Energy minimization server

YASARA Energy Minimization Server^{39 (link)}
was used to attain a minimum energy arrangement of the constructed 3D structure of the HP. Subsequently, the minimized 3D structure was further optimized using GalaxyRefine.^{40 (link)}
After analyzing all the potential structures generated by GalaxyRefine, arguably the one having the best quality and performance was selected.

The 3D structure of human σ2 receptor was built by homology modeling using our previously reported method (Alamri et al., 2020b ). Briefly, the protein sequence of human σ2 receptor amino acids 1–176 (ID: Q5BJF2) in FASTA format was retrieved from UniProtKB database. The 3D structure of σ2 receptor was determined by homology modeling using the I-TASSER (Iterative threading assembly refinement) webserver (https://zhanglab.dcmb.med.umich.edu/I-TASSER/). This hierarchical approach is an integrated online platform for automated protein structure and function prediction starting from the primary amino acid sequence and based on the sequence to structure to function approach (Zhang, 2008 ). The structure of the mitochondrial translocator protein (PDB ID: 2MGY) was identified to be a closely related protein, so it was used as a template for the structure (Jaremko et al., 2014 (link)). The predicted structure contained was composed of 7 α helices. The model was subjected to energy minimization by YASARA Energy Minimization Server (http://www.yasara.org/minimizationserver.htm) using YASARA force field to remove all bad contacts and reduce the model energy globally (Krieger et al., 2002 (link), Krieger and Vriend, 2014 (link)). This model was validated by several equations including ERRAT, Verify 3D, ProSA, ProQ, QMEAN, and PROCHECK as we reported previously (Alamri et al., 2020b ).