-
1
-
-
0037881782
-
Metabolic reconstruction using shortest paths
-
Arita M. Metabolic reconstruction using shortest paths. Simulat Pract Theory 2000, 8:109-125.
-
(2000)
Simulat Pract Theory
, vol.8
, pp. 109-125
-
-
Arita, M.1
-
2
-
-
24044545913
-
CO: A chemical ontology for identification of functional groups and semantic comparison of small molecules
-
10.1016/j.febslet.2005.07.039, 16098521
-
Feldman HJ, Dumontier M, Ling S, Haider N, Hogue CW. CO: A chemical ontology for identification of functional groups and semantic comparison of small molecules. FEBS Lett 2005, 579:4685-4691. 10.1016/j.febslet.2005.07.039, 16098521.
-
(2005)
FEBS Lett
, vol.579
, pp. 4685-4691
-
-
Feldman, H.J.1
Dumontier, M.2
Ling, S.3
Haider, N.4
Hogue, C.W.5
-
3
-
-
0141850380
-
PathMiner: predicting metabolic pathways by heuristic search
-
10.1093/bioinformatics/btg217, 2709535, 12967966
-
McShan DC, Rao S, Shah I. PathMiner: predicting metabolic pathways by heuristic search. Bioinformatics 2003, 19:1692-1698. 10.1093/bioinformatics/btg217, 2709535, 12967966.
-
(2003)
Bioinformatics
, vol.19
, pp. 1692-1698
-
-
McShan, D.C.1
Rao, S.2
Shah, I.3
-
4
-
-
15744396035
-
Heuristic search for metabolic engineering: de novo synthesis of vanillin
-
McShan DC, Shah I. Heuristic search for metabolic engineering: de novo synthesis of vanillin. Comput Chem Eng 2005, 29:499-507.
-
(2005)
Comput Chem Eng
, vol.29
, pp. 499-507
-
-
McShan, D.C.1
Shah, I.2
-
5
-
-
0028534521
-
META. 1. A program for the evaluation of metabolic transformation of chemicals
-
Klopman G, Dimayuga M, Talafous J. META. 1. A program for the evaluation of metabolic transformation of chemicals. J Chem Inf Comput Sci 1994, 34:1320-1325.
-
(1994)
J Chem Inf Comput Sci
, vol.34
, pp. 1320-1325
-
-
Klopman, G.1
Dimayuga, M.2
Talafous, J.3
-
6
-
-
8744224466
-
OptStrain: a computational framework for redesign of microbial production systems
-
10.1101/gr.2872004, 525696, 15520298
-
Pharkya P, Burgard AP, Maranas CD. OptStrain: a computational framework for redesign of microbial production systems. Genome Res 2004, 14:2367-2376. 10.1101/gr.2872004, 525696, 15520298.
-
(2004)
Genome Res
, vol.14
, pp. 2367-2376
-
-
Pharkya, P.1
Burgard, A.P.2
Maranas, C.D.3
-
7
-
-
0024027564
-
Predicting metabolic pathways by logic programming
-
Darvas F. Predicting metabolic pathways by logic programming. J Mol Graph 1988, 6:80-86.
-
(1988)
J Mol Graph
, vol.6
, pp. 80-86
-
-
Darvas, F.1
-
8
-
-
0032619762
-
Knowledge-based expert systems for toxicity and metabolism prediction: DEREK, StAR and METEOR
-
10.1080/10629369908039182, 10491855
-
Greene N, Judson PN, Langowski JJ, Marchant CA. Knowledge-based expert systems for toxicity and metabolism prediction: DEREK, StAR and METEOR. SAR QSAR Environ Res 1999, 10:299-314. 10.1080/10629369908039182, 10491855.
-
(1999)
SAR QSAR Environ Res
, vol.10
, pp. 299-314
-
-
Greene, N.1
Judson, P.N.2
Langowski, J.J.3
Marchant, C.A.4
-
9
-
-
0037498035
-
Microbial pathway prediction: a functional group approach
-
Hou BK, Wackett LP, Ellis LB. Microbial pathway prediction: a functional group approach. J Chem Inf Comput Sci 2003, 43:1051-1057.
