödinger Software Suite, Schrodinger LLC.

Kundu S, & Wu S. (2021). A Structure Based Study of Selective Inhibition of Factor IXa over Factor Xa. Molecules, 26(17), 5372.

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Molecular Modeling of AMPA Receptor Ligands

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The affinity of the studied ligands for the ligand-binding domain of the AMPA receptor was assessed using molecular modeling methods as previously described [36 (link),37 (link),38 (link),39 (link)]. All calculations were performed using Schrodinger Suite software [40 ].
The calculations are based on a physical model with the assumption that the permeability is dominated by the free energy of the desolvation and change in state (neutralization and tautomerization) on passing into the membrane. The membrane is modeled as a low-dielectric continuum, and water as a high-dielectric continuum [41 (link)].

Borozdenko D.A., Ezdoglian A.A., Shmigol T.A., Gonchar D.I., Lyakhmun D.N., Tarasenko D.V., Golubev Y.V., Cherkashova E.A., Namestnikova D.D., Gubskiy I.L., Lagunin A.A., Gubsky L.V., Chekhonin V.P., Borisevich S.S., Gureev M.A., Shagina A.D., Kiseleva N.M., Negrebetsky V.V, & Baukov Y.I. (2021). A Novel Phenylpyrrolidine Derivative: Synthesis and Effect on Cognitive Functions in Rats with Experimental Ishemic Stroke. Molecules, 26(20), 6124.

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Protein Preparation for Molecular Modeling

Cited 1 time

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All protein models were
prepared in Schrodinger suite software under the OPLS_2005 force field.^{45 (link)} Hydrogen atoms were added to the repaired crystal
structures at physiological pH (7.4) with the PROPKA^{46 (link)} tool to optimize the hydrogen bond network provided by
the Protein Preparation tool in Schrodinger. The highly conserved
D80^2.50 has been found to be deprotonated. Since we only
study the initial binding process of D2R, D2.50 in GPCR is always
in a deprotnated state as indicated by previous study.^{34 (link),47 (link)} Thus, we kept the deprotonated state for D80^2.50 during
MD simulations. Constrained energy minimizations were carried out
on the full-atomic models, until the RMSD of heavy atoms coveraged
to 0.4 Å.

Chan H.C., Xu Y., Tan L., Vogel H., Cheng J., Wu D, & Yuan S. (2020). Enhancing the Signaling of GPCRs via Orthosteric Ions. ACS Central Science, 6(2), 274-282.

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Molecular Docking with Maestro

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Maestro (Schrödinger Release 2021-2: Maestro, Schrödinger, LLC, New York, NY, USA, 2020-3.) was applied to XP program (extra precision) site-specific super molecular docking. After the completion of XP (extra precision), molecular docking by Maestro Tool (https://www.schrodinger.com/products/maestro, accessed on 26 July 2022) of Schrödinger Suite Software (https://www.schrodinger.com/, accessed on 26 July 2022), every protein–ligand complex structure in PDB format was taken from the docked post-viewing file for post-docking visualization, investigation of non-bond interactions, and evaluation of hydrophobicity and bioactivity.

Biswas P., Bibi S., Yousafi Q., Mehmood A., Saleem S., Ihsan A., Dey D., Hasan Zilani M.N., Hasan M.N., Saleem R., Awaji A.A., Fahmy U.A, & Abdel-Daim M.M. (2023). Study of MDM2 as Prognostic Biomarker in Brain-LGG Cancer and Bioactive Phytochemicals Inhibit the p53-MDM2 Pathway: A Computational Drug Development Approach. Molecules, 28(7), 2977.

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Structural Modeling of BTK Inhibitors

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Structural modeling of BTK was performed with UCSF ChimeraX.10 (link) The published structures of ibrutinib (Protein Data Bank ID, 5P9J11 (link)) and ARQ-531 bound to BTK (Protein Data Bank ID, 6E4F4 (link)) were used to map mutations found in patients onto the BTK kinase domain. Pirtobrutinib was modeled into the BTK structure with the use of induced fit docking and binding pose nietadynamics12 (link) with Schrödinger Suite software, version 2021–1 (Schrödinger).

