메뉴 건너뛰기




Volumn 1268, Issue , 2015, Pages 43-66

Improved methods for classification, Prediction, And design of antimicrobial peptides

(1)  Wang, Guangshun a  

a NONE

Author keywords

Ab initio design; Database filtering tech; Database screen; Peptide design; Peptide prediction; Universal peptide classification

Indexed keywords

ADENOSINE PHOSPHATE; POLYPEPTIDE ANTIBIOTIC AGENT; ANTIMICROBIAL CATIONIC PEPTIDES;

EID: 84955083930     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-2285-7_3     Document Type: Article
Times cited : (104)

References (58)
  • 1
    • 0037165196 scopus 로고    scopus 로고
    • Antimicrobial peptides of multicellullar organisms
    • ZasloffM (2002) Antimicrobial peptides of multicellullar organisms. Nature 415:359–365
    • (2002) Nature , vol.415 , pp. 359-365
    • Zasloff, M.1
  • 2
    • 33845349605 scopus 로고    scopus 로고
    • Multispecific myeloid defensins
    • Lehrer RI (2007) Multispecific myeloid defensins. Curr Opin Hematol 14:16–21
    • (2007) Curr Opin Hematol , vol.14 , pp. 16-21
    • Lehrer, R.I.1
  • 3
    • 0042830450 scopus 로고    scopus 로고
    • Antibacterial peptides: Basic facts and emerging concepts
    • Boman HG (2003) Antibacterial peptides: basic facts and emerging concepts. J Intern Med 254:197–215
    • (2003) J Intern Med , vol.254 , pp. 197-215
    • Boman, H.G.1
  • 4
    • 33845699790 scopus 로고    scopus 로고
    • Antimicrobial and host-defense peptides as new anti-infective therapeutic strategies
    • Hancock RE, Sahl HG (2006) Antimicrobial and host-defense peptides as new anti-infective therapeutic strategies. Nat Biotechnol 24:1551–1557
    • (2006) Nat Biotechnol , vol.24 , pp. 1551-1557
    • Hancock, R.E.1    Sahl, H.G.2
  • 5
    • 61349169039 scopus 로고    scopus 로고
    • AMPed up immunity: How antimicrobial peptides have multiple roles in immune defense
    • Lai Y, Gallo RL (2009) AMPed up immunity: how antimicrobial peptides have multiple roles in immune defense. Trends Immunol 30: 131–141
    • (2009) Trends Immunol , vol.30 , pp. 131-141
    • Lai, Y.1    Gallo, R.L.2
  • 7
    • 0019386682 scopus 로고
    • Sequence and specificity of two antibacterial proteins involved in insect immunity
    • Steiner H, Hultmark D, Engström Å, Bennich H, Boman HG (1981) Sequence and specificity of two antibacterial proteins involved in insect immunity. Nature 292:246–248
    • (1981) Nature , vol.292 , pp. 246-248
    • Steiner, H.1    Hultmark, D.2    Engström, Å.3    Bennich, H.4    Boman, H.G.5
  • 9
    • 2042513493 scopus 로고
    • Magainins, a class of antimicrobial peptides from Xenopus skin: Isolation, characterization of two active forms, and partial cDNA sequence of a precursor
    • ZasloffM (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
    • (1987) Proc Natl Acad Sci U S A , vol.84 , pp. 5449-5453
    • Zasloff, M.1
  • 10
    • 0347755460 scopus 로고    scopus 로고
    • APD: The antimicrobial peptide database
    • Wang Z, Wang G (2004) APD: the antimicrobial peptide database. Nucleic Acids Res 32:D590–D592
    • (2004) Nucleic Acids Res , vol.32 , pp. D590-D592
    • Wang, Z.1    Wang, G.2
  • 11
    • 58149187882 scopus 로고    scopus 로고
    • The updated antimicrobial peptide database and its application in peptide design
