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Improving the representation of peptide‐like inhibitor and antibiotic molecules in the Protein Data Bank
Author(s) -
Dutta Shuchismita,
Dimitropoulos Dimitris,
Feng Zukang,
Persikova Irina,
Sen Sanchayita,
Shao Chenghua,
Westbrook John,
Young Jasmine,
Zhuravleva Marina A.,
Kleywegt Gerard J.,
Berman Helen M.
Publication year - 2014
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.22434
Subject(s) - protein data bank , protein data bank (rcsb pdb) , peptide , representation (politics) , chemistry , consistency (knowledge bases) , sequence (biology) , computational biology , antibiotics , computer science , combinatorial chemistry , biochemistry , protein structure , artificial intelligence , biology , political science , law , politics
ABSTRACT With the accumulation of a large number and variety of molecules in the Protein Data Bank (PDB) comes the need on occasion to review and improve their representation. The Worldwide PDB (wwPDB) partners have periodically updated various aspects of structural data representation to improve the integrity and consistency of the archive. The remediation effort described here was focused on improving the representation of peptide‐like inhibitor and antibiotic molecules so that they can be easily identified and analyzed. Peptide‐like inhibitors or antibiotics were identified in over 1000 PDB entries, systematically reviewed and represented either as peptides with polymer sequence or as single components. For the majority of the single‐component molecules, their peptide‐like composition was captured in a new representation, called the subcomponent sequence. A novel concept called “group” was developed for representing complex peptide‐like antibiotics and inhibitors that are composed of multiple polymer and nonpolymer components. In addition, a reference dictionary was developed with detailed information about these peptide‐like molecules to aid in their annotation, identification and analysis. Based on the experience gained in this remediation, guidelines, procedures, and tools were developed to annotate new depositions containing peptide‐like inhibitors and antibiotics accurately and consistently. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 659–668, 2014.