Improving the representation of peptide‐like inhibitor and antibiotic molecules in the Protein Data Bank

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.

Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive

“…A related PDB chemical reference dictionary is the Biologically Interesting molecule Reference Dictionary (BIRD) [48], which contains information about oligopeptide-like molecules in the PDB archive. BIRD entries include molecular weight and chemical formula, polymer sequence and connectivity, descriptions of structural features and functional classification, natural source, and external references to corresponding UniProt [49] or Norine [50] archived amino acid sequences.…”

OUP accepted manuscript

“…In addition to FTP file access, data files are now accessible through both HTTP and secure HTTPS protocols (http://www.rcsb.org/pdb/static.do?p=download/http/index.html) to simplify access by other web resources. This functionality provides access to PDB atomic coordinates (.pdb, .cif, .xml), experimental data (structure factors for X-ray, restraints and chemical shifts for NMR) and small molecule data files [Chemical Components (35) and Biologically Interesting Molecules (36,37)].…”

OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive

“…The Biocurator can then accept the matched CCD entry, or launch a ligand editor to define a new chemical component when no appropriate CCD match is found (Sen et al, 2014; Young et al, 2013). Additional modules permit representation changes between polymeric and non-polymeric forms for peptide-like inhibitors/antibiotics (Dutta et al, 2014), value-added annotation such as secondary structure or connectivity between a ligand and neighboring polymer residues, method-specific annotation, etc. The Validation Module performs format and data consistency checks and generates the official wwPDB Validation Report.…”