    • Wang G, Li X, Wang Z (2009) The updated antimicrobial peptide database and its application in peptide design. Nucleic Acids Res 37:D933–D937
    • (2009) Nucleic Acids Res , vol.37 , pp. D933-D937
    • Wang, G.1    Li, X.2    Wang, Z.3
  • 12
    • 0036257512 scopus 로고    scopus 로고
    • Molecular diversity in gene-coded, cationic antimicrobial polypeptides
    • Tossi A, Sandri L (2002) Molecular diversity in gene-coded, cationic antimicrobial polypeptides. Curr Pharm Des 8:743–761
    • (2002) Curr Pharm Des , vol.8 , pp. 743-761
    • Tossi, A.1    Sandri, L.2
  • 16
    • 33846108632 scopus 로고    scopus 로고
    • Defensins knowledgebase: A manually curated database and information source focused on the defensins family of antimicrobial peptides
    • Seebah S, Suresh A, Zhou S, Choong YH, Chua H, Chuon D, Beuerman R, 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
    • (2007) Nucleic Acids Res , vol.35 , pp. D265-D268
    • Seebah, S.1    Suresh, A.2    Zhou, S.3    Choong, Y.H.4    Chua, H.5    Chuon, D.6    Beuerman, R.7    Verma, C.8
  • 17
    • 38349095584 scopus 로고    scopus 로고
    • BACTIBASE: A new web-accessible database for bacteriocin characterization
    • Hammami R, Zouhir A, Ben Hamida J, Fliss I (2007) BACTIBASE: a new web-accessible database for bacteriocin characterization. BMC Microbiol 7:89
    • (2007) BMC Microbiol , vol.7 , pp. 89
    • Hammami, R.1    Zouhir, A.2    Ben Hamida, J.3    Fliss, I.4
  • 18
    • 38549134937 scopus 로고    scopus 로고
    • Cybase: A database of cyclic protein sequences and structures, with applications in protein discovery and engineering
    • Wang CK, Kaas Q, Chiche L, Craik DJ (2008) Cybase: a database of cyclic protein sequences and structures, with applications in protein discovery and engineering. Nucleic Acids Res 36:D206–D210
    • (2008) Nucleic Acids Res , vol.36 , pp. D206-D210
    • Wang, C.K.1    Kaas, Q.2    Chiche, L.3    Craik, D.J.4
  • 19
    • 58149200923 scopus 로고    scopus 로고
    • PhytAMP: A database dedicated to antimicrobial plant peptides
    • Hammami R, Ben Hamida J, Vergoten G, Fliss I (2009) PhytAMP: a database dedicated to antimicrobial plant peptides. Nucleic Acids Res 37:D963–D968
    • (2009) Nucleic Acids Res , vol.37 , pp. D963-D968
    • Hammami, R.1    Ben Hamida, J.2    Vergoten, G.3    Fliss, I.4
  • 20
    • 56649106249 scopus 로고    scopus 로고
    • RAPD: A database of recombinantly-produced antimicrobial peptides
    • Li Y, Chen Z (2008) RAPD: a database of recombinantly-produced antimicrobial peptides. FEMS Microbiol Lett 289:126–129
    • (2008) FEMS Microbiol Lett , vol.289 , pp. 126-129
    • Li, Y.1    Chen, Z.2
  • 23
    • 84866676209 scopus 로고    scopus 로고
    • ThioFinder: A webbased tool for the identification of thiopeptide gene clusters in DNA sequences
    • Li J, Qu X, He X, Duan L, Wu G, Bi D, Deng Z, Liu W, Ou HY (2012) ThioFinder: a webbased tool for the identification of thiopeptide gene clusters in DNA sequences. PLoS One 7:e45878
    • (2012) PLoS One , vol.e45878 , pp. 7
    • Li, J.1    Qu, X.2    He, X.3    Duan, L.4    Wu, G.5    Bi, D.6    Deng, Z.7    Liu, W.8    Ou, H.Y.9
  • 24
    • 34249858459 scopus 로고    scopus 로고
    • AMPer: A database and an automated discovery tool for antimicrobial peptides
    • Fjell CD, Hancock RE, Cherkasov A (2007) AMPer: a database and an automated discovery tool for antimicrobial peptides. Bioinformatics 23:1148–1155
