A Critical Guide to the PDB

This Critical Guide in the Introduction to Bioinformatics series provides a brief outline of the Protein Data Bank – the PDB – the world’s primary repository of biological macromolecular structures. The rationale for creating the resource and the kinds of information it provides are discussed, and issues relating to its evolution and growth are explored.
Specifically, this Guide introduces the principal features of the PDB, the nature (and quality) of its contents and how these may be interrogated. On reading this Guide, users will be able to: i) explain some of the ways in which knowledge of protein structures is useful; ii) identify the constituent databases of the wwPDB; iii) explain key features of the RCSB PDB in terms of its data distribution, growth and redundancy statistics; iv) search the PDB using simple and advanced keywords and full sequences, and analyse differences between them; and v) explain various structural quality criteria, and infer the quality of individual PDB entries.

Scientific topics: Database management

Keywords: Introduction bioinformatics, Introduction pdb, Protein structure analysis, Protein structure databases, Protein structures

Target audience: Beginners

Authors: Terri Attwood

Remote created date: 2018-09-08

A Critical Guide to the PDB https://tess.elixir-europe.org/materials/a-critical-guide-to-the-pdb This Critical Guide in the Introduction to Bioinformatics series provides a brief outline of the Protein Data Bank – the PDB – the world’s primary repository of biological macromolecular structures. The rationale for creating the resource and the kinds of information it provides are discussed, and issues relating to its evolution and growth are explored. Specifically, this Guide introduces the principal features of the PDB, the nature (and quality) of its contents and how these may be interrogated. On reading this Guide, users will be able to: i) explain some of the ways in which knowledge of protein structures is useful; ii) identify the constituent databases of the wwPDB; iii) explain key features of the RCSB PDB in terms of its data distribution, growth and redundancy statistics; iv) search the PDB using simple and advanced keywords and full sequences, and analyse differences between them; and v) explain various structural quality criteria, and infer the quality of individual PDB entries. Database management Introduction bioinformatics, Introduction pdb, Protein structure analysis, Protein structure databases, Protein structures Beginners 2018-09-08