PickPocket statistics

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Citations per year

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Popular tool citations

chevron_left MHC class I epitope prediction chevron_right
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Tool usage distribution map

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Associated diseases

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PickPocket specifications

Information


Unique identifier OMICS_17947
Name PickPocket
Interface Web user interface
Restrictions to use None
Input data A protein sequence.
Input format FASTA
Computer skills Basic
Version 1.1
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Morten Nielsen <>

Additional information


The standalone version of the tool is available upon request at http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?pickpocket

Information


Unique identifier OMICS_17947
Name PickPocket
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A protein sequence.
Input format FASTA
Operating system Unix/Linux
Computer skills Advanced
Version 1.1
Stability Stable
Maintained Yes

Versioning


Add your version

Documentation


Maintainer


  • person_outline Morten Nielsen <>

Additional information


The standalone version of the tool is available upon request at http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?pickpocket

Publication for PickPocket

PickPocket in publications

 (4)
PMCID: 5320590
PMID: 28348866
DOI: 10.1099/mgen.0.000071

[…] of binding-prediction algorithms we are for the moment constrained by availability of quality pan-specific methods. tepitopepan was implemented because of its simplicity and the robustness of the pickpocket method () when the similarity to mhc molecules with known binding specificity is low. tepitopepan [using the propred () implementation] has already been used in several studies relating […]

PMCID: 4654883
PMID: 26589500
DOI: 10.1186/s13073-015-0245-0

[…] methods are netmhcpan [], pick-pocket [], tepitopepan [], adt [], unitope [] and kiss []. multi-pred trains one predictor per super-class (alleles with similar binding properties), whereas pickpocket and tepitopepan calculate the binding specificities of the hla molecule by comparing the pocket-residues with the hlas in their library and calculating a weighted average score, and kiss […]

PMCID: 4570239
PMID: 26370412
DOI: 10.1186/s12859-015-0724-8

[…] evaluated (pam and blosum) for scoring pocket similarity and identifying the best human match. the accuracy of the pigmatrices was compared to available online swine epitope prediction tools such as pickpocket and netmhcpan., pigmatrices that used ssc to define the pocket sequences and pam30 to score pocket similarity demonstrated the best predictive performance and were able to accurately […]

PMCID: 3908610
PMID: 24565049
DOI: 10.1186/1477-5956-11-S1-S15

[…] and hla-ii alleles and 26 hla supertypes. it can be regarded as a combination of the multipred, pepvac, netmhcpan and netmhciipan methods. the tepitopepan [] method, which builds on the tepitope and pickpocket [] methods, enables prediction for more than 700 hla-dr molecules., here, we propose a new mhc ii binding prediction method, which we call owa-pssm. a preliminary study of a special case […]


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PickPocket institution(s)
Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
PickPocket funding source(s)
Supported by National Institutes of Health contracts (HHSN26620 0400025C, HHSN266200400083C and HHSN26620040006C).

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