    • (2007) Bioinformatics , vol.23 , pp. 1148-1155
    • Fjell, C.D.1    Hancock, R.E.2    Cherkasov, A.3
  • 25
    • 0036220024 scopus 로고    scopus 로고
    • Synthetic antibiotic peptides database
    • Wade D, Englund J (2002) Synthetic antibiotic peptides database. Protein Pept Lett 9:53–57
    • (2002) Protein Pept Lett , vol.9 , pp. 53-57
    • Wade, D.1    Englund, J.2
  • 26
    • 0346494756 scopus 로고    scopus 로고
    • The Peptaibol Database: A database for sequences and structures of naturally occurring peptaibols
    • Whitmore L, Wallace BA (2004) The Peptaibol Database: a database for sequences and structures of naturally occurring peptaibols. Nucleic Acids Res 32:D593–D594
    • (2004) Nucleic Acids Res , vol.32 , pp. D593-D594
    • Whitmore, L.1    Wallace, B.A.2
  • 27
    • 84859512521 scopus 로고    scopus 로고
    • EnzyBase: A novel database for enzybiotic studies
    • Wu H, Lu H, Huang J, Li G, Huang Q (2012) EnzyBase: a novel database for enzybiotic studies. BMC Microbiol 12:54
    • (2012) BMC Microbiol , vol.12 , pp. 54
    • Wu, H.1    Lu, H.2    Huang, J.3    Li, G.4    Huang, Q.5
  • 28
    • 84894137189 scopus 로고    scopus 로고
    • MilkAMP: A comprehensive database of antimicrobial peptides of dairy origin
    • Theolier J, Fliss I, Jean J, Hammami R (2013) MilkAMP: a comprehensive database of antimicrobial peptides of dairy origin. Dairy Sci Technol 94:181–193
    • (2013) Dairy Sci Technol , vol.94 , pp. 181-193
    • Theolier, J.1    Fliss, I.2    Jean, J.3    Hammami, R.4
  • 31
    • 84879184644 scopus 로고    scopus 로고
    • LAMP: A database linking antimicrobial peptides
    • Zhao X, Wu H, Lu H, Li G, Huang Q (2013) LAMP: a database linking antimicrobial peptides. PLoS One 8:e66557
    • (2013) PLoS One , vol.8 , pp. e66557
    • Zhao, X.1    Wu, H.2    Lu, H.3    Li, G.4    Huang, Q.5
  • 35
    • 0014669335 scopus 로고
    • New concepts of kingdoms of organisms
    • Whittaker RH (1969) New concepts of kingdoms of organisms. Science 163:150–160
    • (1969) Science , vol.163 , pp. 150-160
    • Whittaker, R.H.1
  • 36
    • 0001271789 scopus 로고
    • Phylogenetic structure of the prokaryotic domain: The primary kingdoms
    • Woese CR, Fox GE (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci U S A 74:5088–5090
    • (1977) Proc Natl Acad Sci U S A , vol.74 , pp. 5088-5090
    • Woese, C.R.1    Fox, G.E.2
  • 37
    • 84878402118 scopus 로고    scopus 로고
    • Chemical modifications of natural antimicrobial peptides and strategies for peptide engineering
    • Wang G (2012) Chemical modifications of natural antimicrobial peptides and strategies for peptide engineering. Curr Biotechnol 1:72–79
    • (2012) Curr Biotechnol , vol.1 , pp. 72-79
    • Wang, G.1
  • 38
    • 0032717048 scopus 로고    scopus 로고
    • Diversity of antimicrobial peptides and their mechanisms of action
    • Epand RM, Vogel HJ (1999) Diversity of antimicrobial peptides and their mechanisms of action. Biochim Biophys Acta 1462:11–28
    • (1999) Biochim Biophys Acta , vol.1462 , pp. 11-28
    • Epand, R.M.1    Vogel, H.J.2
  • 39
    • 0027199706 scopus 로고
    • Genetics of bacteriocins produced by lactic acid bacteria
    • Klaenhammer TR (1993) Genetics of bacteriocins produced by lactic acid bacteria. FEMS Microbiol Rev 12:39–85
