-
1
-
-
80054069179
-
A comprehensive genome-scale reconstruction of Escherichia coli metabolism–2011
-
Orth JD, et al. (2011) A comprehensive genome-scale reconstruction of Escherichia coli metabolism–2011. Mol Syst Biol 7:535.
-
(2011)
Mol Syst Biol
, vol.7
, pp. 535
-
-
Orth, J.D.1
-
2
-
-
85016149190
-
KEGG: New perspectives on genomes, pathways, diseases and drugs
-
Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K (2017) KEGG: New perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res 45:D353–D361.
-
(2017)
Nucleic Acids Res
, vol.45
, pp. D353-D361
-
-
Kanehisa, M.1
Furumichi, M.2
Tanabe, M.3
Sato, Y.4
Morishima, K.5
-
3
-
-
84903906147
-
Profiling the orphan enzymes
-
Sorokina M, Stam M, Médigue C, Lespinet O, Vallenet D (2014) Profiling the orphan enzymes. Biol Direct 9:10.
-
(2014)
Biol Direct
, vol.9
, pp. 10
-
-
Sorokina, M.1
Stam, M.2
Médigue, C.3
Lespinet, O.4
Vallenet, D.5
-
4
-
-
84901320984
-
Finding sequences for over 270 orphan enzymes
-
Shearer AG, Altman T, Rhee CD (2014) Finding sequences for over 270 orphan enzymes. PLoS One 9:e97250.
-
(2014)
PLoS One
, vol.9
-
-
Shearer, A.G.1
Altman, T.2
Rhee, C.D.3
-
5
-
-
75549089640
-
The University of Minnesota Biocatalysis/Bio-degradation Database: Improving public access
-
Gao J, Ellis LBM, Wackett LP (2010) The University of Minnesota Biocatalysis/Bio-degradation Database: Improving public access. Nucleic Acids Res 38(Suppl 1): D488–D491.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. D488-D491
-
-
Gao, J.1
Ellis, L.B.M.2
Wackett, L.P.3
-
6
-
-
17444382016
-
Exploring the diversity of complex metabolic networks
-
Hatzimanikatis V, et al. (2005) Exploring the diversity of complex metabolic networks. Bioinformatics 21:1603–1609.
-
(2005)
Bioinformatics
, vol.21
, pp. 1603-1609
-
-
Hatzimanikatis, V.1
-
9
-
-
79961116083
-
A retrosynthetic biology approach to metabolic pathway design for therapeutic production
-
Carbonell P, Planson A-G, Fichera D, Faulon J-L (2011) A retrosynthetic biology approach to metabolic pathway design for therapeutic production. BMC Syst Biol 5:122.
-
(2011)
BMC Syst Biol
, vol.5
, pp. 122
-
-
Carbonell, P.1
Planson, A.-G.2
Fichera, D.3
Faulon, J.-L.4
-
10
-
-
54949140438
-
Desharky: Automatic design of metabolic pathways for optimal cell growth
-
Rodrigo G, Carrera J, Prather KJ, Jaramillo A (2008) DESHARKY: Automatic design of metabolic pathways for optimal cell growth. Bioinformatics 24:2554–2556.
-
(2008)
Bioinformatics
, vol.24
, pp. 2554-2556
-
-
Rodrigo, G.1
Carrera, J.2
Prather, K.J.3
Jaramillo, A.4
-
11
-
-
77953329895
-
Prediction of novel synthetic pathways for the production of desired chemicals
-
Cho A, Yun H, Park JH, Lee SY, Park S (2010) Prediction of novel synthetic pathways for the production of desired chemicals. BMC Syst Biol 4:35.
-
(2010)
BMC Syst Biol
, vol.4
, pp. 35
-
-
Cho, A.1
Yun, H.2
Park, J.H.3
Lee, S.Y.4
Park, S.5
-
12
-
-
79959374585
-
Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol
-
Yim H, et al. (2011) Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol. Nat Chem Biol 7:445–452.
-
(2011)
Nat Chem Biol
, vol.7
, pp. 445-452
-
-
Yim, H.1
-
13
-
-
84907350970
-
Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path
-
Campodonico MA, Andrews BA, Asenjo JA, Palsson BO, Feist AM (2014) Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path. Metab Eng 25:140–158.
