Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: Application to Recon 3D

Journal of Cheminformatics

Volumn 9, Issue 1, 2017, Pages

  Preciat Gonzalez, German A ^a   El Assal, Lemmer R P ^a   Noronha, Alberto ^a   Thiele, Ines ^a   Haraldsdóttir, Hulda S ^a   Fleming, Ronan M T ^a  

^a UNIVERSITY OF LUXEMBOURG   (Luxembourg)

Author keywords

Atom mapping; AutoMapper; Automation; CLCA; DREAM; ICMAP; Metabolic network reconstruction; MWED; RDT; Recon 3D

Indexed keywords

EID: 85027856736     PISSN: None     EISSN: 17582946     Source Type: Journal    
DOI: 10.1186/s13321-017-0223-1     Document Type: Article

References (43)

1. Forster M, Pick A, Raitner M, Schreiber F, Brandenburg FJ (2002) The system architecture of the BioPath system. In Silico Biol 2(3):415-426
2. Shimizu Y, Hattori M, Goto S, Kanehisa M (2008) Generalized reaction patterns for prediction of unknown enzymatic reactions. Genome informatics. international conference on genome informatics, vol 20, pp 149-158
3. Rahman SA, Cuesta SM, Furnham N, Holliday GL, Thornton JM (2014) ECBLAST: a tool to automatically search and compare enzyme reactions. Nat Methods 11(2):171-174. doi:10.1038/nmeth.2803
4. Caspi R, Altman T, Dreher K, Fulcher CA, Subhraveti P, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Pujar A, Shearer AG, Travers M, Weerasinghe D, Zhang P, Karp PD (2012) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res 40(Database issue):742-753. doi:10.1093/nar/gkr1014
5. Kumar A, Suthers PF, Maranas CD (2012) MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases. BMC Bioinform 13:6. doi:10.1186/1471-2105-13-6
6. Palsson BO (2015) Systems biology: constraint-based reconstruction and analysis. Cambridge University Press, Cambridge
7. Thiele I, Palsson BO (2010) A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protoc 5(1):93-121. doi:10.1038/nprot.2009.203.00367
8. Magnusdottir S, Heinken A, Kutt L, Ravcheev DA, Bauer E, Noronha A, Greenhalgh K, Jager C, Baginska J, Wilmes P, Fleming RMT, Thiele I (2017) Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota. Nat Biotech 35(1):81-89. doi:10.1038/nbt.3703
9. Brunk E, Sahoo S, Daniel Z, Altunkaya A, Prlic A, Mih N, Sastry A, Preciat Gonzalez GA, Danielsdottir AD, Noronha A, Aurich M, Rose P, Fleming RMT, Thiele I, Palsson BO Recon 3D: A resource enabling a three-dimensional view of gene variation in human metabolism (submitted)
10. Rahman SA, Torrance G, Baldacci L, Cuesta SM, Fenninger F, Gopal N, Choudhary S, May JW, Holliday GL, Steinbeck C, Thornton JM (2016) Reaction Decoder Tool (RDT): extracting features from chemical reactions. Bioinformatics 32(13):2065-2066. doi:10.1093/bioinformatics/btw096
11. First EL, Gounaris CE, Floudas CA (2012) Stereochemically consistent reaction mapping and identification of multiple reaction mechanisms through integer linear optimization. J Chem Inf Model 52:84-92. doi:10.1021/ci200351b
12. ChemAxon:Standardizer, was used for structure canonicalization and transformation. J Chem 16.1.11.0, 2015, ChemAxon. http://www.chemaxon. com (2015)
13. Kumar A, Maranas CD (2014) CLCA: maximum common molecular substructure queries within the MetRxn database. J Chem Inf Model 54(12):3417-38. doi:10.1021/ci5003922
