PSI PepcDB

Target Search Help

Content and Report Formats:

Definitions of the various data terms used in the PepcDB query:

Project Target ID

A unique identifier for the target sequence defined by each structural genomics center.

Examples:
  • WR90EC
  • NYSGRC-P007
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Target Category

Targets of biomedical significance, metagenomics targets, targets nominated by community, and other category.

Examples:
  • biomedical
  • membrane protein
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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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Site

Name of the Structural Genomics Center responsible for the target.

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

The PSI Structural Genomics Centers: Other Projects: Asia: Europe:
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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
  • Crystallized
  • Diffraction-quality Crystals
  • Diffraction
  • HSQC
  • NMR Assigned
  • Crystal Structure
  • NMR Structure
  • In PDB
  • Work Stopped
  • Test Target
  • Other
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Any Status in the Status Histrory

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

Examples:
  • Selected
  • Cloned
  • Expressed
  • Soluble
  • Purified
  • Crystallized
  • Diffraction-quality Crystals
  • Diffraction
  • HSQC
  • NMR Assigned
  • Crystal Structure
  • NMR Structure
  • 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 reason.

Examples:
  • Expression failed
  • Cloning failed
  • Purification failed
  • Crystallization failed
  • poor NMR
  • sequencing failed
  • mass spec failed
  • Poor diffraction
  • Duplicate target found
  • Other
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Include Data From

The range of centers to include in your target search.

To search only target data provided by the PSI Structural Genomics Centers, select Only PSI Centers.
To include sequences from worldwide Structural Genomics Centers in a query, select All Structural Genomics Centers.
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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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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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Protocol Type

Search experiments that reference selected types of protocols.

Examples:
  • Cloning Protocol
  • Purification Protocol
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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 to see the list of the identified protocols please use link at top of the query result.

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 "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: expression AND (wheat OR yeast OR baculovirus) will return protocols that contain word "expression" and either "wheat", "yeast", or "baculovirus" anywhere in the text.

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Target Sequence

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



Examples:
MKTIIALSYIFCLVFAQDLPGNDNNSTATLCLGHH
AVPNGTLVKTITNDQIEVTNATELVQSSSTGKICN
NPHRILDGINCTLIDALLGDPHCDGFQNEKWDLFV
ERSKAFSNCYPYDVPDYASLRSLVASSGTLEFINE
GFNWTGVTQNGGSSACKRGPDSGFFSRLNWLYKSG
STYPVQNVTMPNNDNSDKLYIWGVHHPSTDKEQTN
LYVQASGKVTVSTKRSQQTIIPNVGSRPWVRGLSS
RISIYWTIVKPGDILVINSNGNLIAPRGYFKMRTG
KSSI
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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.

FASTA is available from http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml.



Examples:

0.01

0.0001

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