PDBpaint specifications

Information


Unique identifier OMICS_13977
Name PDBpaint
Interface Application programming interface
Restrictions to use None
Input data A structure, A PDB or UniProt ID and the position to tag
Input format PDB
Output data Properties of the protein (from top to bottom, PDB code, name of protein, function of protein, species).
Programming languages Javascript, Perl
Computer skills Advanced
Stability Stable
Requirements
Java, Jmol program
Maintained Yes

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Maintainer


  • person_outline David Fournier

Publication for PDBpaint

PDBpaint citations

 (2)
library_books

PyMine: a PyMOL plugin to integrate and visualize data for drug discovery

2015
BMC Res Notes
PMCID: 4590260
PMID: 26429562
DOI: 10.1186/s13104-015-1483-3

[…] on and analysis of molecular structures and related data []. Both Cytoscape and Chimera are stand-alone software packages and were not developed exclusively for drug discovery purpose. Aquaria [] and PDBpaint [] were developed to retrieve features from various databases and map them onto the protein structures. Both programs focus primarily on structural features such secondary structures and doma […]

library_books

Functional and Genomic Analyses of Alpha Solenoid Proteins

2013
PLoS One
PMCID: 3837014
PMID: 24278209
DOI: 10.1371/journal.pone.0079894

[…] pplied it to protein sequences with structures in the Protein Data Bank (see below). The results were validated by mapping the ARD2 hits on the corresponding PDB structure for visual inspection using PDBpaint . Positives were used to determine the precision and recall of each combination of parameters and training datasets.We selected the combination that had the best recall for a precision of 100 […]

PDBpaint institution(s)
Max Delbrück Center for Molecular Medicine, Berlin, Germany
PDBpaint funding source(s)
This work was supported by the Collaborative Research Center for Theoretical Biology “Robustness, Modularity and Evolutionary Design of Living Systems” (Sonderforschungsbereich 618 (SFB 618)), and the Humboldt-University of Berlin, Germany

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