14. Latendresse M, Malerich JP, Travers M, Karp PD (2012) Accurate atommapping computation for biochemical reactions. J Chem Inf Model 52(11):2970-82. doi:10.1021/ci3002217
15. Kraut H, Eiblmaier J, Grethe G, Low P, Matuszczyk H, Saller H (2013) Algorithm for reaction classification. J Chem Inf Model 53(11):2884-2895. doi:10.1021/ci400442f
16. Tipton KF (1994) Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB). Enzyme nomenclature. Recommendations 1992. Supplement: corrections and additions. Eur J Biochem/FEBS 223(1):1-5
17. Anderson E, Veith GD, Weininger D (1987). SMILES: A line notation and computerized interpreter for chemical structures. Duluth, MN: U.S. EPA, Environmental Research Laboratory-Duluth. Report No. EPA/600/M-87/021
18. Dalby A, Nourse JG, Hounshell WD, Gushurst AKI, Grier DL, Leland BA, Laufer J (1992) Description of several chemical structure file formats used by computer programs developed at Molecular Design Limited. J Chem Inf Model 32(3):244-255. doi:10.1021/ci00007a012
19. First EL, Gounaris CE, Floudas CA (2012) Stereochemically consistent reaction mapping and identification of multiple reaction mechanisms through integer linear optimization. J Chem Inf Model 52(1):84-92. doi:10.1021/ci200351b
20. ChemAxon: Standardizer, Was Used for Structure Canonicalization and Transformation. J Chem 16.1.11.0, 2015. ChemAxon (http://www.chemaxon.com 2015)
21. Kumar A, Maranas CD (2014) CLCA: maximum common molecular substructure queries within the MetRxn database. J Chem Inf Model 54(12):3417-3438. doi:10.1021/ci5003922
22. Latendresse M, Malerich JP, Travers M, Karp PD (2012) Accurate atommapping computation for biochemical reactions. J Chem Inf Model 52(11):2970-2982. doi:10.1021/ci3002217
23. Karp PD, Paley S, Romero P (2002) The pathway tools software. Bioinformatics 18(Suppl 1):225-232
24. Wiechert W (2001) 13c metabolic flux analysis. Metab Eng 3(3):195-206. doi:10.1006/mben.2001.0187
25. Pey J, Planes FJ, Beasley JE (2014) Refining carbon flux paths using atomic trace data. Bioinformatics 30(7):975-980. doi:10.1093/bioinformatics/btt653
26. Haraldsdottir HS, Fleming RMT (2016) Identification of Conserved Moieties in Metabolic Networks by Graph Theoretical Analysis of Atom Transition Networks. PLOS Computational Biology 12(11):e1004999. doi:10.1371/journal.pcbi.1004999
27. Haraldsdottir HS, Thiele I, Fleming RM (2014) Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2. J Cheminform 6(1):2. doi:10.1186/1758-2946-6-2
28. Thiele I, Swainston N, Fleming RMT, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, Bolling C, Bordel S, Chavali AK, Dobson P, Dunn WB, Endler L, Hala D, Hucka M, Hull D, Jameson D, Jamshidi N, Jonsson JJ, Juty N, Keating S, Nookaew I, Le Novere N, Malys N, Mazein A, Papin JA, Price ND, Selkov E Sr, Sigurdsson MI, Simeonidis E, Sonnenschein N, Smallbone K, Sorokin A, van Beek JHGM, Weichart D, Goryanin I, Nielsen J, Westerhoff HV, Kell DB, Mendes P, Palsson BO (2013) A community-driven global reconstruction of human metabolism. Nat Biotech 31(5):419-425. doi:10.1038/nbt.2488
29. Kim S, Thiessen PA, Bolton EE, Chen J, Fu G, Gindulyte A, Han L, He J, He S, Shoemaker BA, Wang J, Yu B, Zhang J, Bryant SH (2016) PubChem substance and compound databases. Nucleic Acids Res 44(D1):1202-1213. doi:10.1093/nar/gkv951
30. Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28(1):27-30
31. Hastings J, de Matos P, Dekker A, Ennis M, Harsha B, Kale N, Muthukrishnan V, Owen G, Turner S, Williams M, Steinbeck C (2013) The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. Nucleic Acids Res 41(D1):456-463. doi:10.1093/nar/gks1146
32. Sud M, Fahy E, Cotter D, Brown A, Dennis EA, Glass CK, Merrill AH, Murphy RC, Raetz CRH, Russell DW, Subramaniam S (2007) LMSD: LIPID MAPS structure database. Nucleic Acids Res 35(Database issue):52732. doi:10.1093/nar/gkl838
33. Forster M, Pick A, Raitner M, Schreiber F, Brandenburg FJ (2002) The system architecture of the BioPath system. Silico Biol (Gedrukt) 2(3):415-426
34. Williams AJ, Tkachenko V, Golotvin S, Kidd R, McCann G (2010) ChemSpider- building a foundation for the semantic web by hosting a crowd sourced databasing platform for chemistry. J Cheminform 2(Suppl 1):16. doi:10.1186/1758-2946-2-S1-O16
35. Wishart DS, Tzur D, Knox C, Eisner R, Guo AC, Young N, Cheng D, Jewell K, Arndt D, Sawhney S, Fung C, Nikolai L, Lewis M, Coutouly M-A, Forsythe I, Tang P, Shrivastava S, Jeroncic K, Stothard P, Amegbey G, Block D, Hau DD, Wagner J, Miniaci J, Clements M, Gebremedhin M, Guo N, Zhang Y, Duggan GE, MacInnis GD, Weljie AM, Dowlatabadi R, Bamforth F, Clive D, Greiner R, Li L, Marrie T, Sykes BD, Vogel HJ, Querengesser L (2007) HMDB: the Human Metabolome DataBase. Nucl Acids Res 35(suppl 1):521-526. doi:10.1093/nar/gkl923
36. Chen WL, Chen DZ, Taylor KT (2013) Automatic reaction mapping and reaction center detection. Wiley Interdiscip Rev Comput Mol Sci 3(6):560-593. doi:10.1002/wcms.1140
37. Schellenberger J, Que R, Fleming RMT, Thiele I, Orth JD, Feist AM, Zielinski DC, Bordbar A, Lewis NE, Rahmanian S, Kang J, Hyduke DR, Palsson BO (2011) Quantitative prediction of cellular metabolism with constraintbased models: the COBRA Toolbox v2.0. Nat Protoc 6(9):1290-1307. doi:10.1038/nprot.2011.308
38. Kotera M, Okuno Y, Hattori M, Goto S, Kanehisa M (2004) Computational assignment of the EC numbers for genomic-scale analysis of enzymatic reactions. J Am Chem Soc 126(50):16487-16498. doi:10.1021/ja0466457
39. Pey J, Planes FJ, Beasley JE (2014) Refining carbon flux paths using atomic trace data. Bioinformatics (Oxford, England) 30(7):97580. doi:10.1093/ bioinformatics/btt653
40. O'Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR, Weininger D, Murray-Rust P, Rzepa H, Murray-Rust P, Rzepa HS, Murray-Rust P, Rzepa H, Wright M, Murray-Rust P, Rzepa H, Holliday GL, Murray-Rust P, Rzepa HS, Fogel K, Bender A, Mussa HY, Glen RC, Reiling S, Filimonov D, Poroikov V, Borodina Y, Gloriozova T, Morgan HL, McKay BD, Gakh A, Burnett M, Trepalin SV, Yarkov AV, Pletnev IV, Gakh AA, Gakh AA, Burnett MN, Trepalin SV, Yarkov AV, Halgren T, Halgren T, Halgren T, Halgren T, Nachbar R, Halgren T, Andronico A, Randall A, Benz RW, Baldi P, Rappe A, Casewit C, Colwell K, Goddard W, Skiff WM, Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA, Wang J, Wang W, Kollman PA, Case DA, O NM, Martin K, Hoffman B, O N, Myers J, Allison T, Bittner S, Didier B, Frenklach M, Green W, Ho Y, Hewson J, Koegler