The Hydropathy – Hopp-Woods track predicts protein antigenic determinants by searching protein sequences for the area of greatest local hydrophilicity. Hopp and Woods, 1981, make two assumptions in using hydrophilicity to find antigenic determinants: 1) antigenic determinants are usually found on regions with a high degree of exposure to solvents and 2) antigenic determinants commonly possess charged hydrophilic side chains. Each residue is assigned a hydrophilicity value and these values are averaged over a hexamer window.
In the Tracks panel, expand Hydropathy and check the box next to Hopp-Woods. The track will now be visible in the Analysis view
Select the track in the Tracks panel. Open the Track Options section, which appears as follows:
- Residues to Average – the size of the window over which hydropathy values are averaged. The Protean 3D default is 7, while the original authors use 6. There is very little difference in antigenic site prediction with this change, except that the larger default value requires a slightly larger antigenic site. The authors recommend setting this value between five and eight. If you set the value below five, too many regions may be falsely predicted. Conversely, values set above eight can create a smooth curve, making it difficult to locate areas of potential antigenic sites.
Click if you wish to return to the default value.
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