-
1
-
-
84962367258
-
Natural products as sources of new drugs from 1981 to 2014
-
Newman DJ, Cragg GM (2016) Natural products as sources of new drugs from 1981 to 2014. J Nat Prod 79(3):629-661.
-
(2016)
J Nat Prod
, vol.79
, Issue.3
, pp. 629-661
-
-
Newman, D.J.1
Cragg, G.M.2
-
2
-
-
70350722394
-
Genomic basis for natural product biosynthetic diversity in the actinomycetes
-
Nett M, Ikeda H, Moore BS (2009) Genomic basis for natural product biosynthetic diversity in the actinomycetes. Nat Prod Rep 26(11):1362-1384.
-
(2009)
Nat Prod Rep
, vol.26
, Issue.11
, pp. 1362-1384
-
-
Nett, M.1
Ikeda, H.2
Moore, B.S.3
-
3
-
-
27544477567
-
Discovery of a new peptide natural product by Streptomyces coelicolor genome mining
-
Lautru S, Deeth RJ, Bailey LM, Challis GL (2005) Discovery of a new peptide natural product by Streptomyces coelicolor genome mining. Nat Chem Biol 1(5):265-269.
-
(2005)
Nat Chem Biol
, vol.1
, Issue.5
, pp. 265-269
-
-
Lautru, S.1
Deeth, R.J.2
Bailey, L.M.3
Challis, G.L.4
-
4
-
-
38949203821
-
Exploiting the mosaic structure of trans-acyltransferase polyketide synthases for natural product discovery and pathway dissection
-
Nguyen T, et al. (2008) Exploiting the mosaic structure of trans-acyltransferase polyketide synthases for natural product discovery and pathway dissection. Nat Biotechnol 26(2):225-233.
-
(2008)
Nat Biotechnol
, vol.26
, Issue.2
, pp. 225-233
-
-
Nguyen, T.1
-
5
-
-
80054865417
-
A mass spectrometry-guided genome mining approach for natural product peptidogenomics
-
Kersten RD, et al. (2011) A mass spectrometry-guided genome mining approach for natural product peptidogenomics. Nat Chem Biol 7(11):794-802.
-
(2011)
Nat Chem Biol
, vol.7
, Issue.11
, pp. 794-802
-
-
Kersten, R.D.1
-
6
-
-
84883615133
-
Comparative genomics of actinomycetes with a focus on natural product biosynthetic genes
-
Doroghazi JR, Metcalf WW (2013) Comparative genomics of actinomycetes with a focus on natural product biosynthetic genes. BMC Genomics 14:611.
-
(2013)
BMC Genomics
, vol.14
, pp. 611
-
-
Doroghazi, J.R.1
Metcalf, W.W.2
-
7
-
-
84922466451
-
A roadmap for natural product discovery based on large-scale genomics and metabolomics
-
Doroghazi JR, et al. (2014) A roadmap for natural product discovery based on large-scale genomics and metabolomics. Nat Chem Biol 10(11):963-968.
-
(2014)
Nat Chem Biol
, vol.10
, Issue.11
, pp. 963-968
-
-
Doroghazi, J.R.1
-
8
-
-
84942761231
-
An automated Genomes-to-Natural Products platform (GNP) for the discovery of modular natural products
-
Johnston CW, et al. (2015) An automated Genomes-to-Natural Products platform (GNP) for the discovery of modular natural products. Nat Commun 6:8421.
-
(2015)
Nat Commun
, vol.6
, pp. 8421
-
-
Johnston, C.W.1
-
9
-
-
84961411746
-
Assembly and clustering of natural antibiotics guides target identification
-
Johnston CW, et al. (2016) Assembly and clustering of natural antibiotics guides target identification. Nat Chem Biol 12(4):233-239.
