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Protocols

PBE specifications

Information


Unique identifier OMICS_22477
Name PBE
Alternative name Protein Block Expert
Software type Toolkit/Suite
Interface Web user interface
Restrictions to use None
Programming languages C, Java
Database management system MySQL
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline Bernard Offmann

Publications for Protein Block Expert

PBE citations

 (5)
call_split

Extension of the classical classification of β turns

2016
Sci Rep
PMCID: 5024104
PMID: 27627963
DOI: 10.1038/srep33191
call_split See protocol

[…] k and l correspond 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). […]

library_books

Assignment of PolyProline II Conformation and Analysis of Sequence – Structure Relationship

2011
PLoS One
PMCID: 3069088
PMID: 21483785
DOI: 10.1371/journal.pone.0018401

[…] rmsd) of 0.42 Å . PB assignment was carried out using an in-house program written in C (available at http://www.dsimb.inserm.fr/~debrevern/DOWN/LECT/), it follows similar rules to assignment done by PBE web server (http://bioinformatics.univ-reunion.fr/PBE/) . […]

library_books

Identification of Local Conformational Similarity in Structurally Variable Regions of Homologous Proteins Using Protein Blocks

2011
PLoS One
PMCID: 3060819
PMID: 21445259
DOI: 10.1371/journal.pone.0017826

[…] tion of local protein 3D structures with a root mean square deviation (rmsd) now evaluated at 0.42 Å , . PBs have been assigned using in-house software. It follows rules similar to assignment done by PBE web server (http://bioinformatics.univ-reunion.fr/PBE/) . […]

library_books

Protein structure search and local structure characterization

2008
BMC Bioinformatics
PMCID: 2529324
PMID: 18721472
DOI: 10.1186/1471-2105-9-349

[…] n consistency in our analysis of various structural alphabets, we applied the same FASTA-based alignment algorithm [] in the alignment tests. We tested the alphabets and substitution matrices used in PBE-align, 3D-BLAST, and SA-FAST on ten difficult cases of previously studied pairwise alignments and compared the results with those produced using VAST, DALI, CE, and FATCAT [,]. Based on the alignm […]

library_books

Discovering structural motifs using a structural alphabet: Application to magnesium binding sites

2007
BMC Bioinformatics
PMCID: 1851716
PMID: 17389049
DOI: 10.1186/1471-2105-8-106

[…] The 3D structures of the 70 Mg2+ and 177 Ca2+ proteins were converted into strings of structural letters using the program PBE published in ref. 9. For a given n- residue protein, n-4 letter assignments were obtained by scanning the protein sequence using a 5-residue sliding window. The structure of each 5-residue segment […]

Citations

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PBE institution(s)
Laboratoire de Biochimie et Génétique Moléculaire, Bioinformatics Team, Université de La Réunion, Saint Denis Messag, La Réunion, France; Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India; INSERM, U726, Equipe de Bioinformatique et Génomique Moléculaire (EBGM), Université Paris 7—Denis Diderot, Paris, France
PBE funding source(s)
Supported by a PhD grant from Conseil Régional de La Réunion.

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