2D-MH

2D-MH: A web-server for generating graphic representation of protein sequences based on the physicochemical properties of their constituent amino acids. Introduction of graphic representation for biological sequences can provide intuitive overall pictures as well as useful insights for performing large-scale analysis. Here, a new two-dimensional graph, called “2D-MH”, is proposed to represent protein sequences. It is formed by incorporating the information of the side-chain mass of each of the constituent amino acids and its hydrophobicity. The graphic curve thus generated is featured by (1) an one-to-one correspondence relation without circuit or degeneracy, (2) better reflecting the innate structure of the protein sequence, (3) clear visibility in displaying the similarity of protein sequences, (4) more sensitive for the mutation sites important for drug targeting, and (5) being able to be used as a metric for the “evolutionary distance” of a protein from one species to the other. It is anticipated that the presented graphic method may become a useful vehicle for large-scale analysis of the avalanche of protein sequences generated in the post-genomic age. As a web-server, 2D-MH is freely accessible at http://icpr.jci.jx.cn/bioinfo/pplot/2D-MH, by which one can easily generate the two-dimensional graphs for any number of protein sequences and compare the evolutionary distances between them.


References in zbMATH (referenced in 14 articles )

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  1. Wu, Chuanyan; Gao, Rui; De Marinis, Yang; Zhang, Yusen: A novel model for protein sequence similarity analysis based on spectral radius (2018)
  2. Pai, Priyadarshini P.; Dash, Tirtharaj; Mondal, Sukanta: Sequence-based discrimination of protein-RNA interacting residues using a probabilistic approach (2017)
  3. Ping, Pengyao; Zhu, Xianyou; Wang, Lei: Similarities/dissimilarities analysis of protein sequences based on PCA-FFT (2017)
  4. Yang, Lei; Wang, Shiyuan; Zhou, Meng; Chen, Xiaowen; Zuo, Yongchun; Lv, Yingli: Characterization of bioplex network by topological properties (2016)
  5. Marrero-Ponce, Yovani; Contreras-Torres, Ernesto; García-Jacas, César R.; Barigye, Stephen J.; Cubillán, Néstor; Alvarado, Ysaías J.: Novel 3D bio-macromolecular bilinear descriptors for protein science: predicting protein structural classes (2015)
  6. Dai, Qi; Guo, Xiaodong; Li, Lihua: Sequence comparison via polar coordinates representation and curve tree (2012)
  7. He, Ping-an; Li, Dan; Zhang, Yanping; Wang, Xin; Yao, Yuhua: A 3D graphical representation of protein sequences based on the Gray code (2012)
  8. Qin, Wenli; Li, Yizhou; Li, Juan; Yu, Lezheng; Wu Di; Jing, Runyu; Pu, Xuemei; Guo, Yanzhi; Li Menglong: Predicting deleterious non-synonymous single nucleotide polymorphisms in signal peptides based on hybrid sequence attributes (2012)
  9. Gong, Binsheng; Liu, Tao; Zhang, Xiaoyu; Chen, Xi; Li, Jiang; Lv, Hongchao; Zou, Yi; Li, Xia; Rao, Shaoqi: Disease embryo development network reveals the relationship between disease genes and embryo development genes (2011)
  10. González-Díaz, Humberto; Prado-Prado, Francisco; Sobarzo-Sánchez, Eduardo; Haddad, Mohamed; Maurel Chevalley, Séverine; Valentin, Alexis; Quetin-Leclercq, Joëlle; Dea-Ayuela, María A.; Teresa Gomez-Muños, María; Munteanu, Cristian R.; José Torres-Labandeira, Juan; García-Mera, Xerardo; Tapia, Ricardo A.; Ubeira, Florencio M.: NL MIND-BEST: a web server for ligands and proteins discovery -- theoretic-experimental study of proteins of \itGiardia lamblia and new compounds active against \itPlasmodium falciparum (2011)
  11. Huang, Yujuan; Yang, Lianping; Wang, Tianming: Phylogenetic analysis of DNA sequences based on the generalized pseudo-amino acid composition (2011)
  12. Qi, Zhao-Hui; Li, Ling; Zhang, Zhi-Meng; Qi, Xiao-Qin: Self-similarity analysis of eubacteria genome based on weighted graph (2011)
  13. Xie, Guosen; Mo, Zhongxi: Three 3D graphical representations of DNA primary sequences based on the classifications of DNA bases and their applications (2011)
  14. Zhou, Guo-Ping: The disposition of the LZCC protein residues in wenxiang diagram provides new insights into the protein-protein interaction mechanism (2011)