Biochemical reactions

BiGGKing Z. A., Lu J., Dräger A., Miller P., Federowicz S., Lerman J. A., Ebrahim A., Palsson B. O., Lewis N. E., BiGG Models: A platform for integrating, standardizing and sharing genome-scale models. Nucleic Acids Research, 2016, 44, D515–D522. Abstract
BRENDAChang A., Jeske L., Ulbrich S., Hofmann J., Koblitz J., Schomburg I., Neumann-Schaal M., Jahn D., Schomburg D., BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Research, 2021, 49, D498–D508. Abstract
CAZyDrula E., Garron M.-L., Dogan S., Lombard V., Henrissat B., Terrapon N., The carbohydrate-active enzyme database: functions and literature. Nucleic Acids Research, 2022, 50, D571–D577. Abstract
ClusterMine360Conway K. R., Boddy C. N., ClusterMine360: A database of microbial PKS/NRPS biosynthesis. Nucleic Acids Research, 2013, 41, D402-D407. Abstract
CSDB_GTEgorova K. S., Toukach P. V., CSDB_GT: a new curated database on glycosyltransferases. Glycobiology, 2017, 27, 285-290. Abstract
db-CAN-seqHuang L., Zhang H., Wu P., Entwistle S., Li X., Yohe T., Yi H., Yang Z., Yin Y., dbCAN-seq: a database of carbohydrate-active enzyme (CAZyme) sequence and annotation. Nucleic Acids Research, 2018, 46, D516–D521. Abstract
ENZYMEBairoch A., The ENZYME database in 2000. Nucleic Acids Research, 2000, 28, 304-305. Abstract
Enzyme PortalAlcántara R., Onwubiko J., Cao H., de Matos P., Cham J. A., Jacobsen J., Holliday G. L., Fischer J. D., Rahman S. A., Jassal B., Goujon M., Rowland R., Velankar S., López R., Overington J. P., Kleywegt G. J., Hermjakob H., O’Donovan C., Martín M. J., Thornton J. M., Steinbeck C., The EBI enzyme portal. Nucleic Acids Research, 2013, 41, D773–D780. Abstract
eQuilibratorBeber M. E., Gollub M. G., Mozaffari D., Shebek K. M., Flamholz A. I., Milo R., Noor E., eQuilibrator 3.0: a database solution for thermodynamic constant estimation. Nucleic Acids Research, 2022, 50, D603–D609. Abstract
ExplorEnzMcDonald A. G., Boyce S., Tipton K. F., ExplorEnz: the primary source of the IUBMB enzyme list. Nucleic Acids Research, 2009, 37, D593-D597. Abstract
EzCatDBNagano N., Nakayama N., Ikeda K., Fukuie M., Yokota K., Doi T., Kato T., Tomii K., EzCatDB: the enzyme reaction database, 2015 update. Nucleic Acids Research, 2015, D453–D458. Abstract
FEDADeckers M., Van Braeckel J., Vanneste K., Deforce D., Fraiture M.-A., Roosens N. H. C., Food Enzyme Database (FEDA): a web application gathering information about food enzyme preparations available on the European market. Database, 2021, Article No baab060. Abstract
GTDGoldberg R. N., Tewari Y. B., Bhat T. N., Thermodynamics of enzyme-catalyzed reactions-a database for quantitative biochemistry. Bioinformatics, 2004, 20, 2874-2877. Abstract
GTDBZhou C., Xu Q., He S., Ye W., Cao R., Wang P., Ling Y., Yan X., Wang Q., Zhang G., GTDB: an integrated resource for glycosyltransferase sequences and annotations. Database, 2020, Article No baaa047. Abstract
INTEDEYin J., Li F., Zhou Y., Mou M., Lu Y., Chen K., Xue J., Luo Y., Fu J., He X., Gao J., Zeng S., Yu L., Zhu F., INTEDE: interactome of drug-metabolizing enzymes. Nucleic Acids Research, 2021, 49, D1233–D1243. Abstract
IntEnzFleischmann A., Darsow M., Degtyarenko K., Fleischmann W., Boyce, S., Axelsen K. B., Bairoch A., Schomburg D. C., Tipton K. F., Apweiler R., IntEnz, the integrated relational enzyme database. Nucleic Acids Research, 2004, 32, D434-D437. Abstract
KEGG reactionKanehisa M., Furumichi M., Sato Y., Ishiguro-Watanabe M., Tanabe M., KEGG: integrating viruses and cellular organisms. Nucleic Acids Research, 2021, 49, D545–D551. Abstract
