PBxplore specifications

Information


Unique identifier OMICS_18198
Name PBxplore
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Reads PDB structure files48, PDBx/mmCIF structure files49, and MD trajectory formats from most MD engines.
Input format PDB
Output data Protein Blocks assignment, Protein Blocks frequency, Statistical analysis.
Output format FASTA
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
License MIT License
Computer skills Advanced
Version 1.3.6
Stability Stable
Requirements
Numpy, Matplotlib, MDAnalysis
Source code URL https://codeload.github.com/pierrepo/PBxplore/tar.gz/v1.3.6
Maintained Yes

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Maintainers


  • person_outline Alexandre G. de Brevern <>
  • person_outline Pierre Poulain <>

Publication for PBxplore

PBxplore in publications

 (4)
PMCID: 5897735
PMID: 29681798
DOI: 10.3389/fnmol.2018.00113

[…] this produced 2000 models of each region., the complex ensemble of structures for each linker variant was further analyzed in terms of protein blocks (pb; de brevern et al., ) assigned using the pbxplore package (barnoud et al., ). for easier pb “sequence” processing, three “letters” of the alphabet were redefined to contain only standard one letter aa codes (b → q, j → s, o → r) allowing us […]

PMCID: 5556033
PMID: 28808266
DOI: 10.1038/s41598-017-08408-w

[…] n-caps and pbs e and f representing β-strand c-caps; pbs a to j are specific to coils; pbs k and l to α-helix n-caps while pbs n to p to α-helix c-caps. pb assignment was carried out using our pbxplore tool at github., pb assignments are done for each residue of the calf-1 domain and over every snapshot extracted from md simulations. the equivalent number of pbs (n eq) is a statistical […]

PMCID: 5024104
PMID: 27627963
DOI: 10.1038/srep33191

[…] to the n cap of an α-helix, and pbs n through p correspond to c-caps. pbs were assigned by using in-house python software, although similar assignment can be performed through the pbe web server or pbxplore (https://github.com/pierrepo/pbxplore)., a specific clustering approach was designed to cluster type iv β-turns by using the classical rule, allowing +/− 30° for all angles, […]

PMCID: 4445325
PMID: 26075209
DOI: 10.3389/fmolb.2015.00020

[…] corresponding position for that window. this pb captures the overall local conformation and approximates the transition along the main-chain smoothly., pb assignments can be done using the python pbxplore tool (https://github.com/pierrepo/pbxplore, in preparation). the result is a translation of a 3d structure into a 1d sequence of pbs., interestingly, the subtle differences between protein […]


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PBxplore institution(s)
INSERM, DSIMB, Paris, France; Univ. Paris Diderot, Sorbonne Paris Cite, UMR-S 1134, Paris, France; Institut National de la Transfusion Sanguine (INTS), Paris, France; Laboratoire d’Excellence GR-Ex, Paris, France; Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands; The Scripps Research Institute, Department of Integrative Structural and Computational Biology, La Jolla, CA, USA; Birkbeck College, University of London, Malet Street, London, UK; INTS, Platelet Unit, Paris, France; Mitochondria, Metals and Oxidative Stress Group, Institut Jacques Monod, UMR 7592, Univ. Paris Diderot, CNRS, Sorbonne Paris Cite, Paris, France
PBxplore funding source(s)
Supported by grants from National Institute for Blood Transfusion (INTS, France) and Lab of Excellence GR-Ex from the Ministry of Research (France), University Paris Diderot, Sorbonne Paris Cite (France), National Institute for Health and Medical Research (INSERM, France), the program ”Investissements d’avenir” of the French National Research Agency, reference ANR-11-IDEX-0005-02 and Indo-French Centre for the Promotion of Advanced Research / CEFIPRA for collaborative grant (number 5302-2).

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