-
(2016)
Nat Chem Biol
, vol.12
, Issue.4
, pp. 233-239
-
-
Johnston, C.W.1
-
10
-
-
0034013269
-
Predictive, structure-based model of amino acid recognition by nonribosomal peptide synthetase adenylation domains
-
Challis GL, Ravel J, Townsend CA (2000) Predictive, structure-based model of amino acid recognition by nonribosomal peptide synthetase adenylation domains. Chem Biol 7(3):211-224.
-
(2000)
Chem Biol
, vol.7
, Issue.3
, pp. 211-224
-
-
Challis, G.L.1
Ravel, J.2
Townsend, C.A.3
-
11
-
-
3442896886
-
NRPS-PKS: A knowledge-based resource for analysis of NRPS/PKS megasynthases
-
Ansari MZ, Yadav G, Gokhale RS, Mohanty D (2004) NRPS-PKS: A knowledge-based resource for analysis of NRPS/PKS megasynthases. Nucleic Acids Res 32(Web Server issue):W405-W413.
-
(2004)
Nucleic Acids Res
, vol.32
, Issue.WEB SERVER ISSUE
, pp. W405-W413
-
-
Ansari, M.Z.1
Yadav, G.2
Gokhale, R.S.3
Mohanty, D.4
-
12
-
-
64249084052
-
Methods for in silico prediction of microbial polyketide and nonribosomal peptide biosynthetic pathways from DNA sequence data
-
Chapter 8
-
Bachmann BO, Ravel J (2009) Chapter 8. Methods for in silico prediction of microbial polyketide and nonribosomal peptide biosynthetic pathways from DNA sequence data. Methods Enzymol 458:181-217.
-
(2009)
Methods Enzymol
, vol.458
, pp. 181-217
-
-
Bachmann, B.O.1
Ravel, J.2
-
13
-
-
84864566650
-
PKMiner: A database for exploring type II polyketide synthases
-
Kim J, Yi GS (2012) PKMiner: A database for exploring type II polyketide synthases. BMC Microbiol 12:169.
-
(2012)
BMC Microbiol
, vol.12
, pp. 169
-
-
Kim, J.1
Yi, G.S.2
-
14
-
-
84859078407
-
The natural product domain seeker NaPDoS: A phylogeny based bioinformatic tool to classify secondary metabolite gene diversity
-
Ziemert N, et al. (2012) The natural product domain seeker NaPDoS: A phylogeny based bioinformatic tool to classify secondary metabolite gene diversity. PLoS One 7(3):e34064.
-
(2012)
PLoS One
, vol.7
, Issue.3
-
-
Ziemert, N.1
-
15
-
-
84876566794
-
ClusterMine360: A database of microbial PKS/NRPS biosynthesis
-
Conway KR, Boddy CN (2013) ClusterMine360: A database of microbial PKS/NRPS biosynthesis. Nucleic Acids Res 41(Database issue):D402-D407.
-
(2013)
Nucleic Acids Res
, vol.41
, Issue.DATABASE ISSUE
, pp. D402-D407
-
-
Conway, K.R.1
Boddy, C.N.2
-
16
-
-
84876517188
-
DoBISCUIT: A database of secondary metabolite biosynthetic gene clusters
-
Ichikawa N, et al. (2013) DoBISCUIT: A database of secondary metabolite biosynthetic gene clusters. Nucleic Acids Res 41(Database issue):D408-D414.
-
(2013)
Nucleic Acids Res
, vol.41
, Issue.DATABASE ISSUE
, pp. D408-D414
-
-
Ichikawa, N.1
-
17
-
-
67650898253
-
Automated genome mining for natural products
-
Li MH, Ung PM, Zajkowski J, Garneau-Tsodikova S, Sherman DH (2009) Automated genome mining for natural products. BMC Bioinformatics 10:185.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 185
-
-
Li, M.H.1
Ung, P.M.2
Zajkowski, J.3
Garneau-Tsodikova, S.4
Sherman, D.H.5
-
18
-
-
84949999706
-
Genomes to natural products prediction informatics for secondary metabolomes (PRISM)
-
Skinnider MA, et al. (2015) Genomes to natural products prediction informatics for secondary metabolomes (PRISM). Nucleic Acids Res 43(20):9645-9662.
