Project: iedb_v5
Class Epitope Structure

Concrete Class Extends 
        :THING
 
Direct Instances:
None
 
Direct Subclasses:
None
 
Class Documentation:
Epitope structure capture the physical and chemical features of an epitope


Template Slots
Slot name Documentation Type Allowed Values/Classes Cardinality Default
Epitope Name Name of the Epitope as specified in the reference

String    0:1   
Chemical Type Categorization of epitope compound as lipid, carbohydrate, DNA, RNA, peptide, organic, inorganic, etc.

String    0:1   
Conformational Type Specifies whether epitope is recognized by cells in a linear conformation, or as 3-D conformation (B-cell). Conformational epitopes, or discontinuous epitopes, on a protein antigen are formed from several separate regions in the primary sequence of a protein brought together by protein folding. Antibodies that bind conformational epitopes bind only native folded proteins.

String    0:1   
SMILES Structure SMILES notation for 2-D structure of epitope. SMILES stand for Simplified Molecular Input Line Entry Specification. SMILES is widely used as a general-purpose chemical nomenclature and data exchange format

String    0:1   
Linear Sequence Linear sequence of amino acids, if molecule is a peptide. Other chemical structures will be captured using SMILES structure.

String    0:1   
Conformational Sequence Sometimes epitopes that contain conformational determinant consists of amino acid residues that are not contiguous within the protein, but are brought together on the surface by folding of the protein. In such cases the non continuous amino acid sequence constituting the epitope are entered in alphanumeric or position notation.

String    0:1   
Post Translational Modification Post-translational modification is the enzymatic processing of a polypeptide chain after translation from messenger RNA and after peptide bond formation has occurred. IEDB will conform to the SWISS-PROT standard list of common modification categories

String    0:1   
Modified Sequence Modified epitope sequence with identified site(s) of post-translational modification

String    0:1   
Author Identified Mimetopes Mimetope is a structure unrelated to elicit antigen that is recognized by the same antigen receptor.

String    0:1   
Epitopic Region/Domain If the exact location of the epitope in its source is unknown, but the region or domain that it is present in is described in the reference, we capture those details and flag the entry as "Contained Within" so that the user is informed that the structure fields don't represent the epitope, but rather the region in which it is present. This field is of Boolean type.

Boolean    0:1   
Comments General Comments

String    0:1   

Return to class hierarchy


Generated on Thu Jun 02 12:31:05 PDT 2005