-
(2014)
Metab Eng
, vol.25
, pp. 140-158
-
-
Campodonico, M.A.1
Andrews, B.A.2
Asenjo, J.A.3
Palsson, B.O.4
Feist, A.M.5
-
14
-
-
53049109464
-
De novo biosynthetic pathways: Rational design of microbial chemical factories
-
Prather KLJ, Martin CH (2008) De novo biosynthetic pathways: Rational design of microbial chemical factories. Curr Opin Biotechnol 19:468–474.
-
(2008)
Curr Opin Biotechnol
, vol.19
, pp. 468-474
-
-
Prather, K.L.J.1
Martin, C.H.2
-
15
-
-
85038207858
-
Retropath2.0: A retrosynthesis workflow for metabolic engineers
-
Delépine B, Duigou T, Carbonell P, Faulon J-L (2017) RetroPath2.0: A retrosynthesis workflow for metabolic engineers. Metab Eng 45:158–170.
-
(2017)
Metab Eng
, vol.45
, pp. 158-170
-
-
Delépine, B.1
Duigou, T.2
Carbonell, P.3
Faulon, J.-L.4
-
16
-
-
84936966835
-
Design of computational retrobiosynthesis tools for the design of de novo synthetic pathways
-
Hadadi N, Hatzimanikatis V (2015) Design of computational retrobiosynthesis tools for the design of de novo synthetic pathways. Curr Opin Chem Biol 28:99–104.
-
(2015)
Curr Opin Chem Biol
, vol.28
, pp. 99-104
-
-
Hadadi, N.1
Hatzimanikatis, V.2
-
17
-
-
84904817527
-
XTMS: Pathway design in an eXTended metabolic space
-
Carbonell P, Parutto P, Herisson J, Pandit SB, Faulon JL (2014) XTMS: Pathway design in an eXTended metabolic space. Nucleic Acids Res 42:W389–W394.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. W389-W394
-
-
Carbonell, P.1
Parutto, P.2
Herisson, J.3
Pandit, S.B.4
Faulon, J.L.5
-
18
-
-
84896872039
-
A computational framework for integration of lipidomics data into metabolic pathways
-
Hadadi N, et al. (2014) A computational framework for integration of lipidomics data into metabolic pathways. Metab Eng 23:1–8.
-
(2014)
Metab Eng
, vol.23
, pp. 1-8
-
-
Hadadi, N.1
-
19
-
-
80053375237
-
The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions
-
Rolfsson O, Palsson BØ, Thiele I (2011) The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions. BMC Syst Biol 5:155.
-
(2011)
BMC Syst Biol
, vol.5
, pp. 155
-
-
Rolfsson, O.1
Palsson, B.Ø.2
Thiele, I.3
-
20
-
-
19244366327
-
Call for an enzyme genomics initiative
-
Karp PD (2004) Call for an enzyme genomics initiative. Genome Biol 5:401.
-
(2004)
Genome Biol
, vol.5
, pp. 401
-
-
Karp, P.D.1
-
21
-
-
78651335279
-
Systematizing the generation of missing metabolic knowledge
-
Orth JD, Palsson BO (2010) Systematizing the generation of missing metabolic knowledge. Biotechnol Bioeng 107:403–412.
-
(2010)
Biotechnol Bioeng
, vol.107
, pp. 403-412
-
-
Orth, J.D.1
Palsson, B.O.2
-
22
-
-
0037398732
-
Missing genes in metabolic pathways: A comparative genomics approach
-
Osterman A, Overbeek R (2003) Missing genes in metabolic pathways: A comparative genomics approach. Curr Opin Chem Biol 7:238–251.
-
(2003)
Curr Opin Chem Biol
, vol.7
, pp. 238-251
-
-
Osterman, A.1
Overbeek, R.2
-
23
-
-
0033055062
-
The use of gene clusters to infer functional coupling
-
Overbeek R, Fonstein M, D’Souza M, Pusch GD, Maltsev N (1999) The use of gene clusters to infer functional coupling. Proc Natl Acad Sci USA 96:2896–2901.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 2896-2901
-
-
Overbeek, R.1
Fonstein, M.2
D’Souza, M.3
Pusch, G.D.4
Maltsev, N.5
-
24
-
-
0033551248
-
Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles
-
Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO (1999) Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles. Proc Natl Acad Sci USA 96:4285–4288.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 4285-4288
-
-
Pellegrini, M.1
Marcotte, E.M.2
Thompson, M.J.3
Eisenberg, D.4
Yeates, T.O.5
-
25
-
-
33745035630
-
Predicting genes for orphan metabolic activities using phylogenetic profiles
-
Chen L, Vitkup D (2006) Predicting genes for orphan metabolic activities using phylogenetic profiles. Genome Biol 7:R17.
