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Opls 2005

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OPLS_2005 is a force field developed by Schrödinger for the simulation of molecular systems. It is designed to provide accurate and efficient modeling of a wide range of organic and inorganic compounds.

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Lab products found in correlation

Protein preparation wizard, by Schrödinger (9 mentions) Ligprep module, by Schrödinger (4 mentions) Ligprep 2.3 module, by Schrödinger (3 mentions) Glide module, by Schrödinger (3 mentions) Ligprep wizard, by Schrödinger (2 mentions) Prime module, by Schrödinger (1 mentions)

23 protocols using opls 2005

1

Meleagrin 3D Structure Generation

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The chemical structure of meleagrin was sketched on the Maestro 9.3 panel interface (Maestro, version 9.3, 2012, Schrödinger, New York, USA). The LigPrep 2.3 module (LigPrep, version 2.3, 2012, Schrödinger, New York, USA) of the Schrödinger suite was implemented to generate the 3D structure and search for different conformers. The Optimized Potentials for Liquid Simulation (OPLS_2005, Schrödinger, New York, USA) force field was applied to geometrically optimize the ligand structure and to compute partial atomic charges. Finally, at most, 32 poses per ligand were generated with different steric features for the subsequent docking studies.
Mady M.S., Mohyeldin M.M., Ebrahim H.Y., Elsayed H.E., Houssen W.E., Haggag E.G., Soliman R.F, & El Sayed K.A. (2015). The indole alkaloid meleagrin, from the olive tree endophytic fungus Penicillium chrysogenum, as a novel lead for the control of c-Met-dependent breast cancer proliferation, migration and invasion. Bioorganic & medicinal chemistry, 24(2), 113-122.
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2

Structural Optimization and Conformer Generation

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The structures of (−)-oleocanthal and tamoxifen were sketched in the Maestro 9.3 panel (Maestro, version 9.3, 2012, Schrödinger, New York, USA). The Lig Prep 2.3 module (LigPrep, version 2.3, 2012, Schrödinger, New York, USA) of the Schrödinger suite was used to generate the 3D structures and to search for different conformers. The Optimized Potentials for Liquid Simulation (OPLS_2005, Schrödinger, New York, USA) force field was applied to geometrically optimize the structures of (−)-oleocanthal and tamoxifen and compute partial atomic charges. Finally, at most, 32 poses were generated with different steric features for subsequent docking studies.
Ayoub N.M., Siddique A.B., Ebrahim H.Y., Mohyeldin M.M, & El Sayed K.A. (2017). The olive oil phenolic (−)-oleocanthal modulates estrogen receptor expression in luminal breast cancer in vitro and in vivo and synergizes with tamoxifen treatment. European journal of pharmacology, 810, 100-111.
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3

AMA1-RON2 Complex Structural Optimization

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As an initial step, the crystal coordinates of AMA1 in complex with a surface-exposed region of RON2 (PDB ID: 2Y8T) was pre-processed using Protein Preparation Wizard of the Schrödinger (New York, NY, USA) suite towards optimizing the stereochemistry by assigning proper bond order, removing steric clashes, adding hydrogen atoms, fixing the disulfide bonds and missing residues and loops. Furthermore, optimization of the protein structure was also performed by adjusting the terminal chi rotation of asparagine, glutamine, and histidine residues. Optimal protonation states for histidine residues were also assigned, followed by the removal of unwanted hetero groups. Finally, energy minimization was performed with OPLS_2005 (Schrödinger) to obtain the optimal geometry.
Vetrivel U., Muralikumar S., Mahalakshmi B., Lily Therese K., Madhavan H., Alameen M, & Thirumudi I. (2016). Multilevel Precision-Based Rational Design of Chemical Inhibitors Targeting the Hydrophobic Cleft of Toxoplasma gondii Apical Membrane Antigen 1 (AMA1). Genomics & Informatics, 14(2), 53-61.
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4

