05.12.11 Data reading

Name
Antigen

Accession number (and link to raw data):
Light chain Heavy chain

Sequence of:
L1 L2 L3 H1 H2 H3

Length of:
L1 L2 L3 H1 H2 H3

Canonical Class of:
L1 L2 L3 H1 H2

Light chain sequence
Heavy chain sequence
Light chain class
Light chain sub-group (Only valid for Human sequences!)
Heavy chain sub-group (Only valid for Human sequences!)
Animal Source
References

PIR Sequence (Note all other options will be switched off!)

What filters do you wish to apply to the data?

Complete (i.e. has both light & heavy chains)
Note that this will always be ANDed with any other filters.

Name includes the text
Antigen includes the text (Use * to mean any known antigen)
Make this as brief as possible! It is not a keyword-type match, but a literal string match. You should not use inverted commas or wildcards.

CDR contains a specified amino acid sequence:

CDR L1 includes
CDR L2 includes
CDR L3 includes
CDR H1 includes
CDR H2 includes
CDR H3 includes
Note you may use a % as a wildcard to match a single amino acid

CDR matches specified length:

CDR L1 = != < >
CDR L2 = != < >
CDR L3 = != < >
CDR H1 = != < >
CDR H2 = != < >
CDR H3 = != < >

Canonical class of CDR is:

Class of CDR L1 is
Class of CDR L2 is
Class of CDR L3 is
Class of CDR H1 is
Class of CDR H2 is

Light chain includes amino acid sequence (Use * to mean sequence is known)
Heavy chain includes amino acid sequence (Use * to mean sequence is known)
Note you may use a % as a wildcard to match a single amino acid. There must be NO SPACES in the sequence specfication.

References include the string
Make this as brief as possible! It is not a keyword-type match, but a literal string match. You should not use inverted commas or wildcards.

Animal source (e.g. human, mouse, shark, etc.) includes the string
Light chain class: Any Lambda Kappa

Human Subgroup   Light: Any I II III IV V VI Heavy: Any I II III
If you specify either of these you will only get Human sequences!

Combine the filters

Combine the above filters using AND OR
Note that the 'Complete' filter will always be ANDed with any other filters even if you select 'or' here.

Which options do you wish to set?

Loop definition: Kabat Chothia AbM

Should insertions be displayed in the CDRs? Yes No

Which key residue definitions do you wish to use?
Default (essentially as used by AbM)
Strict (from combining the exact definitions as they appear in Chothia's 5 papers)
Auto (As derived by an automated analysis of loop conformation and key residues).

Delimiter: , | ; + \ /

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