Peptides: A package for data mining of antimicrobial peptides

R Journal

Volumn 7, Issue 1, 2015, Pages 4-14

  Osorio, Daniel ^a   Rondón Villarreal, Paola ^a   Torres, Rodrigo ^a  

^a UNIVERSIDAD INDUSTRIAL DE SANTANDER   (Colombia)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84934767390     PISSN: None     EISSN: 20734859     Source Type: Journal    
DOI: 10.32614/rj-2015-001     Document Type: Article

References (26)

1. F. C. Bernstein, T. F. Koetzle, G. J. Williams, E. F. Meyer, M. D. Brice, J. R. Rodgers, O. Kennard, T. Shimanouchi, and M. Tasumi. The Protein Data Bank: A computer-based archival file for macromolecular structures. Archives of Biochemistry and Biophysics, 185(2):584-591, 1978.
2. H. G. Boman. Antibacterial peptides: Basic facts and emerging concepts. Journal of Internal Medicine, 254(3):197-215, 2003.
3. D. Eisenberg. Three-dimensional structure of membrane and surface proteins. Annual Review of Biochemistry, 53:595-623, 1984.
4. D. Eisenberg, R. M.Weiss, and T. C. Terwilliger. The helical hydrophobic moment: A measure of the amphiphilicity of a helix. Nature, 299(5881):371-374, 1982.
5. C. D. Fjell, J. Hiss, R. E.W. Hancock, and G. Schneider. Designing antimicrobial peptides: Form follows function. Nature Reviews. Drug Discovery, 11(1):37-51, 2012.
6. P. Gaillard, P.-A. Carrupt, B. Testa, and A. Boudon. Molecular lipophilicity potential, a tool in 3D QSAR: Method and applications. Journal of Computer-Aided Molecular Design, 8(2):83-96, 1994.
7. E. Gasteiger, C. Hoogland, A. Gattiker, M. R. Wilkins, R. D. Appel, A. Bairoch, et al. Protein identification and analysis tools on the ExPASy server. In The Proteomics Protocols Handbook, pages 571-607. Springer, 2005.
8. K. Guruprasad, B. V. Reddy, and M. W. Pandit. Correlation between stability of a protein and its dipeptide composition: A novel approach for predicting in vivo stability of a protein from its primary sequence. Protein Engineering, 4(2):155-61, 1990.
9. R. E. W. Hancock. Cationic peptides: Effectors in innate immunity and novel antimicrobials. The Lancet. Infectious Diseases, 1(3):153-164, 2001.
10. T. Hessa, N. M. Meindl-Beinker, A. Bernsel, H. Kim, Y. Sato, M. Lerch-Bader, I. Nilsson, S. H. White, and G. von Heijne. Molecular code for transmembrane-helix recognition by the Sec61 translocon. Nature, 450(7172):1026-1030, 2007.
11. T. A. Holton, G. Pollastri, D. C. Shields, and C. Mooney. CPPpred: Prediction of cell penetrating peptides. Bioinformatics, 29(23):3094-3096, 2013.
12. F. Huang and W. M. Nau. A conformational flexibility scale for amino acids in peptides. Angewandte Chemie, 115(20):2371-2374, 2003.
13. A. Ikai. Thermostability and aliphatic index of globular proteins. Journal of Biochemistry, 88(6): 1895-1898, 1980.
14. S. Kawashima, P. Pokarowski, M. Pokarowska, A. Kolinski, T. Katayama, and M. Kanehisa. AAindex: Amino acid index database, progress report 2008. Nucleic Acids Research, 36(suppl 1):D202-D205, 2008.
15. H. Kim, J. H. Jang, S. C. Kim, and J. H. Cho. De novo generation of short antimicrobial peptides with enhanced stability and cell specificity. The Journal of Antimicrobial Chemotherapy, 69(1):1-12, 2013.
16. M. Kuhn. caret: Classification and Regression Training, 2014. URL http://CRAN.R-project.org/ package=caret. R package version 6.0-35.
17. K. Matsuzaki. Control of cell selectivity of antimicrobial peptides. Biochimica et Biophysica Acta, 1788 (8):1687-1692, 2009.
18. L. Monincová, J. Slaninová, V. Fučík, O. Hovorka, Z. Voburka, L. Bednárová, P. Maloň, J. Štokrová, and V. Čeřovskỳ. Lasiocepsin, a novel cyclic antimicrobial peptide from the venom of eusocial bee Lasioglossum laticeps (Hymenoptera: Halictidae). Amino Acids, 43(2):751-761, 2012.
19. D. S. Moore. Amino acid and peptide net charges: A simple calculational procedure. Biochemical Education, 13(1):10-11, 1985.
20. S. P. Piotto, L. Sessa, S. Concilio, and P. Iannelli. YADAMP: Yet another database of antimicrobial peptides. International Journal of Antimicrobial Agents, 39(4):346-351, 2012.
21. P. Rice, I. Longden, and A. Bleasby. EMBOSS: The European Molecular Biology Open Software Suite. Trends in Genetics, 16(6):276-277, 2000.
22. J. E. Stajich, D. Block, K. Boulez, S. E. Brenner, S. A. Chervitz, C. Dagdigian, G. Fuellen, J. G. Gilbert, I. Korf, H. Lapp, et al. The Bioperl toolkit: Perl modules for the life sciences. Genome Research, 12 (10):1611-1618, 2002.
23. S. Thomas, S. Karnik, R. S. Barai, V. K. Jayaraman, and S. Idicula-Thomas. CAMP: A useful resource for research on antimicrobial peptides. Nucleic Acids Research, 38:D774-780, 2010.
24. M. Torrent, D. Andreu, V. M. Nogués, and E. Boix. Connecting peptide physicochemical and antimicrobial properties by a rational prediction model. PLoS ONE, 6(2):e16968, 2011.
25. G. Wang, X. Li, and Z. Wang. APD2: The updated antimicrobial peptide database and its application in peptide design. Nucleic Acids Research, 37:D933-937, 2009.
26. M. R. Yeaman and N. Y. Yount. Mechanisms of antimicrobial peptide action and resistance. Pharmacological Reviews, 55(1):27-55, 2003.