PickPocket statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

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


No version available

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 citations

 (5)
library_books

Integrated computational prediction and experimental validation identifies promiscuous T cell epitopes in the proteome of Mycobacterium bovis

2016
Microb Genom
PMCID: 5320590
PMID: 28348866
DOI: 10.1099/mgen.0.000071

[…] ice 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 to […]

library_books

Immunoinformatics and epitope prediction in the age of genomic medicine

2015
Genome Med
PMCID: 4654883
PMID: 26589500
DOI: 10.1186/s13073-015-0245-0

[…] n-specific 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 is […]

library_books

Machine Learning Methods for Predicting HLA–Peptide Binding Activity

2015
Bioinform Biol Insights
PMCID: 4603527
PMID: 26512199
DOI: 10.4137/BBI.S29466

[…] med models are selected and the median value is used as the final consensus score. A similar consensus approach was implemented by NetMHCcons that combines ANN-based NetMHC, NetMHCpan, and PSSM-based PickPocket. Instead of median values, NetMHCcons uses the average log-transformed values as the final prediction scores.The consensus method generally outperforms single models since it can preferably […]

library_books

Development and validation of an epitope prediction tool for swine (PigMatrix) based on the pocket profile method

2015
BMC Bioinformatics
PMCID: 4570239
PMID: 26370412
DOI: 10.1186/s12859-015-0724-8

[…] characteristic (ROC) curve (AUC) using the sensitivity and 1 - specificity values for the same dataset of binders and non-binders.Finally, PigMatrix SLA class I predictions were compared to those of PickPocket 1.1 and NetMHCpan 2.4 and 2.8. A threshold of 500 nM in binding affinity (or 0.426 prediction score based on 1 − log 50K(affinity), was set to classify binders and non-binders as previously […]

library_books

An effective and effecient peptide binding prediction approach for a broad set of HLA DR molecules based on ordered weighted averaging of binding pocket profiles

2013
Proteome Sci
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 of t […]

Citations

Looking to check out a full list of citations?

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).

PickPocket reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review PickPocket