APD3: The antimicrobial peptide database as a tool for research and education

Nucleic Acids Research

Volumn 44, Issue D1, 2016, Pages D1087-D1093

  Wang, Guangshun ^a   Li, Xia ^a   Wang, Zhe ^a  

^a UNIVERSITY OF NEBRASKA MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AUREIN; BREVININ; CATHELICIDIN; CYCLOTIDE; DEFENSIN; DERMASEPTIN; ESCULENTIN; HISTATIN; LANTIBIOTIC; MAXIMIN; POLYPEPTIDE ANTIBIOTIC AGENT; PRO RICH PEPTIDE; TEMPORIN; TRP RICH PEPTIDE; UNCLASSIFIED DRUG; AMINO ACID; ANTIINFECTIVE AGENT; PEPTIDE;

ALGORITHM; AMINO ACID COMPOSITION; AMINO ACID SEQUENCE; ANIMAL; ANTIBACTERIAL ACTIVITY; ANTIFUNGAL ACTIVITY; ANTIMALARIAL ACTIVITY; ANTIMICROBIAL PEPTIDE DATABASE 3; ANTINEOPLASTIC ACTIVITY; ANTIOXIDANT ACTIVITY; ANTIVIRAL ACTIVITY; ARCHAEON; ARTICLE; BACTERIUM; CANDIDA ALBICANS; CHEMICAL MODIFICATION; CHEMOTAXIS; CIRCULAR DICHROISM; COMPUTER INTERFACE; COMPUTER PROGRAM; DATA BASE; ENZYME INHIBITION; ESCHERICHIA COLI; FUNGUS; HEMOLYSIS; HUMAN; INSECTICIDAL ACTIVITY; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PLANT; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN STRUCTURE; PROTIST; STAPHYLOCOCCUS AUREUS; STRUCTURE ACTIVITY RELATION; WOUND HEALING; X RAY DIFFRACTION; CHEMISTRY; DRUG DATABASE; INTERNET; MEDICAL RESEARCH;

AMINO ACIDS; ANIMALS; ANTI-INFECTIVE AGENTS; BIOMEDICAL RESEARCH; DATABASES, PHARMACEUTICAL; INTERNET; PEPTIDES;

EID: 84979498105     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv1278     Document Type: Article

References (53)

