YADAMP: Yet another database of antimicrobial peptides

International Journal of Antimicrobial Agents

Volumn 39, Issue 4, 2012, Pages 346-351

  Piotto, Stefano P ^a   Sessa, Lucia ^a   Concilio, Simona ^a   Iannelli, Pio ^a  

^a UNIVERSITY OF SALERNO   (Italy)

Author keywords

Antimicrobial peptides; QSAR; Web database

Indexed keywords

POLYPEPTIDE ANTIBIOTIC AGENT;

ACCESS TO INFORMATION; ARTICLE; COMPUTER INTERFACE; COMPUTER PREDICTION; CONTENT ANALYSIS; CONTROLLED STUDY; HYDROPHOBICITY; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN MOTIF; SEQUENCE ANALYSIS; STRUCTURE ACTIVITY RELATION; WEB BROWSER;

AMINO ACID SEQUENCE; ANTI-BACTERIAL AGENTS; ANTIMICROBIAL CATIONIC PEPTIDES; COMPUTATIONAL BIOLOGY; DATABASES, FACTUAL; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; INTERNET; MICROBIAL SENSITIVITY TESTS; PROTEIN STRUCTURE, SECONDARY; SEQUENCE ANALYSIS, PROTEIN; STATIC ELECTRICITY; STRUCTURE-ACTIVITY RELATIONSHIP; USER-COMPUTER INTERFACE;

EID: 84858277472     PISSN: 09248579     EISSN: 18727913     Source Type: Journal    
DOI: 10.1016/j.ijantimicag.2011.12.003     Document Type: Article

References (29)

1. Zasloff M. Magainins, a class of antimicrobial peptides from Xenopus skin: isolation, characterization of two active forms, and partial cDNA sequence of a precursor. Proc Natl Acad Sci USA 1987;84:5449-53. (Pubitemid 17129018)
2. Merrifield R, Juvvadi P, Andreu D, Ubach J, Boman A, Boman H. Retro and retroenantio analogs of cecropin-melittin hybrids. Proc Natl Acad Sci USA 1995;92:3449-53.
3. Brogden KA. Antimicrobial peptides: pore formers or metabolic inhibitors in bacteria? Nat Rev Microbiol 2005;3:238-50. (Pubitemid 40298223)
4. Zasloff M. Antimicrobial peptides of multicellular organisms. Nature 2002;415:389-95. (Pubitemid 34100944)
5. Epand RM, Vogel HJ. Diversity of antimicrobial peptides and their mechanisms of action. Biochim Biophys Acta 1999;1462:11-28.
6. Shai Y, Oren Z. From "carpet" mechanism to de-novo designed diastereomeric cell-selective antimicrobial peptides. Peptides 2001;10:1629-41. (Pubitemid 32918242)
7. Piotto S, Concilio S, Iannelli P, Mavelli F. Computer simulations of natural and synthetic polymers in confined systems. Macromol Symp 2009;286:25-33.
8. Boman HG. Antibacterial peptides: basic facts and emerging concepts. J Intern Med 2003;254:197-215. (Pubitemid 37070221)
9. de Jong A, van Hijum SA, Bijlsma JJ, Kok J, Kuipers OP. BAGE L: a web-based bacteriocin genome mining tool. Nucleic Acids Res 2006;34(Web server issue):W273-9.
10. Gueguen Y, Garnier J, Robert L, Lefranc MP, Mougenot I, de Lorgeril J, et al. PenBase, the shrimp antimicrobial peptide penaeidin database: sequence-based classification and recommended nomenclature. Dev Comp Immunol 2006;30:283-8. (Pubitemid 41571268)
11. Hammami R, Ben Hamida J, Vergoten G, Fliss I. PhytAMP: a database dedicated to antimicrobial plant peptides. Nucleic Acids Res 2009;37(Database issue):D963-8.
12. Hammami R, Zouhir A, Ben Hamida J, Fliss I. BACTIBASE: a new web-accessible database for bacteriocin characterization. BMC Microbiol 2007;7:89.
13. Li Y, Chen Z. RAPD: a database of recombinantly-produced antimicrobial peptides. FEMS Microbiol Lett 2008;289:126-9.
14. Seebah S, Suresh A, Zhuo S, Choong YH, Chua H, Chuon D, et al. Defensins knowledgebase: a manually curated database and information source focused on the defensins family of antimicrobial peptides. Nucleic Acids Res 2007;35(Database issue):D265-8. (Pubitemid 46056211)
15. Wade D, Englund J. Synthetic antibiotic peptides database. Protein Pept Lett 2002;9:53-7. (Pubitemid 34293917)
16. Wang Z, Wang G. APD: the antimicrobial peptide database. Nucleic Acids Res 2004;32(Database issue):D590-2. (Pubitemid 38081727)
17. Whitmore L, Wallace BA. The peptaibol database: a database for sequences and structures of naturally occurring peptaibols. Nucleic Acids Res 2004;32(Database issue):D593-4. (Pubitemid 38081728)
18. Thomas S, Karnik S, Shankar Barai R, Jayaraman VK, Idicula-Thomas S. CAMP: a useful resource for research on antimicrobial peptides. Nucleic Acids Res 2010;38(Database issue):D774-80.
19. UniProtKB/Swiss-Prot. http://www.uniprot.org/uniprot [accessed 12 January 2012].
20. Wang G, Li X, Wang Z. APD2: the updated antimicrobial peptide database and its application in peptide design. Nucleic Acids Res 2008;37(Database issue):D933-7.
21. Bjellqvist B, Basse B, Olsen E, Celis JE. Reference points for comparisons of two-dimensional maps of proteins from different human cell types defined in a pH scale where isoelectric points correlate with polypeptide compositions. Electrophoresis 1994;15:529-39. (Pubitemid 24151853)
22. Radzeka A, Wolfenden R. Comparing the polarities of amino acids: side-chain distribution coefficients between vapor phase, cyclohexane, 1-octanol and neutral aqueous solution. Biochemistry 1988;27:1664-70.
23. Eisenberg D, Weiss RM, Terwilliger CT, Wilcox W. Hydrophobic moments and protein structure. Faraday Symp Chem Soc 1982;17:109-20.
24. Tossi A, Sandri L, Giangaspero A. New consensus hydrophobicity scale extended to non-proteinogenic amino acids. In: Peptides 2002. Proceedings of the Twenty-Seventh European Peptide Symposium. Napoli, Italy: Edizioni Ziino; 2002. p. 416-7.
25. Kyte J, Doolittle RF. A simple method for displaying the hydropathic character of a protein. J Mol Biol 1982;157:105-32.
26. King RD, Sternberg MJE. Identification and application of the concepts important for accurate and reliable protein secondary structure prediction. Protein Sci 1996;5:2298-310. (Pubitemid 26384468)
27. Fang H, Werner MN. A conformational flexibility scale for amino acids in peptides. Angew Chem Int Ed Engl 2003;42:2269-72.
28. Guruprasad K, Reddy BVB, Pandit MW. 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 Eng 1990;4: 155-61.
29. Antimicrobial Sequences Database. http://www.bbcm.univ.trieste.it/~tossi/ amsdb.html [accessed 12 January 2012].