LabWorm EnzymesAuthors: Yoav BaumanRoy GranitAlon Vitenshtein
MACiEHolliday G. L., Andreini C., Fischer J. D., Rahman S. A., Almonacid D. E., Williams S. T., Pearson W. R., MACiE: Exploring the diversity of biochemical reactions. Nucleic Acids Research, 2012, 40, D783-D789. Abstract
M-CSARibeiro A. J. M., Holliday G. L., Furnham N., Tyzack J. D., Ferris K., Thornton J. M., Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites. Nucleic Acids Research, 2018, 46, D618–D623. Abstract
MeLADLi G., Su Y., Yan Y.-H., Peng J.-Y., Dai Q.-Q., Ning X.-L., Zhu C.-L., Fu C., McDonough M. A., Schofield C. J., Huang C., Li G.-B., MeLAD: an integrated resource for metalloenzyme-ligand associations. Bioinformatics, 2020, 36, 904-909. Abstract
MEROPSRawlings N. D., Barrett A. J., Thomas P. D., Huang X., Bateman A., Finn R. D., The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database. Nucleic Acids Research, 2018, 46, D624–D632. Abstract
Open TargetsOchoa D., Hercules A., Carmona M., Suveges D., Gonzalez-Uriarte A., Malangone C., Miranda A., Fumis L., Carvalho-Silva D., Spitzer M., Baker J., Ferrer J., Raies A., Razuvayevskaya O., Faulconbridge A., Petsalaki E., Mutowo P., Machlitt-Northen S., Peat G., McAuley E., Ong C. K., Mountjoy E., Ghoussaini M., Pierleoni A., Papa E., Pignatelli M., Koscielny G., Karim M., Schwartzentruber J., Hulcoop D. G., Dunham I., McDonagh E. M., Open Targets Platform: supporting systematic drug–target identification and prioritisation. Nucleic Acids Research, 2021, 49, D1302–D1310. Abstract
OxDBaseArora P. K., Kumar M., Raghava G. P. S., Jain R. K., OxDBase: a database of oxygenases involved in biodegradation. BMC Research Notes, 2009, 2, Article No 67. Abstract
PlantCAZymeEkstrom A., Taujale R., McGinn N., Yin Y., PlantCAZyme: a database for plant carbohydrate-active enzymes, Database, 2014, Article no bau079. Abstract
RheaBansal P., Morgat A., Axelsen K. B., Muthukrishnan V., Coudert E., Aimo L., Hyka-Nouspikel N., Gasteiger E., Kerhornou A., Neto T. B., Pozzato M., Blatter M.-C., Ignatchenko A., Redaschi N., Bridge A., Rhea, the reaction knowledgebase in 2022. Nucleic Acids Research, 2022, 50, D693–D700. Abstract
SABIO-RKWittig U., Rey M., Weidemann A., Kania R., Müller W., SABIO-RK: an updated resource for manually curated biochemical reaction kinetics. Nucleic Acids Research, 2018, 46, D656–D660. Abstract
SFLDHolliday G. L., Brown S. D., Mischel D., Polacco B. J., Babbitt P. C., A strategy for large-scale comparison of evolutionary- and reaction-based classifications of enzyme function. Database, 2020, Article No baaa034. Abstract
STRENDAProvider: Beilstein Institute
SulfAtlasBarbeyron T., Brillet-Guéguen L., Carré W., Carrière C., Caron C., Czjzek M., Hoebeke M., Michel G., Matching the diversity of sulfated biomolecules: creation of a classification database for sulfatases reflecting their substrate specificity. PLoS ONE, 2016, 11, Article No e0164846. Abstract
TECRGoldberg R. N., Tewari Y. B., Bhat T. N., Thermodynamics of Enzyme-Catalyzed Reactions – a database for quantitative biochemistry. Bioinformatics, 2004, 20, 2874-2877. Abstract
TransformerHoffmann M. F., Preissner S. C., Nickel J., Dunkel M., Preissner R., Preissner S., The Transformer database: biotransformation of xenobiotics. Nucleic Acids Research, 2014, 42, D1113–D1117. Abstract
XMetDBSpjuth O., Rydberg P., Willighagen E. L., Evelo C. T., Jeliazkova N., XMetDB: an open access database for xenobiotic metabolism. Journal of Cheminformatics, 2016, 8, Article No 47. Abstract