-
(2015)
Nucleic Acids Res
, vol.43
, Issue.20
, pp. 9645-9662
-
-
Skinnider, M.A.1
-
19
-
-
84979859096
-
antiSMASH 3.0 - A comprehensive resource for the genome mining of biosynthetic gene clusters
-
Weber T, et al. (2015) antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res 43(W1):W237-243.
-
(2015)
Nucleic Acids Res
, vol.43
, Issue.W1
, pp. W237-W243
-
-
Weber, T.1
-
20
-
-
84870918230
-
Ribosomally synthesized and post-translationally modified peptide natural products: Overview and recommendations for a universal nomenclature
-
Arnison PG, et al. (2013) Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature. Nat Prod Rep 30(1):108-160.
-
(2013)
Nat Prod Rep
, vol.30
, Issue.1
, pp. 108-160
-
-
Arnison, P.G.1
-
21
-
-
62449284698
-
Thirteen posttranslational modifications convert a 14-residue peptide into the antibiotic thiocillin
-
Wieland Brown LC, Acker MG, Clardy J, Walsh CT, Fischbach MA (2009) Thirteen posttranslational modifications convert a 14-residue peptide into the antibiotic thiocillin. Proc Natl Acad Sci USA 106(8):2549-2553.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, Issue.8
, pp. 2549-2553
-
-
Wieland Brown, L.C.1
Acker, M.G.2
Clardy, J.3
Walsh, C.T.4
Fischbach, M.A.5
-
22
-
-
84939557642
-
Minimum Information about a Biosynthetic Gene cluster
-
Medema MH, et al. (2015) Minimum Information about a Biosynthetic Gene cluster. Nat Chem Biol 11(9):625-631.
-
(2015)
Nat Chem Biol
, vol.11
, Issue.9
, pp. 625-631
-
-
Medema, M.H.1
-
23
-
-
84927730179
-
Molecular fingerprint similarity search in virtual screening
-
Cereto-Massagué A, et al. (2015) Molecular fingerprint similarity search in virtual screening. Methods 71:58-63.
-
(2015)
Methods
, vol.71
, pp. 58-63
-
-
Cereto-Massagué, A.1
-
24
-
-
84930655650
-
Why is Tanimoto index an appropriate choice for fingerprint-based similarity calculations?
-
Bajusz D, Rácz A, Héberger K (2015) Why is Tanimoto index an appropriate choice for fingerprint-based similarity calculations? J Cheminform 7:20.
-
(2015)
J Cheminform
, vol.7
, pp. 20
-
-
Bajusz, D.1
Rácz, A.2
Héberger, K.3
-
25
-
-
84949867676
-
Pinensins: The first antifungal lantibiotics
-
Mohr KI, et al. (2015) Pinensins: The first antifungal lantibiotics. Angew Chem Int Ed Engl 54(38):11254-11258.
-
(2015)
Angew Chem Int Ed Engl
, vol.54
, Issue.38
, pp. 11254-11258
-
-
Mohr, K.I.1
-
26
-
-
84905466313
-
Radical S-adenosyl methionine epimerases: Regioselective introduction of diverse D-amino acid patterns into peptide natural products
-
Morinaka BI, et al. (2014) Radical S-adenosyl methionine epimerases: Regioselective introduction of diverse D-amino acid patterns into peptide natural products. Angew Chem Int Ed Engl 53(32):8503-8507.
-
(2014)
Angew Chem Int Ed Engl
, vol.53
, Issue.32
, pp. 8503-8507
-
-
Morinaka, B.I.1
-
27
-
-
0027285681
-
DNA sequence and mutational analysis of genes involved in the production and resistance of the antibiotic peptide trifolitoxin
-
Breil BT, Ludden PW, Triplett EW (1993) DNA sequence and mutational analysis of genes involved in the production and resistance of the antibiotic peptide trifolitoxin. J Bacteriol 175(12):3693-3702.
