The homology model for TP15-Fc was calculated using YASARA Structure software (YASARA Biosciences, Vienna, Austria) after removing secretion leader and tags.
Structure software
Manufactured by YASARA
Sourced in Austria
YASARA Structure is a molecular modeling and visualization software used for the analysis and manipulation of molecular structures. It provides tools for the visualization, editing, and simulation of proteins, nucleic acids, and other biomolecules. The software can be used for tasks such as model building, structure optimization, and molecular dynamics simulations.
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Lab products found in correlation
14 protocols using structure software
1
Homology Modeling of TP15-Fc Protein
2
Homology modeling of HER2-specific scFv
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Homology models for the HER2-specific scFv derived from antibody humAb4D5-8 and ULBP2 were calculated using YASARA Structure software (YASARA Biosciences). Secretion leader sequences and tags were not included. Structures for whole molecules were then generated by introducing linker sequences and fusing the best-fitting models obtained for the single subunits. Ribbon drawings were generated using Discovery Studio 2.0 Visualize software (Accelrys Inc.).
3
In silico Modeling of PcAad1p Structure
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In silico modeling of PcAad1p structure was performed using the YASARA Structure software (YASARA Biosciences) with the resolved AKR11C1 structure as the template (64 (link)). Assessment of modeling quality was carried out using the SWISS-MODEL Web server (http://swissmodel.expasy.org/ ). The PcAad1p sequence with key amino acids and motifs thereby revealed was aligned with yeast Aadp proteins (Fig. 2 ).
4
Modeling HM1.24-ETA' Fusion Protein
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A homology model was calculated for HM1.24-ETA′ by modeling the scFv (template: 1H8N) and ETA′ (template: 1IKP) separately using the YASARA Structure software (YASARA Biosciences, Graz, Austria). The individual domains were manually fused using the YASARA Structure software. Ribbon drawings were performed using Discovery Studio 2.0 Visualize software (Accelrys Inc., San Diego, CA, USA).
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Homology Modeling of HER2-specific scFv
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YASARA Structure software (YASARA Biosciences) was employed to calculate the homology models for the HER2-specific scFv derived from antibody humAb4D5-8 and the ligands B7-H6, AICL and PVR individually. Secretion leader sequences and tags were removed. Structures for whole molecules were generated by introducing linker sequences and fusing the best-fitting models obtained for the single subunits. Ribbon drawings were generated using Discovery Studio 2.0 Visualize software (Accelrys Inc.).
6
Molecular Dynamics Analysis of Lipase Mutants
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The MD simulations were performed on computed model of recombinant AMS8 and lid 1 mutant lipases using YASARA structure software (version 11.3.22, Netherlands) following previous MD settings and protocols in water or toluene [7 ,18 (link)] targeting specific temperature of 25 °C and 37 °C. The system was equilibrated at the steepest descent parameters, using a time step of 1 fs for intramolecular forces which calculated the intermolecular forces in every 2 simulation sub-steps. The structure was energy-minimized with AMBER03 force field using a cut off 10.486 Å and the Particle Mesh Ewald algorithm to treat long range electrostatic interactions. After the removal of conformational stress by a short steepest descent minimization via 50 steps of MD in solvent, the procedures continued by simulated annealing and converge as soon as the energy improves by <0.05 kJ/mol per atom within 200 steps. The changes of protein structure were examined using 800 saved trajectories where each 40 simulation snapshots represents 1 ns. The MD simulation was allowed to run until 20 ns. By using final trajectories from MD simulations, the hydrogen-bond networks in recombinant AMS8 and mutant lipases, T52Y and G55Y were explored by BIOVIA Discovery Studio 2017R2 Visualiser version 17.2.0.16,349 (Dassault Systemes, 2016).
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OATP1C1 Homology Modeling Using YASARA
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An OATP1C1 homology model was constructed similarly as we have recently done for MCT8 using YASARA Structure Software (www.yasara.org) (18) (19) (20) . The E.coli
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Molecular Dynamics Simulation of TLR-4 Protein
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Molecular dynamic simulation was performed using YASARA structure software (version 14.12.2) (Wien, Austria) by selecting the AMBER14 force field [35 ]. The whole protein was embedded in the water-filled simulation cell (20 Å). During the entire simulation process, the experimental condition was maintained at a constant pressure (107p) and a temperature of 298 K. The TLR-4 protein and rutin molecule was placed at the center of the cubic box, adding the counterion to adjust the pH to the physiological level (i.e., 7.4) [36 (link)]. The simulation was commenced for 150 ns with a 2.5 fs time step at a constant temperature and pressure (NPT ensemble) [37 (link)]. A pre-established macro script (md run.mcr) within the YASARA package was used during the simulation steps and the output of the conformation was 100 ps [38 (link)]. The results of the simulations were visualized using Discovery Studio Visualizer version 2018.
9
Glycosaminoglycan-Phospholipid Interactions
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HA, CS-4 and CS-6 structure modification with YASARA Structure software (Vienna, Austria) [11 (link)] is described in [12 (link)]. Three types of phospholipids—DPPC, DPPE, and SPH (Figure 3 )—were used to look at their interactions with the abovementioned glycosaminoglycans. Molecules were placed randomly in a simulation box that was followed by system minimization with a time step of 1 fs. Next, water molecules were added, followed with another 1000-step minimization with a 1-fs time step. The total number of atoms in all the cases was ~150,000, including water molecules (4400 of GAGs, and 7500 of PL). Isothermal–isobaric ensemble all-atom simulations were performed under the following conditions: temperature 310 K, pH = 7.0 in 0.9% NaCl (0.154 M) aqueous solution (a four-site (TIP3P) model of water [13 (link)]), with a timestep of 2 fs. Berendsen barostat [14 (link)] with a relaxation time of 1 fs were used to maintain constant temperature and pressure. The final concentrations of HA and CS were the same, CCS = CHA= 5·10−7 M, and both molecules were of the same weight—40 kDa. Concentrations used were chosen to enable PL molecules to bind to GAGs in a relatively short time, and thus they do not refer to any value taken from the literature.
10
Molecular Modeling of Drug-Polymer Complexes
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The structure of NOR, ethyl cellulose (EC), eudragits, oleic acid (OA), sodium lauryl sulphate (SLS) and stearic acid were downloaded from PubChem. Energy minimization of all generated structures were carried out using YASARA-Structure software [30 (link)]. The structures of all ethyl cellulose, eudragits, oleic acid, sodium lauryl sulfate (SLS) and stearic acid polymers were considered as alternative receptors (host) and ligands (guest) to obtain the stable complex of co-polymeric structure, while Norfloxacin was used only as a ligand (guest) structure for the molecular docking simulations. AutoDock Vina was used for molecular docking calculation in PyRx [31 (link)], in which the grid box was set to cover the entire polymer to ensure that all possible interactions with the drug were searched [32 (link)]. The best docked complex between co-polymer and drug was then subjected to molecular dynamics (MD) to divulge its stability in time and under the influence of explicit solvent molecules. MD simulations were carried out in YASARA-Structure program using the YASARA force field with knowledge-based components [30 (link)]. Chimera and Discovery Studio Visualizer were used for the visualization and graphical representations of all co-polymer and drug complex [33 (link)].
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