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Protocol publication

[…] We searched for the keyword ‘Ebola’ in the PDB database ( ). Subsequently, each protein was split based on the chain id, resulting in 146 single chained proteins (See in ). We have not reduced the set based on sequence similarity since the proteins might have different conformations based on their ligands. Note, this list might include non-Ebola proteins which might have been co-crystallized with the Ebola protein. However, they have been put through the same analysis since they might provide insights into the Ebola proteins themselves.These proteins were then analyzed using DSSP , and resulted in 758 helices in all (See in ). These helices were then analyzed using PAGAL. The PAGAL algorithm has been detailed previously . Briefly, the Edmundson wheel is computed by considering a wheel with centre (0,0), radius 5, first residue coordinate (0,5) and advancing each subsequent residue by 100 degrees on the circle, as 3.6 turns of the helix makes one full circle. We compute the hydrophobic moment by connecting the center to the coordinate of the residue and give it a magnitude obtained from the hydrophobic scale (in our case, this scale is obtained from ). These vectors are then added to obtain the final hydrophobic moment.The color coding is as follows: all hydrophobic residues are colored red, while hydrophilic residues are colored in blue: dark blue for positively charged residues, medium blue for negatively charged residues and light blue for amides.The raw file generated by analyzing all 146 proteins through PAGAL is provided as PAGALRAWDATA.txt ( ), and contains the hydrophobic moment, percent of positive charges and the total number of charged residues for every helix. These are then sorted based on the charge (negative or positive) or the hydrophobic moment. We ignore the helices that have none or a single charged residue, and those that are smaller than 10 residues in length. The proportion of charged residues is computed based on the total number of charged residues, and not the length of the helix.All protein structures were rendered by PyMol ( The sequence alignment was done using ClustalW . The alignment images were generated using Seaview . Protein structures have been superimposed using MUSTANG . […]

Pipeline specifications

Software tools DSSP, PAGAL, PyMOL, Clustal W, SeaView, MUSTANG
Application Protein structure analysis
Organisms Homo sapiens