Screening

Three methods are used to perform the final screen on CDR-H3 loops:

• the RMS deviation screen ,
• the accessibility profile screen,
• or energy only (backbone + sidechains).

After aligning your sequence, you should be able to work out the length of the CDR-H3 loop (defined as the residues between the CAR or CTR and the WG). Depending on the length, you should choose the following:

• 4 residue H3s, or 12 residues or more - the VFF energy screen.
• 6,7 or 9 residues , - the accessibility profile screen.
• 5 or 10-11 residues - the RMS deviation screen. (This particularly applies for 5-residue H3s, or 10 or 11 residue H3s which meet certain sequence characteristics).
• 8 residues - if the first residue type is Trp, Gly or Asp, the RMSD screen should be used. (After reading about the RMSD screen, see here as to why this should be). If it is not Trp , use the accessibility screen as for similar-length loops.

NB(1): WAMpredict will automatically predict the most suitable screen for your sequence.

NB(2): The details of these screens, including why certain screens should be used for certain loop lengths, can be found here.

NB(3): For 5-residue H3s, the RMSD screen is particularly recommended, as a series of tentative sequence-structure rules (see here ) have been drawn up. Since the RMSD screen compares putative models to crystal structures of that length, this is particularly beneficial.

In any case, the accessibility screen can only be used on 5-14 residue H3s, and the RMSD screen on 5, or 7-12 residue H3s.

Important note: One feature of many H3 loops is a kink shape at the C terminus. The presence of this is determined by the sequence. The RMS deviation or accessibility screens will not work if your sequence is not expected to be "kinked", so if you submit using those screens in these cases you will be told that you cannot use it. Therefore, submit again using the VFF energy screen.

Sidechain modelling

There are two different sidechain modelling methods: dead end elimination or CONGEN iterative. The optimum method to use ( see here ) is dependent on your screening method:

• RMS deviation screen: dead-end
• Accessibility profile screen: CONGEN
• VFF backbone + sidechain energy: CONGEN

A general guideline is that the dead-end method is slightly more theoretically sound, but the CONGEN method is quicker. Therefore CONGEN should be used in preference to dead-end if there are several conformations to build sidechains on (as in accessibility and VFF) and particularly if the CDR-H3 is aromatic-rich (see here for more details).

Last updated 21/10/02