PMC

The “PDB χ₁ frequency” line represents the accuracy of the NDRD rotamer library without any interactions; this library is used in both Upside and SCWRL4.

Shown are structure ribbons for superposed crystal structure SEI monomer (colored white) and N10P monomer (colored grey). Residue spheres colored orange represent: SEI residues S31, A32, N33, and Q34; and corresponding N10P Upside VLR residues S139, A140, N141, and Q142. Residue spheres colored yellow represent: SEI residues W51and E53; and corresponding N10P Upside VLR residues W106 and E109. The SEI monomer shown was superposed onto N11P tetramer Upside VLR residues using the atoms listed in .

Panel 4A shows structure ribbons representing influenza A N10P [], N11P [], N6N [], IBN []), and SPN [] structures superposed using CNSA118:O, CNSA224:O, and CNSA276:O atoms. Atom spheres shown for each structure are identified by lowercase letters in . Structure ribbons and residue spheres of N10P, N11P, N6N, and IBN are color-coded as in the 'SPATIAL' row in . SPN residues are color coded as in the 'SPNSEQ' and 'SPN<>' rows in . Panel 4B shows substance P-like domains (green and red spheres) in the Upside VLR of N6N. Panel 4C shows E2S-like (green, brown, and orange spheres) and SARSSP-like (purple, red, and yellow spheres) in the Upside VLR of N11P. Panel 4D shows a C-terminal domain common to influenza B viruses (light brown colored spheres) in the Upside VLR of IBN. Panel 4E shows SEI-like domains (orange and yellow spheres) in the Upside VLR of N10P. Panel 4F shows a C-terminal domain common to bacterial viruses (light brown colored spheres) in the Upside VLR of SPN. Medium blue spheres adjacent to the consensus active site region in Panels 4A-4F are CNSR151, CNSR152, and CNSR 178 residues. Sialic acid sticks (colored medium brown) are shown in the consensus active site region of N6N, N10P, N11P, IBN, and SPN (Panel 4A), N6N (Panel 4B), and SPN (Panel 4F).

Consort figure on recruitment and retention in the upside study (n=326).