    • (1993) FEMS Microbiol Rev , vol.12 , pp. 39-85
    • Klaenhammer, T.R.1
  • 42
    • 11344267777 scopus 로고    scopus 로고
    • Insect antimicrobial peptides: Structures, properties and gene regulation
    • Bulet P, Stocklin R (2005) Insect antimicrobial peptides: structures, properties and gene regulation. Protein Pept Lett 12:3–11
    • (2005) Protein Pept Lett , vol.12 , pp. 3-11
    • Bulet, P.1    Stocklin, R.2
  • 43
    • 52049103111 scopus 로고    scopus 로고
    • Reflections on a systematic nomenclature for antimicrobial peptides from the skins of frogs of the family Ranidae
    • Conlon JM (2008) Reflections on a systematic nomenclature for antimicrobial peptides from the skins of frogs of the family Ranidae. Peptides 29:1815–1819
    • (2008) Peptides , vol.29 , pp. 1815-1819
    • Conlon, J.M.1
  • 45
    • 84875074764 scopus 로고    scopus 로고
    • IAMP-2L: A two-level multi-label classifier for identifying antimicrobial peptides and their functional types
    • Xiao X, Wang P, Lin WZ, Jia JH, Chou KC (2013) iAMP-2L: a two-level multi-label classifier for identifying antimicrobial peptides and their functional types. Anal Biochem 436: 168–177
    • (2013) Anal Biochem , vol.436 , pp. 168-177
    • Xiao, X.1    Wang, P.2    Lin, W.Z.3    Jia, J.H.4    Chou, K.C.5
  • 46
    • 84878419915 scopus 로고    scopus 로고
    • Database-guided discovery of potent peptides to combat HIV-1 or superbugs
    • Wang G (2013) Database-guided discovery of potent peptides to combat HIV-1 or superbugs. Pharmaceuticals 6:728–758
    • (2013) Pharmaceuticals , vol.6 , pp. 728-758
    • Wang, G.1
  • 48
    • 84862819407 scopus 로고    scopus 로고
    • Database screening and in vivo efficacy of antimicrobial peptides against methicillin-resistant Staphylococcus aureus USA300
    • Menousek J, Mishra B, Hanke ML, Heim CE, Kielian T, Wang G (2012) Database screening and in vivo efficacy of antimicrobial peptides against methicillin-resistant Staphylococcus aureus USA300. Int J Antimicrob Agents 39:402–406
    • (2012) Int J Antimicrob Agents , vol.39 , pp. 402-406
    • Menousek, J.1    Mishra, B.2    Hanke, M.L.3    Heim, C.E.4    Kielian, T.5    Wang, G.6
  • 49
    • 77149155289 scopus 로고    scopus 로고
    • Identification of novel human immunodeficiency virus type 1 inhibitory peptides based on the antimicrobial peptide database
    • Wang G, Watson KM, Peterkofsky A, Buckheit RW Jr (2010) Identification of novel human immunodeficiency virus type 1 inhibitory peptides based on the antimicrobial peptide database. Antimicrob Agents Chemother 54: 1343–1346
    • (2010) Antimicrob Agents Chemother , vol.54 , pp. 1343-1346
    • Wang, G.1    Watson, K.M.2    Peterkofsky, A.3    Buckheit, R.W.4
  • 50
    • 33750304297 scopus 로고    scopus 로고
    • A linguistic model for the rational design of antimicrobial peptides
    • Loose C, Jensen K, Rigoutsos I, Stephanopoulos G (2006) A linguistic model for the rational design of antimicrobial peptides. Nature 443:867–869
    • (2006) Nature , vol.443 , pp. 867-869
    • Loose, C.1    Jensen, K.2    Rigoutsos, I.3    Stephanopoulos, G.4
  • 52
    • 60749130267 scopus 로고    scopus 로고
    • Use of artificial intelligence in the design of small peptide antibiotics effective against a broad spectrum of highly antibiotic-resistant superbugs