-
(2006)
Genome Biol
, vol.7
, pp. R17
-
-
Chen, L.1
Vitkup, D.2
-
26
-
-
25644458211
-
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
-
Overbeek R, et al. (2005) The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 33:5691–5702.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 5691-5702
-
-
Overbeek, R.1
-
27
-
-
31644444476
-
Mage: A microbial genome annotation system supported by synteny results
-
Vallenet D, et al. (2006) MaGe: A microbial genome annotation system supported by synteny results. Nucleic Acids Res 34:53–65.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 53-65
-
-
Vallenet, D.1
-
28
-
-
33646171940
-
Identifying metabolic enzymes with multiple types of association evidence
-
Kharchenko P, Chen L, Freund Y, Vitkup D, Church GM (2006) Identifying metabolic enzymes with multiple types of association evidence. BMC Bioinformatics 7:177.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 177
-
-
Kharchenko, P.1
Chen, L.2
Freund, Y.3
Vitkup, D.4
Church, G.M.5
-
29
-
-
34247374704
-
Prediction of missing enzyme genes in a bacterial metabolic network. Reconstruction of the lysine-degradation pathway of Pseudomonas aeru-ginosa
-
Yamanishi Y, et al. (2007) Prediction of missing enzyme genes in a bacterial metabolic network. Reconstruction of the lysine-degradation pathway of Pseudomonas aeru-ginosa. FEBS J 274:2262–2273.
-
(2007)
FEBS J
, vol.274
, pp. 2262-2273
-
-
Yamanishi, Y.1
-
30
-
-
79951526289
-
Genome-wide discovery of missing genes in biological pathways of prokaryotes
-
Chen Y, Mao F, Li G, Xu Y (2011) Genome-wide discovery of missing genes in biological pathways of prokaryotes. BMC Bioinformatics 12(Suppl 1):S1.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. S1
-
-
Chen, Y.1
Mao, F.2
Li, G.3
Xu, Y.4
-
31
-
-
84863669933
-
The CanOE strategy: Integrating genomic and metabolic contexts across multiple prokaryote genomes to find candidate genes for orphan enzymes
-
Smith AAT, Belda E, Viari A, Medigue C, Vallenet D (2012) The CanOE strategy: Integrating genomic and metabolic contexts across multiple prokaryote genomes to find candidate genes for orphan enzymes. PLoS Comput Biol 8:e1002540.
-
(2012)
PLoS Comput Biol
, vol.8
-
-
Smith, A.A.T.1
Belda, E.2
Viari, A.3
Medigue, C.4
Vallenet, D.5
-
32
-
-
84883357535
-
An introduction to sequence similarity (“homology”) searching
-
Chapter 3:Unit3.1
-
Pearson WR (2013) An introduction to sequence similarity (“homology”) searching. Curr Protoc Bioinformatics Chapter 3:Unit3.1.
-
(2013)
Curr Protoc Bioinformatics
-
-
Pearson, W.R.1
-
33
-
-
74549221383
-
Annotation error in public databases: Misannotation of molecular function in enzyme superfamilies
-
Schnoes AM, Brown SD, Dodevski I, Babbitt PC (2009) Annotation error in public databases: Misannotation of molecular function in enzyme superfamilies. PLoS Comput Biol 5:e1000605.
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Schnoes, A.M.1
Brown, S.D.2
Dodevski, I.3
Babbitt, P.C.4
-
34
-
-
34547840249
-
Using genome-context data to identify specific types of functional associations in pathway/genome databases
-
Green ML, Karp PD (2007) Using genome-context data to identify specific types of functional associations in pathway/genome databases. Bioinformatics 23:i205–i211.
-
(2007)
Bioinformatics
, vol.23
, pp. i205-i211
-
-
Green, M.L.1
Karp, P.D.2
-
35
-
-
84873311233
-
Ecoh: An enzyme commission number predictor using mutual information and a support vector machine
-
Matsuta Y, Ito M, Tohsato Y (2013) ECOH: An enzyme commission number predictor using mutual information and a support vector machine. Bioinformatics 29:365–372.
