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SAR and QSAR in Environmental Research Volume 19, 2008 - Issue 3-4
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Original Articles

On novel representation of proteins based on amino acid adjacency matrix

M. Randić† National Institute of Chemistry, Hajdrihova, Ljubljana, SloveniaCorrespondence[email protected]
,
M. Novič National Institute of Chemistry, Hajdrihova, Ljubljana, Slovenia
&
M. Vračko National Institute of Chemistry, Hajdrihova, Ljubljana, Slovenia
Pages 339-349 | Received 05 Sep 2007, Accepted 30 Jan 2008, Published online: 04 Dec 2010

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A. El-Lakkani & M. Lashin. (2016) An efficient method for measuring the similarity of protein sequences. SAR and QSAR in Environmental Research 27:5, pages 363-370.
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M. Randić. (2015) On the history of the connectivity index: from the connectivity index to the exact solution of the protein alignment problem. SAR and QSAR in Environmental Research 26:7-9, pages 523-555.
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M.K. Gupta, R. Niyogi & M. Misra. (2013) An alignment-free method to find similarity among protein sequences via the general form of Chou’s pseudo amino acid composition. SAR and QSAR in Environmental Research 24:7, pages 597-609.
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M. Randić, M. Novič, A. Roy Choudhury & D. Plavšić. (2012) On graphical representation of trans-membrane proteins. SAR and QSAR in Environmental Research 23:3-4, pages 327-343.
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P. He. (2010) A new graphical representation of similarity/dissimilarity studies of protein sequences. SAR and QSAR in Environmental Research 21:5-6, pages 571-580.
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A. Roy Choudhury & M. Novič. (2009) Data-driven model for the prediction of protein transmembrane regions. SAR and QSAR in Environmental Research 20:7-8, pages 741-754.
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Articles from other publishers (24)

