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Automatic Identification of Antibodies in the Protein Data Bank
Author(s) -
LI Xun,
WANG Renxiao
Publication year - 2009
Publication title -
chinese journal of chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.28
H-Index - 41
eISSN - 1614-7065
pISSN - 1001-604X
DOI - 10.1002/cjoc.200990021
Subject(s) - protein data bank (rcsb pdb) , protein data bank , antibody , identification (biology) , chemistry , computational biology , computer science , data mining , protein structure , biochemistry , immunology , biology , botany
An automatic method has been developed for identifying antibody entries in the protein data bank (PDB). Our method, called KIAb (Keyword‐based Identification of Antibodies), parses PDB‐format files to search for particular keywords relevant to antibodies, and makes judgment accordingly. Our method identified 780 entries as antibodies on the entire PDB. Among them, 767 entries were confirmed by manual inspection, indicating a high success rate of 98.3%. Our method recovered basically all of the entries compiled in the Summary of Antibody Crystal Structures (SACS) database. It also identified a number of entries missed by SACS. Our method thus provides a more complete mining of antibody entries in PDB with a very low false positive rate.