Structural Preparation of c-Met Kinase

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Four X-ray crystal structures of the c-Met tyrosine kinase domain; (PDB codes: 3CE3 [49 (link)], 3F82 [46 (link)], 4XYF [50 (link)] and 3U6I [51 (link)]) were retrieved from the PDB (www.rcsb.org). The Protein Preparation Wizard was implemented to prepare the kinase domain of each protein. The protein was reprocessed by assigning bond orders, adding hydrogens, creating disulfide bonds and optimizing H-bonding networks using PROPKA (Jensen Research Group, Denmark) [52 (link)]. Finally, energy minimization with RMSD value of 0.3°A was applied using an Optimized Potentials for Liquid Simulation (OPLS_2005, Schrödinger, New York, USA) force field.
Mohyeldin M.M., Busnena B.A., Akl M.R., Dragoi A.M., Cardelli J.A, & El Sayed K.A. (2016). Novel c-Met Inhibitory Olive Secoiridoid Semisynthetic Analogs for the Control of Invasive Breast Cancer. European journal of medicinal chemistry, 118, 299-315.
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5

Structural Insights into MA-IP6 Inhibitor Complex

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The crystal structures of MA with its inhibitor IP6 were retrieved from the RSCB database (PDB IDs: 7E1I, 7E1J, and 7E1K) [44 (link)]. The raw file was prepared for the docking assessment by the PrepWizard module of Maestro. The missing chains were added automatically by Prime and the protonation state was calculated by PropKa at physiological pH. Finally, the receptor–ligand complex was minimized by optimized potential liquid simulation (OPLS_2005 (Schrödinger, LLC, New York, NY, USA, 2016)) force field.
Ciftci H., Sever B., Ayan E., Can M., DeMirci H., Otsuka M., TuYuN A.F., Tateishi H, & Fujita M. (2022). Identification of New L-Heptanoylphosphatidyl Inositol Pentakisphosphate Derivatives Targeting the Interaction with HIV-1 Gag by Molecular Modelling Studies. Pharmaceuticals, 15(10), 1255.
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6

Structural Characterization of Kinase Domains

Cited 1 time
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The X-ray crystal structures of the human kinases JAK2 (PDB code: 4ZIM) [53 (link)], FLT3 (PDB code: 4XUF) [54 (link)], EphB (PDB code: 3ZEW [55 (link)], ABL1 (PDB code: 4WA9) [56 (link)], TIE2 (PDB code: 2WQB) [57 (link)], GSK-3β (PDB code: 3ZRK) [58 (link)], and PLK1 (PDB code: 3THB) [59 (link)], were retrieved from the Protein Data Bank [60 ]. The kinase domain for each protein was prepared using the Protein Preparation Wizard of the Schrödinger molecular modeling suite [61 (link)]. Protein structures were reprocessed by assigning bond orders, adding hydrogens, creating disulfide bonds and optimizing H-bonding networks using PROPKA (Jensen Research Group, Copenhagen, Denmark). Finally, energy minimization with a root mean square deviation (RMSD) value of 0.30 Å was applied using an Optimized Potentials for Liquid Simulation (OPLS_2005, Schrödinger, New York, NY, USA) force field.
Ebrahim H.Y, & El Sayed K.A. (2016). Discovery of Novel Antiangiogenic Marine Natural Product Scaffolds. Marine Drugs, 14(3), 57.
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7

Structural Preparation of c-Met Kinase

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The X-ray crystal structure of huamn c-Met kinase domain (PBD code: 4R1V)40 (link) was retrieved from the Protein Data Bank.41 The Protein Preparation Wizard of Schrödinger suite was used to prepare the kinase domain. The protein was reprocessed by assigning bond orders, adding hydrogens, creating disulfide bonds and optimizing H-bonding networks using PROPKA (Jensen Research Group, Copenhagen, Denmark). Finally, energy minimization with a root mean square deviation (RMSD) value of 0.30 Å was applied using an Optimized Potentials for Liquid Simulation (OPLS_2005, Schrödinger, New York, NY) force field.
Ebrahim H.Y., Moheyldin M.M., Hailat M.M, & El Sayed K.A. (2016). (1S,2E,4S,7E,11E)-2,7,11-Cembratriene-4,6-diol Semisynthetic Analogs as Novel c-Met Inhibitors for The Control of c-Met-Dependent Breast Malignancies. Bioorganic & medicinal chemistry, 24(22), 5748-5761.
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8

