Retrorules: A database of reaction rules for engineering biology

Nucleic Acids Research

Volumn 47, Issue D1, 2019, Pages D1229-D1235

  Duigou, Thomas ^a   Du Lac, Melchior ^a   Carbonell, Pablo ^b   Faulon, Jean Loup ^a,b,c  

^a UMR1319 MICALIS   (France)

^b UNIVERSITY OF MANCHESTER   (United Kingdom)

^c Institute of Systems and Synthetic Biology   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOLOGY; PHOTOSYNTHESIS; STEREOCHEMISTRY; BIOSYNTHESIS; CHEMICAL MODEL; CHEMICAL STRUCTURE; FACTUAL DATABASE; INFORMATION PROCESSING; INTERNET; METABOLIC ENGINEERING; PROCEDURES; STEREOISOMERISM;

BIOSYNTHETIC PATHWAYS; COMPUTATIONAL BIOLOGY; DATA MANAGEMENT; DATABASES, FACTUAL; INTERNET; METABOLIC ENGINEERING; MODELS, CHEMICAL; MOLECULAR STRUCTURE; STEREOISOMERISM;

EID: 85059655505     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gky940     Document Type: Article

References (22)

1. Nielsen, J. and Keasling, J.D. (2016) Engineering cellular metabolism. Cell, 164, 1185-1197
2. de Lorenzo, V., Prather, K.L., Chen, G., ODay, E., von Kameke, C., Oyarzun, D.A., Hosta-Rigau, L., Alsafar, H., Cao, C., Ji, W. et al. (2018) The power of synthetic biology for bioproduction, remediation and pollution control. EMBO Rep., 19, e45658
3. Edlund, A.M., Jones, J., Lewis, R. and Quinn, J.C. (2017) Economic feasibility and environmental impact of synthetic spider silk production from escherichia coli. N. Biotechnol., 42, 12-18
4. Delepine, B., Duigou, T., Carbonell, P. and Faulon, J.-L. (2018) RetroPath2.0: a retrosynthesis workflow for metabolic engineers. Metab. Eng., 45, 158-170
5. Carbonell, P., Wong, J., Swainston, N., Takano, E., Turner, N.J., Scrutton, N.S., Kell, D.B., Breitling, R. and Faulon, J.-L. (2018) Selenzyme: enzyme selection tool for pathway design. Bioinformatics, 34, 2153-2154
6. Plehiers, P.P., Marin, G.B., Stevens, C.V. and Van Geem, K.M. (2018) Automated reaction database and reaction network analysis: extraction of reaction templates using cheminformatics. J. Cheminform., 10, 11
7. Segler, M.H.S., Preuss, M. and Waller, M.P. (2018) Planning chemical syntheses with deep neural networks and symbolic AI. Nature, 555, 604-610
8. Tokic, M., Hadadi, N., Ataman, M., Neves, D., Ebert, B.E., Blank, L.M., Miskovic, L. and Hatzimanikatis, V. (2018) Discovery and evaluation of biosynthetic pathways for the production of five methyl ethyl ketone precursors. ACS Synth. Biol., 7, 1858-1873
9. Kumar, A., Suthers, P.F. and Maranas, C.D. (2012) MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases. BMC Bioinformatics, 13, 6
10. Jeffryes, J.G., Colastani, R.L., Elbadawi-Sidhu, M., Kind, T., Niehaus, T.D., Broadbelt, L.J., Hanson, A.D., Fiehn, O., Tyo, K.E. and Henry, C.S. (2015) MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics. J. Cheminform., 7, 44
11. Tyzack, J.D., Ribeiro, A.J.M., Borkakoti, N., Thornton, J.M. and Wren, J. (2018) Transform-MinER: transforming molecules in enzyme reactions. Bioinformatics, doi:10.1093/bioinformatics/bty394
12. Segler, M.H.S. and Waller, M.P. (2017) Neural-Symbolic machine learning for retrosynthesis and reaction prediction. Chem. - A Eur. J., 23, 5966-5971
13. Carbonell, P., Carlsson, L. and Faulon, J.-L.J.-L. (2013) Stereo signature molecular descriptor. J. Chem. Inf. Model., 53, 887-897
14. Moretti, S., Martin, O., Tran, T.V. Du, Bridge, A., Morgat, A. and Pagni, M. (2016) MetaNetX/MNXref reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks. Nucleic Acids Res., 44, D523-D526
15. Morgat, A., Lombardot, T., Axelsen, K.B., Aimo, L., Niknejad, A., Hyka-Nouspikel, N., Coudert, E., Pozzato, M., Pagni, M., Moretti, S. et al. (2017) Updates in Rhea - an expert curated resource of biochemical reactions. Nucleic Acids Res., 45, D415-D418
16. Bateman, A., Martin, M.J., ODonovan, C., Magrane, M., Alpi, E., Antunes, R., Bely, B., Bingley, M., Bonilla, C., Britto, R. et al. (2017) UniProt: the universal protein knowledgebase. Nucleic Acids Res., 45, D158-D169
17. Fillbrunn, A., Dietz, C., Pfeuffer, J., Rahn, R., Landrum, G.A. and Berthold, M.R. (2017) KNIME for reproducible cross-domain analysis of life science data. J. Biotechnol., 261, 149-156
18. Notebaart, R.A., Kintses, B., Feist, A.M. and Papp, B. (2017) Underground metabolism: network-level perspective and biotechnological potential. Curr. Opin. Biotechnol., 49, 108-114
19. Delepine, B., Libis, V., Carbonell, P. and Faulon, J.-L. (2016) SensiPath: computer-aided design of sensing-enabling metabolic pathways. Nucleic Acids Res., 44, W226-W231
20. Carbonell, P., Parutto, P., Herisson, J., Pandit, S.B. and Faulon, J.-L. (2014) XTMS: pathway design in an eXTended metabolic space. Nucleic Acids Res., 42, W389-W394
21. Koch, M., Duigou, T., Carbonell, P. and Faulon, J.-L. (2017) Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0. J. Cheminform., 9, 64
22. Schomburg, I., Jeske, L., Ulbrich, M., Placzek, S., Chang, A. and Schomburg, D. (2017) The BRENDA enzyme information system-From a database to an expert system. J. Biotechnol., 261, 194-206