-
(1993)
J Bacteriol
, vol.175
, Issue.12
, pp. 3693-3702
-
-
Breil, B.T.1
Ludden, P.W.2
Triplett, E.W.3
-
28
-
-
84866533015
-
Precursor-centric genome-mining approach for lasso peptide discovery
-
Maksimov MO, Pelczer I, Link AJ (2012) Precursor-centric genome-mining approach for lasso peptide discovery. Proc Natl Acad Sci USA 109(38):15223-15228.
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, Issue.38
, pp. 15223-15228
-
-
Maksimov, M.O.1
Pelczer, I.2
Link, A.J.3
-
29
-
-
84924291904
-
Genome mining for ribosomally synthesized and post-translationally modified peptides (RiPPs) in anaerobic bacteria
-
Letzel AC, Pidot SJ, Hertweck C (2014) Genome mining for ribosomally synthesized and post-translationally modified peptides (RiPPs) in anaerobic bacteria. BMC Genomics 15:983.
-
(2014)
BMC Genomics
, vol.15
, pp. 983
-
-
Letzel, A.C.1
Pidot, S.J.2
Hertweck, C.3
-
30
-
-
84945232182
-
The genomic landscape of ribosomal peptides containing thiazole and oxazole heterocycles
-
Cox CL, Doroghazi JR, Mitchell DA (2015) The genomic landscape of ribosomal peptides containing thiazole and oxazole heterocycles. BMC Genomics 16:778.
-
(2015)
BMC Genomics
, vol.16
, pp. 778
-
-
Cox, C.L.1
Doroghazi, J.R.2
Mitchell, D.A.3
-
31
-
-
84904554933
-
Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters
-
Cimermancic P, et al. (2014) Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters. Cell 158(2):412-421.
-
(2014)
Cell
, vol.158
, Issue.2
, pp. 412-421
-
-
Cimermancic, P.1
-
32
-
-
84883572507
-
BAGEL3: Automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptides
-
van Heel AJ, de Jong A, Montalbán-López M, Kok J, Kuipers OP (2013) BAGEL3: Automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptides. Nucleic Acids Res 41(Web Server issue): W448-W453.
-
(2013)
Nucleic Acids Res
, vol.41
, Issue.WEB SERVER ISSUE
, pp. W448-W453
-
-
Van Heel, A.J.1
De Jong, A.2
Montalbán-López, M.3
Kok, J.4
Kuipers, O.P.5
-
33
-
-
84891820094
-
IMG 4 version of the integrated microbial genomes comparative analysis system
-
Markowitz VM, et al. (2014) IMG 4 version of the integrated microbial genomes comparative analysis system. Nucleic Acids Res 42(Database issue):D560-D567.
-
(2014)
Nucleic Acids Res
, vol.42
, Issue.DATABASE ISSUE
, pp. D560-D567
-
-
Markowitz, V.M.1
-
34
-
-
84859436530
-
NCBI Reference Sequences (RefSeq): Current status, new features and genome annotation policy
-
Pruitt KD, Tatusova T, Brown GR, Maglott DR (2012) NCBI Reference Sequences (RefSeq): Current status, new features and genome annotation policy. Nucleic Acids Res 40(Database issue):D130-D135.
-
(2012)
Nucleic Acids Res
, vol.40
, Issue.DATABASE ISSUE
, pp. D130-D135
-
-
Pruitt, K.D.1
Tatusova, T.2
Brown, G.R.3
Maglott, D.R.4
-
35
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
Edgar RC (2004) MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32(5):1792-1797.
-
(2004)
Nucleic Acids Res
, vol.32
, Issue.5
, pp. 1792-1797
-
-
Edgar, R.C.1
-
36
-
-
67650757433
-
trimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses
-
Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T (2009) trimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25(15):1972-1973.