-
(2013)
Bioinformatics
, vol.29
, pp. 365-372
-
-
Matsuta, Y.1
Ito, M.2
Tohsato, Y.3
-
36
-
-
84855290528
-
Divergence and convergence in enzyme evolution
-
Galperin MY, Koonin EV (2012) Divergence and convergence in enzyme evolution. J Biol Chem 287:21–28.
-
(2012)
J Biol Chem
, vol.287
, pp. 21-28
-
-
Galperin, M.Y.1
Koonin, E.V.2
-
37
-
-
33744815655
-
Proteins of the same fold and unrelated sequences have similar amino acid composition
-
Ofran Y, Margalit H (2006) Proteins of the same fold and unrelated sequences have similar amino acid composition. Proteins 64:275–279.
-
(2006)
Proteins
, vol.64
, pp. 275-279
-
-
Ofran, Y.1
Margalit, H.2
-
38
-
-
84947798846
-
RXNSim: A tool to compare biochemical reactions
-
Giri V, Sivakumar TV, Cho KM, Kim TY, Bhaduri A (2015) RxnSim: A tool to compare biochemical reactions. Bioinformatics 31:3712–3714.
-
(2015)
Bioinformatics
, vol.31
, pp. 3712-3714
-
-
Giri, V.1
Sivakumar, T.V.2
Cho, K.M.3
Kim, T.Y.4
Bhaduri, A.5
-
39
-
-
80051936716
-
RXNfinder: Biochemical reaction search engines using molecular structures, molecular fragments and reaction similarity
-
Hu QN, Deng Z, Hu H, Cao DS, Liang YZ (2011) RxnFinder: Biochemical reaction search engines using molecular structures, molecular fragments and reaction similarity. Bioinformatics 27:2465–2467.
-
(2011)
Bioinformatics
, vol.27
, pp. 2465-2467
-
-
Hu, Q.N.1
Deng, Z.2
Hu, H.3
Cao, D.S.4
Liang, Y.Z.5
-
40
-
-
84962467691
-
Identification of enzyme genes using chemical structure alignments of substrate-product pairs
-
Moriya Y, et al. (2016) Identification of enzyme genes using chemical structure alignments of substrate-product pairs. J Chem Inf Model 56:510–516.
-
(2016)
J Chem Inf Model
, vol.56
, pp. 510-516
-
-
Moriya, Y.1
-
41
-
-
84871708278
-
Assignment of EC numbers to enzymatic reactions with reaction difference fingerprints
-
Hu QN, et al. (2012) Assignment of EC numbers to enzymatic reactions with reaction difference fingerprints. PLoS One 7:e52901.
-
(2012)
PLoS One
, vol.7
-
-
Hu, Q.N.1
-
42
-
-
84895071963
-
EC-BLAST: A tool to automatically search and compare enzyme reactions
-
Rahman SA, Cuesta SM, Furnham N, Holliday GL, Thornton JM (2014) EC-BLAST: A tool to automatically search and compare enzyme reactions. Nat Methods 11: 171–174.
-
(2014)
Nat Methods
, vol.11
, pp. 171-174
-
-
Rahman, S.A.1
Cuesta, S.M.2
Furnham, N.3
Holliday, G.L.4
Thornton, J.M.5
-
43
-
-
0004117251
-
-
Version 4.9 DAYLIGHT Chemical Information Systems Inc., Mission Viejo, CA
-
Delany J (2011) Daylight Theory Manual, Version 4.9 (DAYLIGHT Chemical Information Systems Inc., Mission Viejo, CA).
-
(2011)
Daylight Theory Manual
-
-
Delany, J.1
-
44
-
-
37049239596
-
A computer program for classifying plants
-
Rogers DJ, Tanimoto TT (1960) A computer program for classifying plants. Science 132:1115–1118.
-
(1960)
Science
, vol.132
, pp. 1115-1118
-
-
Rogers, D.J.1
Tanimoto, T.T.2
-
46
-
-
84993958585
-
Atlas of biochemistry: A repository of all possible biochemical reactions for synthetic biology and metabolic engineering studies
-
Hadadi N, Hafner J, Shajkofci A, Zisaki A, Hatzimanikatis V (2016) ATLAS of Biochemistry: A repository of all possible biochemical reactions for synthetic biology and metabolic engineering studies. ACS Synth Biol 5:1155–1166.