-
(2003)
J Chem Inf Comput Sci
, vol.43
, pp. 1051-1057
-
-
Hou, B.K.1
Wackett, L.P.2
Ellis, L.B.3
-
11
-
-
17444382016
-
Exploring the diversity of complex metabolic networks
-
10.1093/bioinformatics/bti213, 15613400
-
Hatzimanikatis V, Li C, Ionita JA, Henry CS, Jankowski MD, et al. Exploring the diversity of complex metabolic networks. Bioinformatics 2005, 21:1603-1609. 10.1093/bioinformatics/bti213, 15613400.
-
(2005)
Bioinformatics
, vol.21
, pp. 1603-1609
-
-
Hatzimanikatis, V.1
Li, C.2
Ionita, J.A.3
Henry, C.S.4
Jankowski, M.D.5
-
12
-
-
33751149652
-
Computer-assisted planning of organic syntheses: the second generation of programs
-
Ihlenfeldt WD, Gasteiger J. Computer-assisted planning of organic syntheses: the second generation of programs. Angew Chem Int Ed Engl 1996, 34:2613-2633.
-
(1996)
Angew Chem Int Ed Engl
, vol.34
, pp. 2613-2633
-
-
Ihlenfeldt, W.D.1
Gasteiger, J.2
-
13
-
-
8744251043
-
Computational discovery of biochemical routes to specialty chemicals
-
Li C, Henry CS, Jankowski MD, Ionita JA, Hatzimanikatis V, Broadbelt LJ. Computational discovery of biochemical routes to specialty chemicals. Chem Eng Sci 2004, 59:5051-5060.
-
(2004)
Chem Eng Sci
, vol.59
, pp. 5051-5060
-
-
Li, C.1
Henry, C.S.2
Jankowski, M.D.3
Ionita, J.A.4
Hatzimanikatis, V.5
Broadbelt, L.J.6
-
14
-
-
53049109464
-
De novo biosynthetic pathways: rational design of microbial chemical factories
-
Prather KL, Martin CH. De novo biosynthetic pathways: rational design of microbial chemical factories. Curr Opin Biotechnol 2009, 19:468-474.
-
(2009)
Curr Opin Biotechnol
, vol.19
, pp. 468-474
-
-
Prather, K.L.1
Martin, C.H.2
-
15
-
-
54949140438
-
DESHARKY: automatic design of metabolic pathways for optimal cell growth
-
10.1093/bioinformatics/btn471, 18776195
-
Rodrigo G, Carrera J, Prather KL, Jaramillo A. DESHARKY: automatic design of metabolic pathways for optimal cell growth. Bioinformatics 2008, 24:2554-2556. 10.1093/bioinformatics/btn471, 18776195.
-
(2008)
Bioinformatics
, vol.24
, pp. 2554-2556
-
-
Rodrigo, G.1
Carrera, J.2
Prather, K.L.3
Jaramillo, A.4
-
16
-
-
38049001166
-
Non-fermentative pathways for synthesis of branched chain higher alcohols as biofuels
-
10.1038/nature06450, 18172501
-
Atsumi S, Hanai T, Liao JC. Non-fermentative pathways for synthesis of branched chain higher alcohols as biofuels. Nature 2008, 451:86-89. 10.1038/nature06450, 18172501.
-
(2008)
Nature
, vol.451
, pp. 86-89
-
-
Atsumi, S.1
Hanai, T.2
Liao, J.C.3
-
17
-
-
0023965741
-
SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules
-
Weininger D. SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules. J Chem Inf Comput Sci 1988, 28:31-36.
