Protein structure databases
Encyclopedia
In biology
, a protein structure database is a database
that is modeled
around the various experimentally determined protein structure
s. 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.
of all experimentally determined protein structure data. Today the PDB is maintained by an international consortia collectively known as the Worldwide Protein Data Bank
(wwPDB). The mission of the wwPDB is to maintain a single archive of macromolecular structural data that is freely and publicly available to the global community.
, the data has been used in various other protein structure databases.
Examples of protein structure databases include (in alphabetical order);
Database of Macromolecular Movements : describes the motions that occur in proteins and other macromolecules, particularly using movies
JenaLib : the Jena Library of Biological Macromolecules is aimed at a better dissemination of information on three-dimensional biopolymer structures with an emphasis on visualization and analysis.
ModBase
: a database of three-dimensional protein models calculated by comparative modeling
PDBe : the European resource for the collection, organisation and dissemination of data on biological macromolecular structures, and a member of the Worldwide Protein Data Bank
.
OCA : a browser-database for protein structure/function - The OCA integrates information from KEGG, OMIM, PDBselect, Pfam
, PubMed
, SCOP
, SwissProt, and others.
OPM
: provides spatial positions of protein three-dimensional structures with respect to the lipid bilayer
.
PDB Lite : derived from OCA, PDB Lite was provided to make it as easy as possible to find and view a macromolecule within the PDB
PDBsum : provides an overview macromolecular structures in the PDB, giving schematic diagrams of the molecules in each structure and of the interactions between them
PDBTM : the Protein Data Bank of Transmembrane Proteins
— a selection of the PDB.
PDBWiki
: a community annotated knowledge base of biological molecular structures http://pdbwiki.org
Protein : the NIH protein database, a collection of sequences from several sources, including translations from annotated coding regions in GenBank
, RefSeq
and TPA
, as well as records from SwissProt, PIR
, PRF
, and PDB
Proteopedia
: the collaborative, 3D encyclopedia of proteins and other molecules. A wiki that contains a page for every entry in the PDB (>50,000 pages), with a Jmol
view that highlights functional sites and ligands. Offers an easy-to-use scene-authoring tool so you don't have to learn Jmol script language to create customized molecular scenes. Custom scenes are easily attached to "green links" in descriptive text that display those scenes in Jmol.
SCOP
: the Structural Classification of Proteins http://scop.mrc-lmb.cam.ac.uk/scop/ a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known.
SWISS-MODEL Repository : a database of annotated protein models calculated by homology modeling
TOPSAN : the Open Protein Structure Annotation Network — a wiki designed to collect, share and distribute information about protein three-dimensional structures.
ProtCID
: The Protein Common Interface Database (ProtCID) is a database of similar protein-protein interfaces in crystal structures of homologous proteins.
Biology
Biology is a natural science concerned with the study of life and living organisms, including their structure, function, growth, origin, evolution, distribution, and taxonomy. Biology is a vast subject containing many subdivisions, topics, and disciplines...
, a protein structure database is a database
Database
A database is an organized collection of data for one or more purposes, usually in digital form. The data are typically organized to model relevant aspects of reality , in a way that supports processes requiring this information...
that is modeled
Data modeling
Data modeling in software engineering is the process of creating a data model for an information system by applying formal data modeling techniques.- Overview :...
around the various experimentally determined protein structure
Protein structure
Proteins are an important class of biological macromolecules present in all organisms. Proteins are polymers of amino acids. Classified by their physical size, proteins are nanoparticles . Each protein polymer – also known as a polypeptide – consists of a sequence formed from 20 possible L-α-amino...
s. 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
Sequence database
In the field of bioinformatics, a sequence database is a large collection of computerized nucleic acid sequences, protein sequences, or other sequences stored on a computer...
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.
The Protein Data Bank
The Protein Data Bank (PDB) was established in 1971 as the central archiveArchive
An archive is a collection of historical records, or the physical place they are located. Archives contain primary source documents that have accumulated over the course of an individual or organization's lifetime, and are kept to show the function of an organization...
of all experimentally determined protein structure data. Today the PDB is maintained by an international consortia collectively known as the Worldwide Protein Data Bank
Worldwide Protein Data Bank
The Worldwide Protein Data Bank, wwPDB, is an organization whose mission, according to its website, is "to maintain a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly available to the global community." Given the open access goal, it is somewhat ironic...
(wwPDB). The mission of the wwPDB is to maintain a single archive of macromolecular structural data that is freely and publicly available to the global community.
List of other protein structure databases
Because the PDB releases data into the public domainPublic domain
Works are in the public domain if the intellectual property rights have expired, if the intellectual property rights are forfeited, or if they are not covered by intellectual property rights at all...
, the data has been used in various other protein structure databases.
Examples of protein structure databases include (in alphabetical order);
Database of Macromolecular Movements : describes the motions that occur in proteins and other macromolecules, particularly using movies
JenaLib : the Jena Library of Biological Macromolecules is aimed at a better dissemination of information on three-dimensional biopolymer structures with an emphasis on visualization and analysis.
ModBase
ModBase
ModBase is a database of annotated comparative protein structure models....