-
(2016)
ACS Synth Biol
, vol.5
, pp. 1155-1166
-
-
Hadadi, N.1
Hafner, J.2
Shajkofci, A.3
Zisaki, A.4
Hatzimanikatis, V.5
-
47
-
-
85008869334
-
Reconstruction of biological pathways and metabolic networks from in silico labeled metabolites
-
Hadadi N, Hafner J, Soh KC, Hatzimanikatis V (2017) Reconstruction of biological pathways and metabolic networks from in silico labeled metabolites. Biotechnol J 12: 1600464.
-
(2017)
Biotechnol J
, vol.12
, pp. 1600464
-
-
Hadadi, N.1
Hafner, J.2
Soh, K.C.3
Hatzimanikatis, V.4
-
48
-
-
85049059297
-
Selenzyme: Enzyme selection tool for pathway design
-
Carbonell P, et al. (2018) Selenzyme: Enzyme selection tool for pathway design. Bioinformatics 34:2153–2154.
-
(2018)
Bioinformatics
, vol.34
, pp. 2153-2154
-
-
Carbonell, P.1
-
49
-
-
84962606868
-
Linalool isomerase, a membrane-anchored enzyme in the anaerobic monoterpene degradation in Thauera linaloolentis 47Lol
-
Marmulla R, Safaric B, Markert S, Schweder T, Harder J (2016) Linalool isomerase, a membrane-anchored enzyme in the anaerobic monoterpene degradation in Thauera linaloolentis 47Lol. BMC Biochem 17:6.
-
(2016)
BMC Biochem
, vol.17
, pp. 6
-
-
Marmulla, R.1
Safaric, B.2
Markert, S.3
Schweder, T.4
Harder, J.5
-
50
-
-
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 215:403–410.
-
(1990)
J Mol Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
51
-
-
85064112383
-
In vitro and in silico affinity fingerprints: Finding similarities beyond structural classes
-
ed Klebe G (Kluwer Academic Publishers, Dordrecht, The Netherlands)
-
Briem H, Lessel UF (2002) In vitro and in silico affinity fingerprints: Finding similarities beyond structural classes. Virtual Screening: An Alternative or Complement to High Throughput Screening? ed Klebe G (Kluwer Academic Publishers, Dordrecht, The Netherlands), pp 231–244.
-
(2002)
Virtual Screening: An Alternative or Complement to High Throughput Screening?
, pp. 231-244
-
-
Briem, H.1
Lessel, U.F.2
-
52
-
-
80053512597
-
Open Babel: An open chemical toolbox
-
O’Boyle NM, et al. (2011) Open Babel: An open chemical toolbox. J Cheminform 3:33.
-
(2011)
J Cheminform
, vol.3
, pp. 33
-
-
O’Boyle, N.M.1
-
53
-
-
0023965741
-
SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules
-
Weininger D (1988) SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules. J Chem Inf Comput Sci 28:31–36.
-
(1988)
J Chem Inf Comput Sci
, vol.28
, pp. 31-36
-
-
Weininger, D.1
-
54
-
-
38349112826
-
On the normalization and visualization of author co-citation data: Salton’s Cosine versus the Jaccard index
-
Leydesdorff L (2008) On the normalization and visualization of author co-citation data: Salton’s Cosine versus the Jaccard index. J Am Soc Inf Sci Technol 59:77–85.
-
(2008)
J Am Soc Inf Sci Technol
, vol.59
, pp. 77-85
-
-
Leydesdorff, L.1
-
55
-
-
84964509986
-
Development of a commercial scale process for production of 1,4-butanediol from sugar
-
Burgard A, Burk MJ, Osterhout R, Van Dien S, Yim H (2016) Development of a commercial scale process for production of 1,4-butanediol from sugar. Curr Opin Biotechnol 42:118–125.
-
(2016)
Curr Opin Biotechnol
, vol.42
, pp. 118-125
-
-
Burgard, A.1
Burk, M.J.2
Osterhout, R.3
Van Dien, S.4
Yim, H.5
-
56
-
-
84969351865
-
Identification of metabolic engineering targets for the enhancement of 1,4-butanediol production in recombinant E. Coli using large-scale kinetic models
-
Andreozzi S, et al. (2016) Identification of metabolic engineering targets for the enhancement of 1,4-butanediol production in recombinant E. coli using large-scale kinetic models. Metab Eng 35:148–159.
-
(2016)
Metab Eng
, vol.35
, pp. 148-159
-
-
Andreozzi, S.1
|