Wang E., Mi X., Thompson M.C., Montoya S., Notti R.Q., Afaghani J., Durham B.H., Penson A., Witkowski M.T., Lu S.X., Bourcier J., Hogg S.J., Erickson C., Cui D., Cho H., Singer M., Totiger T.M., Chaudhry S., Geyer M., Alencar A., Linley A.J., Palomba M.L., Coombs C.C., Park J.H., Zelenetz A., Roeker L., Rosendahl M., Tsai D.E., Ebata K., Brandhuber B., Hyman D.M., Aifantis I., Mato A., Taylor J, & Abdel-Wahab O. (2022). Mechanisms of Resistance to Noncovalent Bruton’s Tyrosine Kinase Inhibitors. The New England journal of medicine, 386(8), 735-743.

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Molecular modeling of CIN-HPβCD complexes

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The molecular modeling studies of CIN with HPβCD in the presence and absence of TA were carried out using the Schrödinger software suite (Schrödinger, LLC, New York) in the Maetsro module (version 11.1).
Structure collection: CIN and TA structures were drawn and optimized using Ligprep module. Finally, the geometry optimization was carried out using the OPLS2005 force field. HPβCD structure was drawn by adding 2‑hydroxy propyl chain to native βCD structure imported from PDB (PDB ID: 1BFN). Geometry of HPβCD was optimized using Macro model module.
Generation of supramolecular inclusion complex models: The Glide module was used for generating HP-β-CD inclusion complexes. The grid was generated using the Glide Grid Generation panel in Glide. For generating HPβCD binary supramolecular inclusion complex, CIN was docked with standard precision (SP) mode on HPβCD. The ternary supramolecular inclusion complex was generated by docking the binary inclusion complex with TA in SP mode.
Binding affinity calculation: The binding affinity “ΔG” was calculated using the Prime MM-GBSA module (version 4.5, Schrödinger), which calculates the free energy change upon formation of the complex in comparison to total individual energy based on change in the solvent accessible surface area [27] (link).

Patel M, & Hirlekar R. (2018). Multicomponent cyclodextrin system for improvement of solubility and dissolution rate of poorly water soluble drug. Asian Journal of Pharmaceutical Sciences, 14(1), 104-115.

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Evaluating Compound Drug-Likeness

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To evaluate the drug-likeness of compounds, physicochemical and other drug-related properties, including compliance with Lipinski’s Ro5 and Jorgensen’s Rule of 3 (Ro3), were calculated using QikProp^{25 (link)} (v. 4.0) within the Schrödinger software suite (Schrödinger, LLC). Adherence to the Ghose and Veber filters was calculated as described^{26 (link), 27 (link)}.

Tanenbaum D.M., Wang Y., Williams S.P, & Sigler P.B. (1998). Crystallographic comparison of the estrogen and progesterone receptor’s ligand binding domains. Proceedings of the National Academy of Sciences of the United States of America, 95(11), 5998-6003.

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Homology Modeling of HelD ATPase Domain

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The amino acid sequence of HelD from B. subtilis was retrieved from UniProt database and the closest structural homologs were identified using BLAST search against the Protein Data Bank database. The ATPase domain of HelD (residue range 539–641) shares 29% sequence identity with the E. coli UvrD. The C-terminal domain (residue range 606–774) shares 39% sequence identity with Lactobacillus planetarium (PDB ID 3DMN). No sequence similarity was observed for the N-terminal domain. The homology model was built only for the ATPase and the C-terminal domain using Prime 3.1 module (Jacobson et al., 2004 (link)) in Schrödinger software suite (Schrödinger, LLC, New York, NY, United States). SSpro program in Prime was used to predict the secondary structure of HelD. Initially, four models were generated and the model with the least energy was selected for the loop refinement. For refinement of loops comprising of <5 and >5 amino acids, the number of output structures was set to 10 and 5, respectively. After loop refinement, the OPLS3 force field (Harder et al., 2016 (link)) was used to minimize the model which was further validated by PROCHECK (Laskowski et al., 1993 (link)) for the evaluation of Ramachandran plot (Ramachandran et al., 1963 (link)).

Kaur G., Kapoor S, & Thakur K.G. (2018). Bacillus subtilis HelD, an RNA Polymerase Interacting Helicase, Forms Amyloid-Like Fibrils. Frontiers in Microbiology, 9, 1934.

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