1. Zasloff, M. (2002) Antimicrobial peptides of multicellular organisms. Nature., 415, 389-395.
2. Boman, H.G. (2003) Antibacterial peptides: basic facts and emerging concepts. J. Intern. Med., 254, 197-215.
3. Hancock, R.E. and Sahl, H.G. (2006) Antimicrobial and host-defense peptides as new anti-infective therapeutic strategies. Nat. Biotechnol., 24, 1551-1557.
4. Lai, Y. and Gallo, R.L. (2009) AMPed up immunity: how antimicrobial peptides have multiple roles in immune defense. Trends Immunol., 30, 131-141.
5. Yeaman, M.R. (2014) Platelets: at the nexus of antimicrobial defence. Nat. Rev. Microbiol., 12, 426-437.
6. Epand, R.M. and Vogel, H.J. (1999) Diversity of antimicrobial peptides and their mechanisms of action. Biochim. Biophys. Acta, 1462, 11-28.
7. Mangoni, M.L. and Shai, Y. (2011) Short native antimicrobial peptides and engineered ultrashort lipopeptides: similarities and differences in cell specificities and modes of action. Cell. Mol. Life Sci., 68, 2267-2280.
8. van Hoek, M.L. (2013) Biofilms: an advancement in our understanding of Francisella species. Virulence, 4, 833-846.
9. Wang, G. (ed). (2010) Antimicrobial Peptides: Discovery, Design and Novel Therapeutic Strategies. CABI, Oxfordshire.
10. Selsted, M.E., Harwig, S.S., Ganz, T., Schilling, J.W. and Lehrer, R.I. (1985) Primary structures of three human neutrophil defensins. J. Clin. Invest., 76, 1436-1439.
11. Zasloff, M (1987) 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. U.S.A., 84, 5449-5453.
12. Steiner, H., Hultmark, D., Engström, Å., Bennich, H. and Boman, H.G. (1981) Sequence and specificity of two antibacterial proteins involved in insect immunity. Nature, 292, 246-248.
13. Tossi, A. and Sandri, L. (2002) Molecular diversity in gene-coded, cationic antimicrobial polypeptides. Curr. Pharm. Des., 8, 743-761.
14. Brahmachary, M., Krishnan, S.P., Koh, J.L., Khan, A.M., Seah, S.H., Tan, T.W., Brusic, V. and Bajic, V.B. (2004) ANTIMIC: a database of antimicrobial sequences. Nucleic Acids Res., 32, D586-D589.
15. Seshadri Sundararajan, V., Gabere, M.N., Pretorius, A., Adam, S., Christoffels, A., Lehväslaiho, M., Archer, J.A. and Bajic, V.B. (2012) DAMPD: a manually curated antimicrobial peptide database. Nucleic Acids Res., 40, D1108-D1112.
16. Wang, Z. and Wang, G. (2004) APD: the Antimicrobial peptide database. Nucleic Acids Res., 32, D590-D592.
17. Wang, G, Li, X and Wang, Z (2009) The updated antimicrobial peptide database and its application in peptide design. Nucleic Acids Res., 37, D933-D937.
18. Whitmore, L. and Wallace, B.A. (2004) The Peptaibol Database: a database for sequences and structures of naturally occurring peptaibols. Nucleic Acids Res., 32, D593-D594.
19. Gueguen, Y., Garnier, J., Robert, L., Lefranc, M.P., Mougenot, I., de Lorgeril, J., Janech, M., Gross, P.S., Warr, G.W., Cuthbertson, B. et al. (2006) PenBase, the shrimp antimicrobial peptide penaeidin database: sequence-based classification and recommended nomenclature. Dev. Comp. Immunol., 30, 283-288.
20. Hammami, R., Zouhir, A., Ben Hamida, J. and Fliss, I. (2007) BACTIBASE: a new web-accessible database for bacteriocin characterization. BMC Microbiol., 7, 89.
21. Hammami, R., Ben Hamida, J., Vergoten, G. and Fliss, I. (2009) PhytAMP: a database dedicated to antimicrobial plant peptides. Nucleic Acids Res., 37, D963-D968.
22. Novković, M., Simunić, J., Bojović, V., Tossi, A. and Juretić, D. (2012) DADP: the database of anuran defense peptides. Bioinformatics, 28, 1406-1407.
23. Seebah, S., Suresh, A., Zhou, S., Choong, Y.H., Chua, H., Chuon, D., Beuerman, R. and Verma, C. (2007) Defensins knowledgebase: a manually curated database and information source focused on the defensins family of antimicrobial peptides. Nucleic Acids Res., 35, D265-D268.
24. Wang, C.K., Kaas, Q., Chiche, L. and Craik, D.J. (2008) Cybase: a database of cyclic protein sequences and structures, with applications in protein discovery and engineering. Nucleic Acids Res., 36, D206-D210.
25. Waghu, FH, Barai, RS, Gurung, P and Idicula-Thomas, S. (2015) CAMPR3: a database on sequences, structures and signatures of antimicrobial peptides. Nucleic Acids Res., doi:10.1093/nar/gkv1051.
26. Piotto, S.P., Sessa, L., Concilio, S. and Iannelli, P. (2012) YADAMP: yet another database of antimicrobial peptides. Int. J. Antimicrob. Agents, 39, 346-351.
27. Zhao, X., Wu, H., Lu, H., Li, G. and Huang, Q. (2013) LAMP: A Database Linking Antimicrobial Peptides. PLoS One, 8, e66557.