: a database of three-dimensional protein models calculated by comparative modeling
PDBe : the European resource for the collection, organisation and dissemination of data on biological macromolecular structures, and a member of the Worldwide Protein Data Bank
Worldwide Protein Data Bank
The Worldwide Protein Data Bank, wwPDB, is an organization whose mission, according to its website, is "to maintain a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly available to the global community." Given the open access goal, it is somewhat ironic...
.
OCA : a browser-database for protein structure/function - The OCA integrates information from KEGG, OMIM, PDBselect, Pfam
Pfam
Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models.- Features :For each family in Pfam one can:* Look at multiple alignments* View protein domain architectures...
, PubMed
PubMed
PubMed is a free database accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine at the National Institutes of Health maintains the database as part of the Entrez information retrieval system...
, SCOP
SCOP
SCOP may refer to:* Structural Classification of Proteins* Suprachiasmatic nucleus circadian oscillatory protein, a member of the leucine-rich repeat protein family* Société coopérative, a type of corporation in France...
, SwissProt, and others.
OPM
Orientations of Proteins in Membranes database
Orientations of Proteins in Membranes database provides spatial positions of membrane protein structures with respect to the lipid bilayer. Positions of the proteins are calculated using an implicit solvation model of the lipid bilayer...
: provides spatial positions of protein three-dimensional structures with respect to the lipid bilayer
Lipid bilayer
The lipid bilayer is a thin membrane made of two layers of lipid molecules. These membranes are flat sheets that form a continuous barrier around cells. The cell membrane of almost all living organisms and many viruses are made of a lipid bilayer, as are the membranes surrounding the cell nucleus...
.
PDB Lite : derived from OCA, PDB Lite was provided to make it as easy as possible to find and view a macromolecule within the PDB
PDBsum : provides an overview macromolecular structures in the PDB, giving schematic diagrams of the molecules in each structure and of the interactions between them
PDBTM : the Protein Data Bank of Transmembrane Proteins
Membrane protein
A membrane protein is a protein molecule that is attached to, or associated with the membrane of a cell or an organelle. More than half of all proteins interact with membranes.-Function:...
— a selection of the PDB.
PDBWiki
PDBWiki
PDBWiki is a wiki that functions as a user-contributed database of protein structure annotations, listing all the protein structures currently available in the Protein Data Bank...
: a community annotated knowledge base of biological molecular structures http://pdbwiki.org
Protein : the NIH protein database, a collection of sequences from several sources, including translations from annotated coding regions in GenBank
GenBank
The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. This database is produced and maintained by the National Center for Biotechnology Information as part of the International Nucleotide Sequence...
, RefSeq
RefSeq
The Reference Sequence database is an open access, annotated and curated collection of publicly available nucleotide sequences and their protein products. This database is built by National Center for Biotechnology Information , and, unlike GenBank, provides only single record for each natural...
and TPA
TPA
TPA may refer to:* Third-Party Audit, an Audit performed by a specialized & independent Organization* TaxPayers' Alliance, a British free-market lobby group* Tempe Preparatory Academy, a preparatory secondary school in Arizona, USA...
, as well as records from SwissProt, PIR
Protein Information Resource
The Protein Information Resource , located at Georgetown University Medical Center , is an integrated public bioinformatics resource to support genomic and proteomic research, and scientific studies-History:...
, PRF
PRF
PRF is an acronym and can stand for:* Platelet Rich Fibrin, A combination of platelets and fibrin used to regenerate tissue* PRF-3, the call letters of the now defunct TV Tupi, Brazil's first television station* Pain Relief Foundation...
, and PDB
Protein Data Bank
The Protein Data Bank is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids....
Proteopedia
Proteopedia
Proteopedia is a wiki, 3D encyclopedia of proteins and other molecules..The site contains a page for every entry in the Protein Data Bank , as well as pages that are more descriptive of protein structures in general such as acetylcholinesterase, hemoglobin, and the photosystem II with a Jmol view...
: the collaborative, 3D encyclopedia of proteins and other molecules. A wiki that contains a page for every entry in the PDB (>50,000 pages), with a Jmol
Jmol
Jmol is an open-source Java viewer for chemical structures in 3D,that does not require 3D acceleration plugins.Jmol returns a 3D representation of a molecule that may be used as a teaching tool, or for research e.g...
view that highlights functional sites and ligands. Offers an easy-to-use scene-authoring tool so you don't have to learn Jmol script language to create customized molecular scenes. Custom scenes are easily attached to "green links" in descriptive text that display those scenes in Jmol.
SCOP
Structural Classification of Proteins
The Structural Classification of Proteins database is a largely manual classification of protein structural domains based on similarities of their structures and amino acid sequences. A motivation for this classification is to determine the evolutionary relationship between proteins...
: the Structural Classification of Proteins http://scop.mrc-lmb.cam.ac.uk/scop/ a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known.
SWISS-MODEL Repository : a database of annotated protein models calculated by homology modeling
TOPSAN : the Open Protein Structure Annotation Network — a wiki designed to collect, share and distribute information about protein three-dimensional structures.
ProtCID
ProtCID
The Protein Common Interface Database is a database of similar protein-protein interfaces in crystal structures of homologous proteins....
: The Protein Common Interface Database (ProtCID) is a database of similar protein-protein interfaces in crystal structures of homologous proteins.