Physicochemical determinants of antimicrobial activity

5th International Conference on Bioinformatics and Computational Biology 2013, BICoB 2013

Volumn , Issue , 2013, Pages 253-259

  Veltri, Daniel ^a   Shehu, Amarda ^b  

^a GEORGE MASON UNIVERSITY   (United States)

^b Krasnow Institute for Advanced Study   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTI-MICROBIAL ACTIVITY; ANTIBACTERIAL DRUGS; ANTIMICROBIAL PEPTIDE; DE NOVO DESIGN; FEATURE PROFILES; MACHINE LEARNING TECHNIQUES; PHYSICOCHEMICAL PROPERTY; RATIONAL DESIGN;

CLASSIFICATION (OF INFORMATION); LEARNING SYSTEMS;

BIOINFORMATICS;

EID: 84883633978     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (32)

1. M. Blaber, X.J. Zhang, and B.W. Matthews. Structural basis of amino acid alpha helix propensity. Science, 260(5114):1637, 1993.
2. A. Bundi and K. Wüthrich. Use of amide 1h-nmr titration shifts for studies of polypeptide conformation. Biopolymers, 18(2):299-311, 1979.
3. Y. Chen and C. Lin. Combining SVMs with various feature selection strategies. In Isabelle Guyon, Masoud Nikravesh, Steve Gunn, and Lotfi Zadeh, editors, Feature Extraction, Volume 207 of Studies in Fuzziness and Soft Computing, pages 315-324. Springer Berlin, Heidelberg, 2006.
4. A. Cherkasov and B. Jankovic. Application of 'inductive' QSAR descriptors for quantification of antibacterial activity of cationic polypeptides. Molecules, 9(12):1034-1052, 2004.
5. R.-E. Fan, P.-H. Chen, and C.-J. Lin. Working set selection using the second order information for training SVM. J. Mach. Learn. Res., 6(1532-4435):1889-1918, 2005.
6. J. Fauchère, M. Charton, L.B. Kier, A. Verloop, and V. Pliska. Amino acid side chain parameters for correlation studies in biology and pharmacology. International journal of peptide and protein research, 32(4):269-278, 1988.
7. Fabiano C. Fernandes, Daniel J. Rigden, and Octavio L. Franco. Prediction of antimicrobial pep-tides based on the adaptive neuro-fuzzy inference system application. Peptide Science, 98(4):280-287, 2012.
8. A. Finkelstein, A. Badretdinov, and O. Ptitsyn. Physical reasons for secondary structure stability: alpha-helices in short peptides. Proteins, 10(4):287-99, 1991.
9. C. Fjell, R. Hancock, and A. Cherkasov. AM-Per: a database and an automated discovery tool for antimicrobial peptides. Bioinformatics, 23(9):1148-1155, 2007.
10. C. Fjell, H. Jenssen, K. Hilpert, W. A. Cheung, N. Pante, R. E. Hancock, and A Cherkasov. Identification of novel antibacterial peptides by chemoinformatics and machine learning. J. Med. Chem., 52(7):2006-2015, 2009.
11. R. Gautier, D. Douguet, B. Antonny, and Drin G. HELIQUEST: a web server to screen sequences with specific α-helical properties. Bioinformatics, 24(18):2101-2102, 2008.
12. R.A. George and J. Heringa. An analysis of protein domain linkers: their classification and role in protein folding. Protein engineering, 15(11):871-879, 2002.
13. Y. Igarashi, A. Eroshkin, S. Gramatikova, G. Gramatikoff, Y. Zhang, J. W. Smith, A. L. Osterman, and Godzik A. CutDB: a proteolytic event database. Nucl. Acids Res., 35:D546-D549, 2007.
14. C.J. Jameson. Understanding NMR chemical shifts. Annual review of phys chem, 47(1):135-169, 1996.
15. J. Janin. Surface and inside volumes in globular proteins. Nature, 277:491-492, 1979.
16. U. Kamath, J. Compton, R. Islamaj-Dogan, De Jong K.A., and A. Shehu. An evolutionary algorithm approach for feature generation from sequence data and its application to dna splice-site prediction. Trans Comp Biol and Bioinf, 2012.
17. S. Kawashima and M. Kanehisa. AAindex: amino acid index database. Nucl. Acids Res., 28(1):374, 2000.
18. S. Lata, N. K. Mishra, and G. P. Raghava. AntiBP2: improved version of antibacterial peptide prediction. BMC Bioinformatics, 11(Suppl 1):S1-S19, 2010.
19. S. Lata, B. K. Sharma, and G. P. Raghava. Analysis and prediction of antibacterial peptides. BMC Bioinformatics, 23(8):263-272, 2007.
20. M. Magrane and the UniProt consortium. UniProt knowledgebase: a hub of integrated protein data. Database, 2011(bar009):1-13, 2011.
21. J.L. Meek. Prediction of peptide retention times in high-pressure liquid chromatography on the basis of amino acid composition. Proceedings of the National Academy of Sciences, 77(3):1632-1636, 1980.
22. K.T. O'Neil and W.F. DeGrado. A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids. Science, 250(4981):646, 1990.
23. R Development Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria, 2010.
24. B. Robson and E. Suzuki. Conformational properties of amino acid residues in globular proteins. Journal of molecular biology, 107(3):327, 1976.
25. P. Sneath. Relations between chemical structure and biological activity in peptides. Journal of theoretical biology, 12(2):157-195, 1966.
26. S. Thomas, S. Karnik, R. S. Barai, V. K. Jayaraman, and S. I. Thomas. CAMP: a useful resource for research on antimicrobial peptides. Nucl. Acids Res., 38(Suppl 1):D774-D780, 2009.
27. M. Torrent, P. Di Tommaso, D. Pulido, M. V. Nogues, Notredame. C., E. Boix, and D. Andreu. AMPA: An automated web server for prediction of protein antimicrobial regions. Bioinformatics, 28(1):130-1, 2011.
28. A. Tossi, L. Sandri, and A. Giangaspero. Amphipathic, α-helical antimicrobial peptides. Peptide Science, 55(1):4-30, 2000.
29. G. Wang. Antimicrobial Peptides: Discovery, Design and Novel Therapeutic Strategies. CABI Bookshop, Wallingford, England, 2010.
30. G. Wang, X. Li, and Z. Wang. APD2: the updated antimicrobial peptide database and its application in peptide design. Nucl. Acids Res., 37(Sup. 1):D933-D937, 2009.
31. M. Wilce, M. Aguilar, and Milton T. Hearn. Physicochemical basis of amino acid hydropho-bicity scales: Evaluation of four new scales of amino acid hydrophobicity coefficients derived from rp-hplc of peptides. Analytical Chemistry, 67(7):1210-1219, 1995.
32. Igor Zelezetsky, Alessandra Pontillo, Luca Puzzi, Nikolinka Antcheva, Ludovica Segat, Sabrina Pacor, Sergio Crovella, and Alessandro Tossi. Evolution of the primate cathelicidin. J. of Biological Chemistry, 281(29):19861-19871, 2006.