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Basic Structure Sequence
Align DNA/Protein Distributions
Statistics Definitions Manual
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Basic
Data Source
Source ID or Accession     Help: Text searches
Name
Antigen     (Kabat sequences only)
Clone     (EMBL format sequence sources only)
Reference
Author
Publication Year
Organism
Exclude sequences
with warnings
Exclude unclassified
sequences
Exclude unpaired
sequences
Exclude un-numbered
sequences
Structure
Heavy Chain
Sequences with a predicted canonical class
Match
Region Method Canonical Class
CDR-H1
CDR-H2
Residues within x Ångströms of your chosen position in known structures
Distance Measure
Chothia Position Constraint Amino Acids Distance (Å)
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add row
Residues within x Ångströms of your chosen position in known structures and predicted in sequences
Distance Measure
C-alpha
Chothia Position Constraint Amino Acids Distance (Å) Plus nσ
 delete row
add row
Light Chain
Sequences with a predicted canonical class
Match
Region Method Canonical Class
CDR-L1
CDR-L2
CDR-L3
Residues within x Ångströms of your chosen position in known structures
Distance Measure
Chothia Position Constraint Amino Acids Distance (Å)
 delete row
add row
Residues within x Ångströms of your chosen position in known structures and predicted in sequences
Distance Measure
C-alpha
Chothia Position Constraint Amino Acids Distance (Å) Plus nσ
 delete row
add row
Sequence
Heavy Chain
Search for chosen motifs within complete sequences
Fragment/Regex
Search for chosen motifs within specific regions
Region Definition
Region Fragment/Regex
HFR1
CDR-H1
HFR2
CDR-H2
HFR3
CDR-H3
HFR4
Specify minimum and maximum lengths for regions
Region Definition
Region Minimum Maximum
HFR1
CDR-H1
HFR2
CDR-H2
HFR3
CDR-H3
HFR4
Constrain amino acids at required positions
Numbering Scheme
Required Position Constraint Amino Acids
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add row
Light Chain
Search for chosen motifs within complete sequences
Fragment/Regex
Search for chosen motifs within specific regions
Region Definition
Region Fragment/Regex
LFR1
CDR-L1
LFR2
CDR-L2
LFR3
CDR-L3
LFR4
Specify minimum and maximum lengths for regions
Region Definition
Region Minimum Maximum
LFR1
CDR-L1
LFR2
CDR-L2
LFR3
CDR-L3
LFR4
Constrain amino acids at required positions
Numbering Scheme
Required Position Constraint Amino Acids
 delete row
add row
Restrict to Antibody Class
Heavy Chain
Light Chain
Add Annotation:
Canonical Classes
Display
Region Auto AbM Strict
CDR-H1
CDR-H2

CDR-L1
CDR-L2
CDR-L3

Environment of selected positions for results with known structures
Distance Measure
Chain Chothia Position Display Distance (A)
 
Environment of selected positions using distance distributions.
Distance Measure
C-alpha
Chain Chothia Position Display Distance (A) Plus nσ
 
Region sequences and/or lengths
Region Definition
Region Sequence Length
HFR1
CDR-H1
HFR2
CDR-H2
HFR3
CDR-H3
HFR4

LFR1
CDR-L1
LFR2
CDR-L2
LFR3
CDR-L3
LFR4

Amino Acids at selected positions
Numbering Scheme
Chain Position
 

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Download results and selected annotation to a local file in one of the following formats:
Tab separated text file
Protein sequences in abYsis FASTA format
Protein + DNA sequences in abYsis FASTA format
abYsis XML short format (no atom coordinates or DNA sequences)
abYsis XML full format

Download is limited to the first 1000 chains or chain pairs.

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