title: Chemical annotation of small and peptide-like molecules at the Protein Data Bank.
abstract: Over the past decade, the number of polymers and their complexes with small molecules in the Protein Data Bank archive (PDB) has continued to increase significantly. To support scientific advancements and ensure the best quality and completeness of the data files over the next 10 years and beyond, the Worldwide PDB partnership that manages the PDB archive is developing a new deposition and annotation system. This system focuses on efficient data capture across all supported experimental methods. The new deposition and annotation system is composed of four major modules that together support all of the processing requirements for a PDB entry. In this article, we describe one such module called the Chemical Component Annotation Tool. This tool uses information from both the Chemical Component Dictionary and Biologically Interesting molecule Reference Dictionary to aid in annotation. Benchmark studies have shown that the Chemical Component Annotation Tool provides significant improvements in processing efficiency and data quality. Database URL: http://wwpdb.org.
authors.affiliation: Department of Chemistry and Chemical Biology, and Center for Integrative Proteomics Research, Rutgers The State University of New Jersey, 174 Frelinghuysen Rd, Piscataway, NJ 08854-8087, USA and San Diego Supercomputer Centre and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0743, USA.
authors.forename: Jasmine Y
authors.initials: JY
authors.lastname: Young
authors.forename: Zukang
authors.initials: Z
authors.lastname: Feng
authors.forename: Dimitris
authors.initials: D
authors.lastname: Dimitropoulos
authors.forename: Raul
authors.initials: R
authors.lastname: Sala
authors.forename: John
authors.initials: J
authors.lastname: Westbrook
authors.forename: Marina
authors.initials: M
authors.lastname: Zhuravleva
authors.forename: Chenghua
authors.initials: C
authors.lastname: Shao
authors.forename: Martha
authors.initials: M
authors.lastname: Quesada
authors.forename: Ezra
authors.initials: E
authors.lastname: Peisach
authors.forename: Helen M
authors.initials: HM
authors.lastname: Berman
mesh_terms: D019295:Computational Biology; D030562:Databases, Protein; D004014:Dictionaries as Topic; D058977:Molecular Sequence Annotation; D010455:Peptides / Q000737:chemistry*; D012015:Reference Standards; D015203:Reproducibility of Results; D009626:Terminology as Topic
chemical_list: D010455:Peptides