PTools specifications

Information


Unique identifier OMICS_23431
Name PTools
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++, Python
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Maintainers


  • person_outline Sebastian Schneider <>
  • person_outline Adrien Saladin <>

Additional information


https://github.com/ptools/ptools/tree/master/Tutorial

Publications for PTools

PTools in publications

 (17)
PMCID: 5813426
PMID: 29444634
DOI: 10.1186/s12859-018-2050-4

[…] institutes of health., metaflux is a module of pathway tools, which is freely available to academic users; it is available for a fee to commercial users. a license can be obtained at biocyc.org/ptools, including the ecocyc database., one file was used with metaflux to generate the results presented in this paper, namely ecocyc-20.0-gem-cs-glucose-tea-oxygen.fba. this is the description […]

PMCID: 5861410
PMID: 29390145
DOI: 10.1093/nar/gky048

[…] to 150 ns. the final 50 and 100 ns of the production phase were considered in the analyses of the filament and the isolated protein trajectories, respectively., in-house python scripts based on the ptools library () were used to compute the number of contacts between different regions of the system. for each contact pair, both the contact occurrence and the persistence time of the contact […]

PMCID: 5031960
PMID: 27653669
DOI: 10.1038/srep33782

[…] homology search (blast) against the uniprot database., a metabolic pathway database, rhacyc, was created for rhazya using the pathologic component of pathway tools (http://bioinformatics.ai.sri.com/ptools/). this program inferred metabolic pathways by comparing the annotated rhazya genes to the metacyc 2.0 reference pathway database (http://www.metacyc.org). the rhacyc database contains […]

PMCID: 5015936
PMID: 27412985
DOI: 10.1534/g3.116.032953

[…] proteome comparison tool in patric (https://www.patricbrc.org) ()., a pathway genome database (pgdb) was constructed using the pathologic module of the pathway tools software (http://brg.ai.sri.com/ptools/) (; ). genes and proteins were imported into pathologic from the annotated genome sequences in genbank file format and metacyc () was selected as the reference pathway database. comparisons […]

PMCID: 4751476
PMID: 26868929
DOI: 10.1038/srep21429

[…] with twice the height of the pentamers and hexamers. we propose here plausible quaternary structures of such decamers and dodecamers, by performing (with our coarse-grained approach implemented in ptools) single docking calculations of the aβ42 cyclic pentamer and hexamer models onto themselves, respectively. we found that the thirteen and twelve lowest energy predicted structures […]


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PTools institution(s)
Physik-Department, Technische Universität München, Garching, Germany
PTools funding source(s)
Supported by the Deutsche Forschungsgemeinschaft (DFG) (grant Za-153/5-3).

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