-
(2009)
Bioinformatics
, vol.25
, Issue.15
, pp. 1972-1973
-
-
Capella-Gutiérrez, S.1
Silla-Martínez, J.M.2
Gabaldón, T.3
-
37
-
-
80055082271
-
Accelerated profile HMM searches
-
Eddy SR (2011) Accelerated profile HMM searches. PLOS Comput Biol 7(10):e1002195.
-
(2011)
PLOS Comput Biol
, vol.7
, Issue.10
-
-
Eddy, S.R.1
-
38
-
-
79960976768
-
UniProt Knowledgebase: A hub of integrated protein data
-
Magrane M; UniProt Consortium (2011) UniProt Knowledgebase: A hub of integrated protein data. Database (Oxford) 2011:bar009.
-
(2011)
Database (Oxford)
, vol.2011
-
-
Magrane, M.1
-
39
-
-
67849122320
-
MEME SUITE: Tools for motif discovery and searching
-
Bailey TL, et al. (2009) MEME SUITE: Tools for motif discovery and searching. Nucleic Acids Res 37(Web Server issue):W202-W208.
-
(2009)
Nucleic Acids Res
, vol.37
, Issue.WEB SERVER ISSUE
, pp. W202-W208
-
-
Bailey, T.L.1
-
40
-
-
0037361967
-
The Chemistry Development Kit (CDK): An open-source Java library for chemo- and bioinformatics
-
Steinbeck C, et al. (2003) The Chemistry Development Kit (CDK): An open-source Java library for chemo- and bioinformatics. J Chem Inf Comput Sci 43(2):493-500.
-
(2003)
J Chem Inf Comput Sci
, vol.43
, Issue.2
, pp. 493-500
-
-
Steinbeck, C.1
-
41
-
-
77952772341
-
Extended-connectivity fingerprints
-
Rogers D, Hahn M (2010) Extended-connectivity fingerprints. J Chem Inf Model 50(5):742-754.
-
(2010)
J Chem Inf Model
, vol.50
, Issue.5
, pp. 742-754
-
-
Rogers, D.1
Hahn, M.2
-
42
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403-410.
-
(1990)
J Mol Biol
, vol.215
, Issue.3
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
43
-
-
79959931985
-
HMMER web server: Interactive sequence similarity searching
-
Finn RD, Clements J, Eddy SR (2011) HMMER web server: Interactive sequence similarity searching. Nucleic Acids Res 39(Web Server issue):W29-W37.
-
(2011)
Nucleic Acids Res
, vol.39
, Issue.WEB SERVER ISSUE
, pp. W29-W37
-
-
Finn, R.D.1
Clements, J.2
Eddy, S.R.3
-
44
-
-
84870472070
-
BioJava: An open-source framework for bioinformatics in 2012
-
Prlić A, et al. (2012) BioJava: An open-source framework for bioinformatics in 2012. Bioinformatics 28(20):2693-2695.
-
(2012)
Bioinformatics
, vol.28
, Issue.20
, pp. 2693-2695
-
-
Prlić, A.1
-
45
-
-
18644368714
-
The Bioperl toolkit: Perl modules for the life sciences
-
Stajich JE, et al. (2002) The Bioperl toolkit: Perl modules for the life sciences. Genome Res 12(10):1611-1618.
-
(2002)
Genome Res
, vol.12
, Issue.10
, pp. 1611-1618
-
-
Stajich, J.E.1
-
46
-
-
77952299957
-
Prodigal: Prokaryotic gene recognition and translation initiation site identification
-
Hyatt D, et al. (2010) Prodigal: Prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11:119.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 119
-
-
Hyatt, D.1
-
47
-
-
79953300078
-
FIMO: Scanning for occurrences of a given motif
-
Grant CE, Bailey TL, Noble WS (2011) FIMO: Scanning for occurrences of a given motif. Bioinformatics 27(7):1017-1018.
-
(2011)
Bioinformatics
, vol.27
, Issue.7
, pp. 1017-1018
-
-
Grant, C.E.1
Bailey, T.L.2
Noble, W.S.3
|