-
(1988)
J Chem Inf Comput Sci
, vol.28
, pp. 31-36
-
-
Weininger, D.1
-
19
-
-
0033982936
-
KEGG: Kyoto Encyclopedia of Genes and Genomes
-
10.1093/nar/28.1.27, 102409, 10592173
-
Kanehisa M, Goto S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 2000, 28:27-30. 10.1093/nar/28.1.27, 102409, 10592173.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 27-30
-
-
Kanehisa, M.1
Goto, S.2
-
20
-
-
0032919364
-
KEGG: Kyoto Encyclopedia of Genes and Genomes
-
10.1093/nar/27.1.29, 148090, 9847135
-
Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, et al. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 1999, 27:29-34. 10.1093/nar/27.1.29, 148090, 9847135.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 29-34
-
-
Ogata, H.1
Goto, S.2
Sato, K.3
Fujibuchi, W.4
Bono, H.5
-
22
-
-
0037069467
-
Analysis of optimality in natural and perturbed metabolic networks
-
10.1073/pnas.232349399, 137552, 12415116
-
Segre D, Vitkup D. Analysis of optimality in natural and perturbed metabolic networks. Proc Natl Acad Sci USA 2002, 99:15112-15117. 10.1073/pnas.232349399, 137552, 12415116.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 15112-15117
-
-
Segre, D.1
Vitkup, D.2
-
23
-
-
84971332759
-
Top value added chemicals from biomass Volume I - Results of screening for potential candidates from sugars and synthesis gas [Electronic Version]
-
Werpy T, Petersen G. Top value added chemicals from biomass Volume I - Results of screening for potential candidates from sugars and synthesis gas [Electronic Version]. DOE Science and Technology Information 2004,
-
(2004)
DOE Science and Technology Information
-
-
Werpy, T.1
Petersen, G.2
-
24
-
-
63949085600
-
3-hydroxypropionic acid and other organic compounds
-
no. PCT/US2001/043607
-
Gokarn RR, Selifonova OV, Jessen HJ, Steven JG, Selmer T, Buckel W. 3-hydroxypropionic acid and other organic compounds. Patent application 2001, no. PCT/US2001/043607.
-
(2001)
Patent application
-
-
Gokarn, R.R.1
Selifonova, O.V.2
Jessen, H.J.3
Steven, J.G.4
Selmer, T.5
Buckel, W.6
-
25
-
-
63949083313
-
Biosynthetic pathways for 3-hydroxypropionic acid production
-
10.1007/s00253-009-1898-7, 19221732
-
Jing X, Meng X, Xian M. Biosynthetic pathways for 3-hydroxypropionic acid production. Appl Microbiol Biotechnol 2009, 82:995-1003. 10.1007/s00253-009-1898-7, 19221732.
-
(2009)
Appl Microbiol Biotechnol
, vol.82
, pp. 995-1003
-
-
Jing, X.1
Meng, X.2
Xian, M.3
-
26
-
-
0001611357
-
JChem: Java applets and modules supporting chemical database handling from web browsers
-
Csizmadia F. JChem: Java applets and modules supporting chemical database handling from web browsers. J Chem Inf Comput Sci 2000, 40:323-324.
-
(2000)
J Chem Inf Comput Sci
, vol.40
, pp. 323-324
-
-
Csizmadia, F.1
-
28
-
-
0002877326
-
Progress in linear programming
-
Bixby RE. Progress in linear programming. ORSA J Computing 1994, 6:15-22.
-
(1994)
ORSA J Computing
, vol.6
, pp. 15-22
-
-
Bixby, R.E.1
-
29
-
-
77953332855
-
Enzymology and molecular biology of carbonyl metabolism 10
-
Weiner H. Enzymology and molecular biology of carbonyl metabolism 10. Gulf Professional Publishing 2001,
-
(2001)
Gulf Professional Publishing
-
-
Weiner, H.1
-
30
-
-
0035570220
-
Functional group placement in protein binding sites: a comparison of GRID and MCSS
-
10.1023/A:1014309222984, 11918077
-
Bitetti-Putzer R, Joseph-McCarthy D, Hogle JM, Karplus M. Functional group placement in protein binding sites: a comparison of GRID and MCSS. J Comput Aided Mol Des 2001, 15:935-960. 10.1023/A:1014309222984, 11918077.
-
(2001)
J Comput Aided Mol Des
, vol.15
, pp. 935-960
-
-
Bitetti-Putzer, R.1
Joseph-McCarthy, D.2
Hogle, J.M.3
Karplus, M.4
-
31
-
-
77953335453
-
Functional group based ligand binding affinity scoring function at atomic environmental level
-
2646862, 19255647
-
Varadwaj PK, Lahiri T. Functional group based ligand binding affinity scoring function at atomic environmental level. Bioinformation 2009, 3:268-274. 2646862, 19255647.
-
(2009)
Bioinformation
, vol.3
, pp. 268-274
-
-
Varadwaj, P.K.1
Lahiri, T.2
-
32
-
-
84955745094
-
Handbook of Chemoinformatics
-
Wiley-VCH
-
Gasteiger J, Engel T. Handbook of Chemoinformatics. 2003, Wiley-VCH.