Structural Preparation of c-Met Kinase Domain

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Two X-ray crystal structures of the c-Met tyrosine kinase domain; (PDB codes: 2WD1 and 2RF3) were retrieved from the Protein Data Bank (www.rcsb.org). The Protein Preparation Wizard of the Schrödinger suite was implemented to prepare the c-Met kinase domain.31 (link) The protein was reprocessed by assigning bond orders, adding hydrogen, creating disulfide bonds and optimizing H-bonding networks using PROPKA (Jensen Research Group, Copenhagen, Denmark). Finally, energy minimization with a root mean square deviation (RMSD) value of 0.30Å was applied using an Optimized Potentials for Liquid Simulation (OPLS_2005, Schrödinger, New York, USA) force field.
Mady M.S., Mohyeldin M.M., Ebrahim H.Y., Elsayed H.E., Houssen W.E., Haggag E.G., Soliman R.F, & El Sayed K.A. (2015). The indole alkaloid meleagrin, from the olive tree endophytic fungus Penicillium chrysogenum, as a novel lead for the control of c-Met-dependent breast cancer proliferation, migration and invasion. Bioorganic & medicinal chemistry, 24(2), 113-122.
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9

Structural Insights into the hERα Ligand Binding Domain

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The X-ray crystal structure of the human estrogen receptor-alpha ligand binding domain (hERα LBD); residues 297–554, (PDB code: 1A52) (Tanenbaum et al., 1998 (link)) was retrieved from the Protein Data Bank (www.rcsb.org). The Protein Preparation Wizard of the Schrödinger suite was implemented to prepare the binding domain (Olsson et al., 2011 (link)). The protein was reprocessed by assigning bond orders, adding hydrogens, creating disulfide bonds and optimizing H-bonding networks using PROPKA (Jensen Research Group, Copenhagen, Denmark). Finally, energy minimization with a root mean square deviation (RMSD) value of 0.30 Å was applied using an Optimized Potentials for Liquid Simulation (OPLS_2005, Schrödinger, New York, USA) force field.
Ayoub N.M., Siddique A.B., Ebrahim H.Y., Mohyeldin M.M, & El Sayed K.A. (2017). The olive oil phenolic (−)-oleocanthal modulates estrogen receptor expression in luminal breast cancer in vitro and in vivo and synergizes with tamoxifen treatment. European journal of pharmacology, 810, 100-111.
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10

Structural Preparation of PCSK9 Proteins

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The PDB wild-type PCSK9 crystal structures (PDB codes: 4NE9, 4NMX, and 3GCW) and the mutant-type PCSK9 crystal structure PDB code: 3GCX were used. The Protein Preparation Wizard was implemented to prepare the active domain of each protein. The protein was reprocessed by assigning bond orders, adding hydrogens, creating disulfide bonds and optimizing H-bonding networks using PROPKA (Jensen Research Group, Denmark) [28 ]. Finally, energy minimization with RMSD value of 0.3 Å was applied using an Optimized Potentials for Liquid Simulation (OPLS_2005, Schrödinger, New York, USA) force field.
Abdelwahed K.S., Siddique A.B., Mohyeldin M.M., Qusa M.H., Goda A.A., Singh S.S., Ayoub N.M., King J.A., Jois S.D, & El Sayed K.A. (2020). Pseurotin A as a Novel Suppressor of Hormone Dependent Breast Cancer Progression and Recurrence by Inhibiting PCSK9 Secretion and Interaction with LDL Receptor. Pharmacological research, 158, 104847.
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