PSI Structural Biology Knowledgebase

PSI | Structural Biology Knowledgebase
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Glossary

Glossary for the structure report
SectionDescription
Similarity For each matching sequence in the database the percent sequence identity (I) and the BLAST expectation value (E) are provided. The BLAST expectation threshold value used for the search is 10 if your query sequence length is not greater than 50. The expectation threshold value is 0.001 if the query sequence length is greater than 50.
View Alignment Links to a page providing the sequence alignment details for your query sequence and the matching protein sequence. The percent sequence similarity and the expectation value from the BLAST sequence alignment are reported.
Download Download the entry in PDB format for the structure at the RCSB Protein Data Bank (RCSB PDB).
Images Provides a link to molecular images available at the RCSB PDB
RCSB PDB The 4-letter code links to the entry's Structure Summary page at the RCSB PDB.
Authors The list of authors responsible for the structure entry.
Title Author-provided title of the structure entry included in RCSB PDB.
Experimental method The experimental method used to obtain this structure entry such as X-ray crystallography or Nuclear Magnetic Resonance (NMR).
PDB Descriptor A classification of the biological function of the structure used by the RCSB PDB.
PubMed The PubMed identifier code for the primary citation associated with the structure entry. This identifier is linked to the abstract for the publication.
DOI The Document Object Identifier (DOI) for the primary citation associated with this structure entry.
Release date Date the structure was publicly released by the PDB.
Deposition date Date the structure was deposited to the PDB.
Target ID The TargetTrack (formerly TargetDB) identifier code for the protein sequence target related to this structure.
PSI Center The Protein Structure Initiative Center responsible for the structure entry.
View Alignment Links to a page providing the sequence alignment details for your query sequence and the matching protein sequence. The percent similarity and the E-value from BLAST sequence alignment are reported.
BMRB A link to BMRB, Biological Magnetic Resonance Data Bank. A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids and other Biomolecules.

Glossary for the pre-released structures report
SectionDescription
Authors The list of authors responsible for the structure entry.
Title Author-provided title of the structure entry included in RCSB PDB.
Deposition date Date the structure was deposited to the PDB.
Release status Current status of this structure, before its released.
Entity A unique object (sequence) in a PDB structure.


Glossary for the models report
The models section provides links to the PSI Protein Model Portal at the Swiss Institute of Bioinformatics. The Model Portal provides access to the structural models that can be leveraged from PSI targets and other experimental protein structures by comparative modelling methods. The following information is included in the models section:
Section Description
Model Count The number of models satisfying the current query found at the PSI Protein Model Portal.
Providers The source of the model structures satisfying the current query. The PSI Center producing the model or the model database producing the model are identified.

Glossary for the targets & protocols report

SectionDescription
Similarity (Seq search only) For each matching sequence in the database the percent sequence identity (I) and the BLAST expectation value (E) are provided. The BLAST expectation threshold value used for the search is 10 if your query sequence length is not greater than 50. The expectation threshold value is 0.001 if the query sequence length is greater than 50.

View Alignment 

Links to a page providing the sequence alignment details for your query sequence and the matching protein sequence. The percent sequence similarity and the expectation value from the BLAST sequence alignment are reported.
Target Summary A link to the TargetTrack target registration database summary page for this target.
Progress and Protocols The current production status and related protocols used for this target as reported to TargetTrack.
PDB ID The 4-letter code links to the entry's Structure Summary page at the RCSB PDB.
PSI Target Category Scientific category assigned to the target.  A full list of categories can be found on the TargetTrack guidelines site. 


Glossary for the materials report
SectionDescription
Target Summary A link to the TargetTrack target registration database summary page for this target.
Order Clone Links to ordering information for this clone at the PSI:Biology Materials Repository.
Clone Details Links to further information about this clone maintained at the PSI:Biology Materials Repository.
Vector Details Links to further information about this cloning vector maintained at the PSI:Biology Materials Repository.
Structural Biology Knowledgebase ISSN: 1758-1338
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