-
(2003)
-
-
Gasteiger, J.1
Engel, T.2
-
33
-
-
0036249270
-
Grouping of coefficients for the calculation of inter-molecular similarity and dissimilarity using 2D fragment bit-strings
-
Holliday JD, Hu CY, Wilett P. Grouping of coefficients for the calculation of inter-molecular similarity and dissimilarity using 2D fragment bit-strings. Comb Chem High Throughput Screen 2002, 5:155-166.
-
(2002)
Comb Chem High Throughput Screen
, vol.5
, pp. 155-166
-
-
Holliday, J.D.1
Hu, C.Y.2
Wilett, P.3
-
34
-
-
0025701406
-
Group contributions for estimating standard gibbs energies of formation of biochemical compounds in aqueous solution
-
10.1002/bit.260361013, 18595046
-
Mavrovouniotis ML. Group contributions for estimating standard gibbs energies of formation of biochemical compounds in aqueous solution. Biotechnol Bioeng 1990, 36:1070-1082. 10.1002/bit.260361013, 18595046.
-
(1990)
Biotechnol Bioeng
, vol.36
, pp. 1070-1082
-
-
Mavrovouniotis, M.L.1
-
35
-
-
0026353854
-
Estimation of standard Gibbs energy changes of biotransformations
-
Mavrovouniotis ML. Estimation of standard Gibbs energy changes of biotransformations. J Biol Chem 1991, 266:14440-14445.
-
(1991)
J Biol Chem
, vol.266
, pp. 14440-14445
-
-
Mavrovouniotis, M.L.1
-
36
-
-
85013932278
-
Dictionary of distances
-
Elsevier, ISBN 0444520872
-
Deza MM, Deza E. Dictionary of distances. 2006, Elsevier, ISBN 0444520872.
-
(2006)
-
-
Deza, M.M.1
Deza, E.2
-
37
-
-
30344456708
-
Inferring meaningful pathways in weighted metabolic networks
-
10.1016/j.jmb.2005.09.079, 16337962
-
Croes D, Couche F, Wodak SJ, Helden J. Inferring meaningful pathways in weighted metabolic networks. J Mol Biol 2006, 356:222-236. 10.1016/j.jmb.2005.09.079, 16337962.
-
(2006)
J Mol Biol
, vol.356
, pp. 222-236
-
-
Croes, D.1
Couche, F.2
Wodak, S.J.3
Helden, J.4
-
38
-
-
0036306663
-
Homology, Pathway Distance and Chromosomal Localization of the Small Molecule Metabolism Enzymes in Escherichia coli
-
10.1016/S0022-2836(02)00140-7, 12054833
-
Rion SC, Teichmann SA, Thoronton JM. Homology, Pathway Distance and Chromosomal Localization of the Small Molecule Metabolism Enzymes in Escherichia coli. J Mol Biol 2002, 318:911-932. 10.1016/S0022-2836(02)00140-7, 12054833.
-
(2002)
J Mol Biol
, vol.318
, pp. 911-932
-
-
Rion, S.C.1
Teichmann, S.A.2
Thoronton, J.M.3
-
39
-
-
2942704016
-
Analysis of phenetic trees based on metabolic capabilities across the three domains of life
-
10.1016/j.jmb.2004.04.059, 15210350
-
Aguilar D, Aviles FX, Querol E, Sternberg MJ. Analysis of phenetic trees based on metabolic capabilities across the three domains of life. J Mol Biol 2004, 340:491-512. 10.1016/j.jmb.2004.04.059, 15210350.
-
(2004)
J Mol Biol
, vol.340
, pp. 491-512
-
-
Aguilar, D.1
Aviles, F.X.2
Querol, E.3
Sternberg, M.J.4
-
40
-
-
0030982247
-
A molecular view of microbial diversity and the biosphere
-
10.1126/science.276.5313.734, 9115194
-
Pace NR. A molecular view of microbial diversity and the biosphere. Science 1997, 276:734-740. 10.1126/science.276.5313.734, 9115194.
-
(1997)
Science
, vol.276
, pp. 734-740
-
-
Pace, N.R.1
-
41
-
-
77953345650
-
Edit distance for genome comparison based on non-local operations
-
Sankoff D. Edit distance for genome comparison based on non-local operations. Springer Berlin 2006,
-
(2006)
Springer Berlin
-
-
Sankoff, D.1
|