    • Cherkasov A, Hilpert K, Jenssen H, Fjell CD, Waldbrook M, Mullaly SC, Volkmer R, Hancock RE (2008) Use of artificial intelligence in the design of small peptide antibiotics effective against a broad spectrum of highly antibiotic-resistant superbugs. ACS Chem Biol 4:65–74
    • (2008) ACS Chem Biol , vol.4 , pp. 65-74
    • Cherkasov, A.1    Hilpert, K.2    Jenssen, H.3    Fjell, C.D.4    Waldbrook, M.5    Mullaly, S.C.6    Volkmer, R.7    Hancock, R.E.8
  • 53
    • 84874210228 scopus 로고    scopus 로고
    • The importance of amino acid composition in natural AMPs: An evolutional, structural, and functional perspective
    • Mishra B, Wang G (2012) The importance of amino acid composition in natural AMPs: an evolutional, structural, and functional perspective. Front Immunol 3:221
    • (2012) Front Immunol , vol.3 , pp. 221
    • Mishra, B.1    Wang, G.2
  • 54
    • 84864451396 scopus 로고    scopus 로고
    • Ab initio design of potent anti-MRSA peptides based on database filtering technology
    • Mishra B, Wang G (2012) Ab initio design of potent anti-MRSA peptides based on database filtering technology. J Am Chem Soc 134: 12426–12429
    • (2012) J Am Chem Soc , vol.134 , pp. 12426-12429
    • Mishra, B.1    Wang, G.2
  • 55
    • 57749088664 scopus 로고    scopus 로고
    • Structures of human host defense cathelicidin LL-37 and its smallest antimicrobial peptide KR-12 in lipid micelles
    • Wang G (2008) Structures of human host defense cathelicidin LL-37 and its smallest antimicrobial peptide KR-12 in lipid micelles. J Biol Chem 283:32637–32643
    • (2008) J Biol Chem , vol.283 , pp. 32637-32643
    • Wang, G.1
  • 56
    • 0028927655 scopus 로고
    • Elucidation of the primary and three-dimensional structure of the uterotonic polypeptide kalata B1
    • Saether O, Craik DJ, Campbell ID, Sletten K, Juul J, Norman DG (1995) Elucidation of the primary and three-dimensional structure of the uterotonic polypeptide kalata B1. Biochemistry 34:4147–4158
    • (1995) Biochemistry , vol.34 , pp. 4147-4158
    • Saether, O.1    Craik, D.J.2    Campbell, I.D.3    Sletten, K.4    Juul, J.5    Norman, D.G.6
  • 57
    • 0035188391 scopus 로고    scopus 로고
    • Structure determination of human and murine beta-defensins reveals structural conservation in the absence of significant sequence similarity
    • Bauer F, Schweimer K, Klüver E, Conejo- Garcia JR, Forssmann WG, Rösch P, Adermann K, Sticht H (2001) Structure determination of human and murine beta-defensins reveals structural conservation in the absence of significant sequence similarity. Protein Sci 10:2470–2479
    • (2001) Protein Sci , vol.10 , pp. 2470-2479
    • Bauer, F.1    Schweimer, K.2    Klüver, E.3    Conejo-Garcia, J.R.4    Forssmann, W.G.5    Rösch, P.6    Adermann, K.7    Sticht, H.8
  • 58
    • 0034719121 scopus 로고    scopus 로고
    • Structure of the bovine antimicrobial peptide indolicidin bound to dodecylphosphocholine and sodium dodecyl sulfate micelles
    • Rozek A, Friedrich CL, Hancock RE (2000) Structure of the bovine antimicrobial peptide indolicidin bound to dodecylphosphocholine and sodium dodecyl sulfate micelles. Biochemistry 39:15765–15774
    • (2000) Biochemistry , vol.39 , pp. 15765-15774
    • Rozek, A.1    Friedrich, C.L.2    Hancock, R.E.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.