28. Whittaker, R.H. (1969) New concepts of kingdoms of organisms. Science, 163, 150-160.
29. Woese, C.R. and Fox, G.E. (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc. Natl. Acad. Sci. U.S.A., 74, 5088-5090.
30. Rose, P.W., Bi, C., Bluhm, W.F., Christie, C.H., Dimitropoulos, D., Dutta, S., Green, R.K., Goodsell, D.S., Prlic, A., Quesada, M. et al. (2013) The RCSB Protein Data Bank: new resources for research and education. Nucleic Acids Res., 41, D475-D482.
31. Wang, G. (2015) Improved methods for classification, prediction, and design of antimicrobial peptides. Methods Mol. Biol., 1268, 43-66.
32. Wang, G. (2013) Database-guided discovery of potent peptides to combat HIV-1 or superbugs. Pharmaceuticals, 6, 728-758.
33. Conlon, J.M. (2015) Host-defense peptides of the skin with therapeutic potential: From hagfish to human. Peptides, 67, 29-38.
34. Mishra, B. and Wang, G. (2012) The importance of amino acid composition in natural AMPs: an evolutional, structural, and functional perspective. Front. Immunol., 3, 221.
35. Kyte, J. and Doolittle, R.F. (1982) A simple method for displaying the hydropathic character of a protein. J. Mol. Biol., 157, 105-132.
36. O'Shea, E.F., O'Connor, P.M., O'Sullivan, O., Cotter, P.D., Ross, R.P. and Hill, C. (2013) Bactofencin a, a new type of cationic bacteriocin with unusual immunity. MBio, 4, doi:10.1128/mBio.00498-13.
37. Li, Y., Li, X. and Wang, G. (2006) Cloning, expression, isotope labeling, and purification of human antimicrobial peptide LL-37 in Escherichia coli for NMR studies. Protein Expr. Purif., 47, 498-505.
38. Wang, G. (2007) Tool developments for structure-function studies of host defense peptides. Protein Pept. Lett., 14, 57-69.
39. Wang, G., Li, Y. and Li, X. (2005) Correlation of three-dimensional structures with the antibacterial activity of a group of peptides designed based on a nontoxic bacterial membrane anchor. J. Biol. Chem., 280, 5803-5811.
40. Wang, G., Watson, K.M., Peterkofsky, A. and Buckheit, R.W. (2010) Identification of novel human immunodeficiency virus type 1-inhibitory peptides based on the antimicrobial peptide database. Antimicrob. Agents Chemother., 54, 1343-1346.
41. Loose, C., Jensen, K., Rigoutsos, I. and Stephanopoulos, G. (2006) A linguistic model for the rational design of antimicrobial peptides. Nature, 443, 867-869.
42. Mishra, B. and Wang, G. (2012) Ab initio design of potent anti-MRSA peptides based on database filtering technology. J. Am. Chem. Soc., 134, 12426-12429.
43. Chakraborty, S., Liu, R., Hayouka, Z., Chen, X., Ehrhardt, J., Lu, Q., Burke, E., Yang, Y., Weisblum, B., Wong, G.C. et al. (2014) Ternary nylon-3 copolymers as host-defense peptide mimics: beyond hydrophobic and cationic subunits. J. Am. Chem. Soc., 136, 14530-14535.
44. Lata, S., Sharma, B.K. and Raghava, G.P. (2007) Analysis and prediction of antibacterial peptides. BMC Bioinformatics, 8, 263.
45. Xiao, X., Wang, P., Lin, W.Z, Jia, J.H. and Chou, K.C (2013) iAMP-2L: A two-level multi-label classifier for identifying antimicrobial peptides and their functional types. Anal. Biochem., 436, 168-177.
46. Bishop, B.M., Juba, M.L., Devine, M.C., Barksdale, S.M., Rodriguez, C.A., Chung, M.C., Russo, P.S., Vliet, K.A., Schnur, J.M. and van Hoek, M.L. (2015) Bioprospecting the American alligator (Alligator mississippiensis) host defense peptidome. PLoS One, 10, e0117394.
47. Wang, G. (2014) Human antimicrobial peptides and proteins. Pharmaceuticals, 7, 545-594.
48. Wang, G., Mishra, B., Lau, K., Lushnikova, T., Golla, R. and Wang, X. (2015) Antimicrobial peptides in 2014. Pharmaceuticals, 8, 123-150.
49. Wang, G. (2015) Database resources dedicated to antimicrobial peptides. In: Chen, C-Y, Yan, X and Jackson, CR (eds). Antimicrobial Resistance and Food Safety: Methods and Techniques. Academic Press, Boston, pp. 365-384.
50. Gogoladze, G., Grigolava, M., Vishnepolsky, B., Chubinidze, M., Duroux, P., Lefranc, M.P. and Pirtskhalava, M. (2014) DBAASP: Database of Antimicrobial Activity and Structure of Peptides. FEMS Microbiol. Lett., 357, 63-68.
51. Yang, X., Lee, W.H. and Zhang, Y. (2012) Extremely abundant antimicrobial peptides existed in the skins of nine kinds of Chinese odorous frogs. J. Proteome Res., 11, 306-319.
52. Bevins, C.L. and Salzman, N.H. (2011) The potter's wheel: the host's role in sculpting its microbiota. Cell. Mol. Life Sci., 68, 3675-3685.
53. Lee, H.T., Lee, C.C., Yang, J.R., Lai, J.Z. and Chang, K.Y. (2015) A large-scale structural classification of antimicrobial peptides. Biomed. Res. Int., 2015, 475062.