Everything about Protein structure database
In biology, a protein structure database is a database that is modeled around the various experimentally determined protein structures. The aim of most protein structure databases is to organize and annotate the protein structures, providing the biological community access to the experimental data in a useful way. Data included in protein structure databases often includes three-dimensional coordinates as well as experimental information, such as unit cell dimensions and angles for x-ray crystallography determined structures. Though most instances, in this case either proteins or a specific structure determinations of a protein, also contain sequence information and some databases even provide means for performing sequence based queries, the primary attribute of a structure database is structural information, whereas sequence databases focus on sequence information, and contain no structural information for the majority of entries. Protein structure databases are critical for many efforts in computational biology such as structure based drug design, both in developing the computational methods used and in providing a large experimental dataset used by some methods to provide insights about the function of a protein. Wikipedia →
🧭 Start here: a 6-step reading path
- Read the overview: Protein structure databaseA 5-minute orientation
- Skim a recent paper: AlphaFold Protein Structure Database and 3D-Beacons: New Data and CapabilitiesInfluential work since 2022
- Pick up a classic book: Computational Linguistics and Intelligent Text ProcessingThe most-reprinted book on the subject
- Read the landmark paper: AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequencesCited 2,364 times
- Go sideways: Protein Data BankA closely related topic
- Go sideways: PDBsumA closely related topic
📖 Definitions
No dictionary entry for this exact phrase.
🗂️ The subject at a glance
🏆 Landmark papers (most cited)
AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences
HOMSTRAD: A database of protein structure alignments for homologous families
Derivation of rules for comparative protein modeling from a database of protein structure alignments
PrePPI: a structure-informed database of protein–protein interactions
A database of protein structure families with common folding motifs
CyBase: a database of cyclic protein sequence and structure
The CATH Database provides insights into protein structure/function relationships
Development of a heme protein structure electrochemical function database
🆕 Influential since 2022
AlphaFold Protein Structure Database and 3D-Beacons: New Data and Capabilities
BioLiP2: an updated structure database for biologically relevant ligand–protein interactions
AlphaFold Protein Structure Database 2025: a redesigned interface and updated structural coverage
The impact of AlphaFold Protein Structure Database on the fields of life sciences
PrePPI: A Structure Informed Proteome-wide Database of Protein–Protein Interactions
📚 Books worth reading
Computational Linguistics and Intelligent Text ProcessingAlexander Gelbukh · 2003
Mathematical structures for computer scienceJudith L. Gersting · 1982
Bioinformatics and Functional GenomicsJonathan Pevsner · 2003
Statistical Atlases and Computational Models of the Heart. Imaging and Modelling ChallengesOscar Camara · 2012
Bioinformatics for dummiesJean-Michel Claverie · 2003
Essential bioinformaticsJin Xiong · 2006
Computational intelligence and pattern analysis in biology informaticsUjjwal Maulik · 2010
Intelligent Information and Database SystemsAli Selamat · 2013
Ranked by number of editions on Open Library, a rough measure of how lasting a book is.
🔗 Related topics
- Protein Data Bank The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules such as proteins and nucleic acids, which…
- PDBsum PDBsum is a database that provides an overview of the contents of each 3D macromolecular structure deposited in the Protein Data Bank (PDB). The original…
- Structural bioinformatics Structural bioinformatics is the branch of bioinformatics that is related to the analysis and prediction of the three-dimensional structure of biological…
- European Bioinformatics Institute The European Bioinformatics Institute (EMBL-EBI) is an intergovernmental organization (IGO) which, as part of the European Molecular Biology Laboratory…
- Protein Data Bank (file format) The Protein Data Bank (PDB) file format is a textual file format describing the three-dimensional structures of molecules held in the Protein Data Bank…
- Phyre Phyre and Phyre2 (Protein Homology/AnalogY Recognition Engine; pronounced as fire) are free web-based services for protein structure prediction. Phyre…
- Structure validation Macromolecular structure validation is the process of evaluating reliability for 3-dimensional atomic models of large biological molecules such as proteins…
- Biological data visualization Biological data visualization is a branch of bioinformatics concerned with the application of computer graphics, scientific visualization, and information…