W, Lansing C, Lind P, Alm M, Amini A, Shrimpton PJ, Muggleton SH, Sternberg MJE, Arbor S, Marshall GR, Huang Z, Huan J, Smalter A, Lushington GH, Cheng T, Li Q, Wang Y, Bryant SH Mihaleva VV, Verhoeven HA, de Vos RCH, Hall RD, van Ham R, Bas DC, Rogers DM, Jensen JH, Fabian L, Brock CP, Dehmer M, Barbarini N, Varmuza K, Graber A, Langham JJ, Jain AN, Fontaine F, Pastor M, Zamora I, Konyk M, Leon AD Dumontier M, Kogej T, Engkvist O, Blomberg N, Muresan S, Reynes C, Host H, Camproux A-C, Laconde G, Leroux F, Mazars A, Deprez B, Fahraeus R, Villoutreix BO, Sperandio O, Lagorce D, Pencheva T, Villoutreix BO, Miteva MA, Gomez MJ, Pazos F, Guijarro FJ, de Lorenzo V, Valencia A, Kazius J, Nijssen S, Kok J, Back T, IJzerman AP, O NM, Brustle M, Buehler M, Dodson J, van Duin A, Bullock CW, Jacob RB, McDougal OM, Hampikian G, Andersen T, Jiang X, Kumar K, Hu X, Wallqvist A, Reifman J, Lagorce D, Sperandio O, Galons H, Miteva MA, Villoutreix BO, Maunz A, Helma C, Kramer S, Maunz A, Helma C, Kramer S, Helma C, Meineke MA, Vardeman CF, Lin T, Fennell CJ, Gezelter JD, Tosco P, Balle T, Tosco P, Balle T, Filippov IV, Nicklaus MC, Koes DR, Camacho CJ, Jacob CR, Beyhan SM, Bulo RE, Gomes ASP, Gotz AW, Kiewisch K, Sikkema J, Visscher L, Green WH, Allen JW, Ashcraft RW, Beran GJ, Class CA, Gao C, Goldsmith CF, Harper MR, Jalan A, Magoon GR, Matheu DM, Merchant SS, Mo JD, Petway S, Raman S, Sharma S, Song J, Geem KMV, Wen J, West RH, Wong A, Wong H-W, Yelvington PE, Yu J, Karwath A, Raedt LD, Lonie DC, Zurek E, Zonta N, Grimstead IJ, Avis NJ, Brancale A, Chen JH, Linstead E, Swamidass SJ, Wang D, Baldi P, Backman TWH, Cao Y, Girke T, Ahmed J, Worth CL, Thaben P, Matzig C, Blasse C, Dunkel M, Preissner R, Miteva MA, Guyon F, Tuffery P, Sharman JL, Mpamhanga CP, Spedding M, Germain P, Staels B, Dacquet C, Laudet V, Harmar AJ, Esposito R, Ermondi G, Caron G, Wallach I, Lilien R, Poater A, Cosenza B, Correa A, Giudice S, Ragone F, Scarano V, Cavallo L, Yan B-B, Xue M-Z, Xiong B, Liu K, Hu D-Y, Shen J-K, Rydberg P, Gloriam DE, Olsen L, Ingsriswang S, Pacharawongsakda E, Bauer RA, Bourne PE, Formella A, Frommel C, Gille C, Goede A, Guerler A, Hoppe A, Knapp EW, Poschel T, Schmidt U, Struck S, Gruening B, Hossbach J, Jaeger IS, Parol R, Lindequist U, Teuscher E, Preissner R, Bauer RA, Gunther S, Jansen D, Heeger C, Thaben PF, Preissner R, Ahmed J, Preissner S, Dunkel M, Worth CL, Eckert A, Preissner R, Kuhn M, Szklarczyk D, Franceschini A, Campillos M, von Mering C, Jensen LJ, Beyer A, Bork P, Tetko IV, Gasteiger J, Todeschini R, Mauri A, Livingstone D, Ertl P, Palyulin VA, Radchenko EV, Zefirov NS, Makarenko AS, Sperandio O, Petitjean M, Tuffery P (2011) Open babel: an open chemical toolbox. J Cheminform 3(1):33. doi:10.1186/1758-2946-3-33
41. Fleming RMT, Maes CM, Saunders MA, Ye Y, Palsson BO (2012) A variational principle for computing nonequilibrium fluxes and potentials in genome-scale biochemical networks. J Theor Biol 292(71-77):2014. doi:10.1016/j.jtbi.2011.09.029.00019. Accessed-04-02
42. Clayden J, Greeves N, Warren S, Wothers P (2000) Organic chemistry, 1 edn. Oxford University Press, Oxford
43. Loudon GM, Parise J (2016) Organic chemistry. Roberts and Company Publishers, Greenwood Village