PMID: 11604035Oct 18, 2001Paper

On 3-D graphical representation of proteomics maps and their numerical characterization

Journal of Chemical Information and Computer Sciences
M RandićMarjana Novic

Abstract

We consider numerical characterization of proteomics maps by representing a map as a three-dimensional graphical object based on x, y coordinates of the spots and using their relative abundance as the z coordinate. In our representation the protein spots are first ordered based on their relative abundance and labeled accordingly. In the next step a 3-D path is constructed connecting spots having adjacent labels. Finally a matrix is constructed by assigning to each pairs of labels (i, j) matrix element, the numerical value of which is based on the quotients of the Euclidean distance and the distance along the 3-D zigzag between the two points. The approach has been illustrated on a fragment of a proteomics map and compared with 2-D graphical representation of proteomics maps.

References

Aug 1, 1976·Journal of Pharmaceutical Sciences·J A de SilvaC V Puglisi
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Citations

Jun 12, 2003·Journal of Molecular Graphics & Modelling·Zeljko BajzerSubhash C Basak
Feb 24, 2006·Journal of Biomolecular Structure & Dynamics·Fenglan Bai, Tianming Wang
Feb 7, 2003·SAR and QSAR in Environmental Research·M RandićS C Basak
Aug 6, 2004·SAR and QSAR in Environmental Research·M Randić
Aug 6, 2004·SAR and QSAR in Environmental Research·M Randić, J Zupan
Mar 22, 2012·SAR and QSAR in Environmental Research·M RandićD Plavšić
Jan 5, 2014·EURASIP Journal on Bioinformatics & Systems Biology·Sai ZouJunfeng Wang
Feb 25, 2009·Journal of Biomolecular Structure & Dynamics·Wei HuangJianmin Zhang
Jun 15, 2010·Journal of Theoretical Biology·Milan RandićDejan Plavsić
Jun 7, 2008·Proteins·Yu-Hua YaoYao-Zhou Zhang
Jul 11, 2012·Molecular Phylogenetics and Evolution·Takuyo Aita, Koichi Nishigaki
May 4, 2007·Journal of Computational Chemistry·Xizhen ZhangLi Yang
Sep 25, 2009·Journal of Computational Chemistry·Yu-Hua YaoYao-Zhou Zhang
Nov 15, 2011·International Journal of Quantum Chemistry·Ying GuoSheng-Li Zhang
Sep 11, 2003·Chemical Reviews·Milan Randić
Oct 14, 2010·Chemical Reviews·Milan RandićDejan Plavsić
Jul 4, 2019·Journal of Chemical Information and Modeling·Ruimin MaTengfei Luo

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