PSI PepcDB

PepcDB | Description of Search Attributes

Definitions of the Data Terms Used in a PepcDB Query

Target Attributes: Trial Attributes:

PepcDB Target Attributes

Project Target ID

A unique identifier for the target sequence defined by the depositing center.


Examples:
  • WR90EC
  • NYSGRC-P007
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External Database ID

Identifier of external databases including Uniprot, GenBank, PFAM, PDB, CATH, SGD, WormBase.


Examples:

PDB identifiers:

  • 1EKE
  • 1STZ

PFAM identifiers:

  • PF00005
  • PF00137
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Target Category

Targets of biomedical significance, membrane protein targets, metagenomics targets, targets nominated by community, targets arising from PSI-Biology partnerships, and other categories.


Examples:
  • biomedical
  • community nominated
  • legacy
  • membrane protein
  • metagenomic
  • structural coverage
  • technology development
  • PSI Biology partnership
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Target Status

Represents the current experimental status of a target. This is different from query options "Trial Status" and "Any Status in History", which represent status information of specific experiments (trials) associated with a target.

Searching with this item returns all targets in the database whose current state of production is in the selected experimental status.


Examples:
  • Selected
  • Cloned
  • Expressed
  • Soluble
  • Purified
  • Mass Spec Verified
  • Crystallized
  • Diffraction-Quality Crystals
  • Diffraction (Native Diffraction-Data or Phasing Diffraction-Data)
  • Crystal Structure
  • Heteronuclear Single Quantum Coherence (HSQC)
  • NMR Assigned
  • NMR Structure
  • In BMRB
  • In PDB
  • Work Stopped
  • Test Target
  • Other
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Site

Name of the Structural Biology Center responsible for the target.


To search targets from a single Structural Biology center, select one of the project sites from the list below.


PSI-1 and PSI-2 Centers: Other North American Projects: Other Asian and Eureopean Projects: back to top

Include Data From

The range of centers to include in your target search.


To search only target data provided by the PSI Centers in a query, select Only PSI Centers.


To include sequences from worldwide structural biology centers in a query, select All Structural Biology Centers.


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Protein Name

The name of the target protein.


Examples:
  • Glutamate synthase
  • 29-C10
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Source Organism

The scientific name of the source organism from which the target sequence was obtained.


Examples:
  • Arabidopsis thaliana
  • Escherichia coli
  • Caenorhabditis elegans
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Target Sequence

The one-letter code sequence of the target, for FASTA comparison.


Example:
MKTIIALSYIFCLVFAQDLPGNDNNSTATLCLGHH
AVPNGTLVKTITNDQIEVTNATELVQSSSTGKICN
NPHRILDGINCTLIDALLGDPHCDGFQNEKWDLFV
ERSKAFSNCYPYDVPDYASLRSLVASSGTLEFINE
GFNWTGVTQNGGSSACKRGPDSGFFSRLNWLYKSG
STYPVQNVTMPNNDNSDKLYIWGVHHPSTDKEQTN
LYVQASGKVTVSTKRSQQTIIPNVGSRPWVRGLSS
RISIYWTIVKPGDILVINSNGNLIAPRGYFKMRTG
KSSI
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FASTA Sequence Search E-Value

Pearson, W.R. and Lipman, D.J. Improved tools for biological sequence comparison. PNAS 85:2444-2448 (1988).


The E()-value cutoff limits the number of scores and alignments shown based on the expected number of scores. A cutoff value of 2.0 (-E 2.0) will show all library sequences with scores with an expectation value <= 2.0.


For protein searches, matched sequences with E()-values < 0.01 for searches of 10,000 protein sequences are almost always homologous. Frequently sequences with E()-values from 1 - 10 are related as well. However, E()-values also reflect differences between the amino acid composition of the query sequence and that of the "average" database sequence. Therefore, when searches are done with query sequences with "biased" amino-acid composition, unrelated sequences may have "significant" scores because of sequence bias.


Examples:
  • 10
  • 0.01
  • 0.0001

FASTA is available from

http://fasta.bioch.virginia.edu/fasta/fasta_list.html


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PepcDB Trial Attributes

Protocol Keywords

This field allows you to search text of experimental protocols that match the "key words". The query will return the list of experimental trials that reference the identified text protocols. If you are only interested in seeing the list of the identified protocols, please use the link at top of the query results page.

The protocols can be searched with exact phrases or specific words. The phrases and words can be grouped (...) and searched with conjunction (AND) or disjuction (OR) operators. If boolean operators are not provided, the search will be performed with the "AND" operator. To search with exact phrases please include your sentence into the double quotes, example "cell free expression".


Examples:
  • Search: pET21b will return protocols that contain word pET21b in the text.
  • Search: "cell free expression" will return protocols that contain the phrase "cell free expression" in the text.
  • Search: cell AND free AND expression will return protocols that contain all three words anywhere in the text.
  • Search: cell free expression will return protocols that contain all three words anywhere in the text (same as using AND operator as above).
  • Search: expression AND (wheat OR yeast OR baculovirus) will return protocols that contain the word "expression" and either "wheat", "yeast", or "baculovirus" anywhere in the text.
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Experiment Current Status

The current status of the experimental trial. Searching with this item returns all experiments in the database that reached the selected experimental status.


Examples:
  • Selected
  • Cloned
  • Expressed
  • Soluble
  • Purified
  • Mass Spec Verified
  • Crystallized
  • Diffraction-Quality Crystals
  • Diffraction (Native Diffraction-Data or Phasing Diffraction-Data)
  • Crystal Structure
  • Heteronuclear Single Quantum Coherence (HSQC)
  • NMR Assigned
  • NMR Structure
  • In BMRB
  • In PDB
  • Work Stopped
  • Test Target
  • Other
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Experiment Status History

Experimental trial status. Searching with this item returns all experiments in the database that report the selected experimental status in their status history.


Examples:
  • Selected
  • Cloned
  • Expressed
  • Soluble
  • Purified
  • Mass Spec Verified
  • Crystallized
  • Diffraction-Quality Crystals
  • Diffraction (Native Diffraction-Data or Phasing Diffraction-Data)
  • Crystal Structure
  • Heteronuclear Single Quantum Coherence (HSQC)
  • NMR Assigned
  • NMR Structure
  • In BMRB
  • In PDB
  • Work Stopped
  • Test Target
  • Other
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Experiment Stop Status

Experiment status termination code. Search for experiments that were stopped due to experimental failure or other reasons.


Examples:
  • Cloning Failed
  • Sequencing Failed
  • Expression Failed
  • Purification Failed
  • Mass Spec Failed
  • Crystallization Failed
  • Poor Diffraction
  • Poor NMR
  • Duplicate Target Found
  • Internal Duplicate Target Found
  • TargetDB Duplicate Target Found
  • PDB Duplicate Target Found
  • Structure Successful
  • Other
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Experimental Trial Data Updated

Search experimental trials that were updated before and/or after identified date.


Examples:
  • Before: 2001-05-10
  • After : 2001-01-21
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Protocol Type

Search experiments that reference selected types of protocols.


Examples:
  • Cloning Protocol
  • Purification Protocol
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