Wei Li, Lina Yang, Yu Qiu, Yujian Yuan, Xichun Li & Zuqiang Meng. (2022) FFP: joint Fast Fourier transform and fractal dimension in amino acid property-aware phylogenetic analysis. BMC Bioinformatics 23:1.
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Neelesh Babu Thummadi, Mallikarjuna T., Vaibhav Vindal & Manimaran P.. (2021) Prioritizing the candidate genes related to cervical cancer using the moment of inertia tensor. Proteins: Structure, Function, and Bioinformatics 90:2, pages 363-371.
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Mervat M. Abo-Elkhier, Marwa A. Abd Elwahaab & Moheb I. Abo El Maaty. (2019) Measuring Similarity among Protein Sequences Using a New Descriptor. BioMed Research International 2019, pages 1-10.
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Marwa A. Abd Elwahaab, Mervat M. Abo-Elkhier & Moheb I. Abo el Maaty. (2019) A Statistical Similarity/Dissimilarity Analysis of Protein Sequences Based on a Novel Group Representative Vector. BioMed Research International 2019, pages 1-9.
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Milan Randić. (2018) Mathematical chemistry illustrations: a personal view of less known results. Journal of Mathematical Chemistry 57:1, pages 280-314.
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Li Ge, Jiaguo Liu, Yusen Zhang & Matthias Dehmer. (2018) Identifying anticancer peptides by using a generalized chaos game representation. Journal of Mathematical Biology 78:1-2, pages 441-463.
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Jayanta Pal, Soumen Ghosh, Bansibadan Maji & Dilip Kumar Bhattacharya. (2017) WITHDRAWN: A Novel Way of Comparing Protein Sequences Represented Under Physio-Chemical Properties of their Amino Acids. Computational Biology and Chemistry.
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Milan Randic, Marjana Novic & Dejan Plavsic. 2016. Solved and Unsolved Problems of Structural Chemistry. Solved and Unsolved Problems of Structural Chemistry 325 364 .
Soumen Ghosh, Jayanta Pal, Bansibadan Maji & Dilip Kumar Bhattacharya. (2016) Condensed Matrix Descriptor for Protein Sequence Comparison. International Journal of Analytical Mass Spectrometry and Chromatography 04:01, pages 1-13.
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Jayanta Pal, Soumen Ghosh, Bansibadan Maji & Dilip Kumar Bhattacharya. (2016) Use of FFT in Protein Sequence Comparison under Their Binary Representations. Computational Molecular Bioscience 06:02, pages 33-40.
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Amrita Roy Choudhury & Marjana Novi?. (2015) Pred?TM: A Novel ?-Transmembrane Region Prediction Algorithm. PLOS ONE 10:12, pages e0145564.
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Lei Wang, Hui Peng & Jinhua Zheng. (2014) ADLD: A Novel Graphical Representation of Protein Sequences and Its Application. Computational and Mathematical Methods in Medicine 2014, pages 1-15.
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Zengchao Mu, Jing Wu & Yusen Zhang. (2013) A novel method for similarity/dissimilarity analysis of protein sequences. Physica A: Statistical Mechanics and its Applications 392:24, pages 6361-6366.
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Ali El-Lakkani & Seham El-Sherif. (2013) Similarity analysis of protein sequences based on 2D and 3D amino acid adjacency matrices. Chemical Physics Letters 590, pages 192-195.
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Milan Randić, Marjana Novič & Dejan Plavšić. (2013) Milestones in graphical bioinformatics. International Journal of Quantum Chemistry 113:22, pages 2413-2446.
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Amrita Roy Choudhury, Nikolay Zhukov & Marjana Novič. (2013) Mathematical Characterization of Protein Transmembrane Regions. The Scientific World Journal 2013, pages 1-6.
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Milan Randić, Jure Zupan, Alexandru T. Balaban, Dražen Vikić-Topić & Dejan Plavšić. (2010) Graphical Representation of Proteins. Chemical Reviews 111:2, pages 790-862.
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Ambarnil Ghosh & Ashesh Nandy. 2011. Protein Structure and Diseases. Protein Structure and Diseases 1 42 .
Keshari Kishore Jha, Abdul Samad, Yatendra Kumar, Mohd. Shaharyar, Ratan Lal Khosa, Jainendra Jain, Vikash Kumar & Priyanka Singh. (2010) Design, synthesis and biological evaluation of 1,3,4-oxadiazole derivatives. European Journal of Medicinal Chemistry 45:11, pages 4963-4967.
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Ping‐An He, Yan‐Ping Zhang, Yu‐Hua Yao, Yi‐Fa Tang & Xu‐Ying Nan. (2010) The graphical representation of protein sequences based on the physicochemical properties and its applications. Journal of Computational Chemistry 31:11, pages 2136-2142.
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Milan Randić, Tomaž Pisanski, Marjana Novič & Dejan Plavšić. (2010) Novel graph distance matrix. Journal of Computational Chemistry, pages NA-NA.
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Milan Randić, Marjan Vračko, Marjana Novič & Dejan Plavšić. (2009) Spectrum-like graphical representation of RNA secondary structure. International Journal of Quantum Chemistry 109:13, pages 2982-2995.
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H. González-Díaz, L.G. Pérez-Montoto, A. Duardo-Sanchez, E. Paniagua, S. Vázquez-Prieto, R. Vilas, M.A. Dea-Ayuela, F. Bolas-Fernández, C.R. Munteanu, J. Dorado, J. Costas & F.M. Ubeira. (2009) Generalized lattice graphs for 2D-visualization of biological information. Journal of Theoretical Biology 261:1, pages 136-147.
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Milan Randić, Ketij Mehulić, Damir Vukičević, Tomaž Pisanski, Dražen Vikić-Topić & Dejan Plavšić. (2009) Graphical representation of proteins as four-color maps and their numerical characterization. Journal of Molecular Graphics and Modelling 27:5, pages 637-641.
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