As the full three-dimensional structure of none of the proteins was available in the Protein Data Bank (PDB), a homology modelling was performed to predict the three-dimensional structure of each protein using RaptorX web server (http://raptorx.uchicago.edu/StructurePrediction/predict/ ). The server predicts the absolute global quality and comparable global quality for each of the residues of the query sequence. In order to check the three-dimensional structure, we used PyMOL molecular graphics system v. 1.7.4.4 (Schrödinger, LLC, Portland, OR, USA). To perform structure refinement and energy minimization of the three-dimensional modelled protein structures, the online server GalaxyRefine (http://galaxy.seoklab.org/ ) and YASARA software were used, respectively. GalaxyRefine employs the CASP10 assessment to refine the query structure, improving the structural and global quality of the three-dimensional model. This method initially rebuilds side chains and performs side-chain repacking and subsequently uses MD simulation to achieve overall structure relaxation.
Galaxyrefine
Manufactured by YASARA
GalaxyRefine is a high-precision laboratory refining instrument designed for the purification and separation of complex chemical mixtures. The core function of GalaxyRefine is to utilize advanced chromatographic techniques to efficiently isolate and concentrate targeted compounds from diverse sample matrices.
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Lab products found in correlation
2 protocols using galaxyrefine
1
Protein Structure Modeling and Refinement
2
Protein Structure Prediction and Refinement
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As the full three-dimensional (3D) structure of none of the proteins was available in the Protein Data Bank (PDB), a homology modeling was performed to predict the 3D structure of each protein using RaptorX web server (http://raptorx.uchicago.edu/StructurePrediction/predict/). The server predicts the absolute global quality and comparable global quality for each of the residues of the query sequence. In order to check the 3D structure, we used PyMOL molecular graphics system version 1.7.4.4 (Schrödinger, LLC, and Portland, OR, USA). To perform structure refinement and energy minimization of the 3D modeled protein structures, the online server GalaxyRefine (http://galaxy.seoklab.org/) and YASARA software were used, respectively. GalaxyRefine employs the CASP10 assessment to refine the query structure, improving the structural and global quality of the 3D model. This method initially rebuilds side chains and performs side chain repacking and subsequently uses molecular dynamics simulation to achieve overall structure relaxation. server was used to check the reliability of modeled proteins and their overall quality factors.
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