Literature DB >> 18977780

PConPy--a Python module for generating 2D protein maps.

Hui Kian Ho1, Michael J Kuiper, Ramamohanarao Kotagiri.   

Abstract

UNLABELLED: PConPy is an open-source Python module for generating protein contact maps, distance maps and hydrogen bond plots. These maps can be generated in a number of publication-quality vector and raster image formats. Contact maps can be annotated with secondary structure and hydrogen bond assignments. PConPy offers a more flexible choice of contact definition parameters than existing toolkits, most notably a greater choice of inter-residue distance metrics. PConPy can be used as a stand-alone application or imported into existing source code. A web-interface to PConPy is also available for use. AVAILABILITY: The PConPy web-interface and source code can be accessed from its website at http://www.csse.unimelb.edu.au/~hohkhkh1/pconpy/. CONTACT: hohkhkh1@csse.unimelb.edu.au

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Year:  2008        PMID: 18977780     DOI: 10.1093/bioinformatics/btn566

Source DB:  PubMed          Journal:  Bioinformatics        ISSN: 1367-4803            Impact factor:   6.937


  6 in total

1.  SpecP: A tool for spectral partitioning of protein contact graph.

Authors:  Saritha Namboodiri; Kripadas K
Journal:  Bioinformation       Date:  2013-06-08

2.  Automated procedure for contact-map-based protein structure reconstruction.

Authors:  Bogumil M Konopka; Marika Ciombor; Monika Kurczynska; Malgorzata Kotulska
Journal:  J Membr Biol       Date:  2014-03-29       Impact factor: 1.843

3.  Applying PyRosetta molecular energies to separate properly oriented protein models from mirror models, obtained from contact maps.

Authors:  Monika Kurczynska; Ewa Kania; Bogumil M Konopka; Malgorzata Kotulska
Journal:  J Mol Model       Date:  2016-04-23       Impact factor: 1.810

4.  Automated method to differentiate between native and mirror protein models obtained from contact maps.

Authors:  Monika Kurczynska; Malgorzata Kotulska
Journal:  PLoS One       Date:  2018-05-22       Impact factor: 3.240

5.  Tableau-based protein substructure search using quadratic programming.

Authors:  Alex Stivala; Anthony Wirth; Peter J Stuckey
Journal:  BMC Bioinformatics       Date:  2009-05-19       Impact factor: 3.169

6.  RNAmap2D - calculation, visualization and analysis of contact and distance maps for RNA and protein-RNA complex structures.

Authors:  Michal J Pietal; Natalia Szostak; Kristian M Rother; Janusz M Bujnicki
Journal:  BMC Bioinformatics       Date:  2012-12-21       Impact factor: 3.169

  6 in total

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