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
ClusterCADTao X. B., LaFrance S., Xing Y.,, Nava A. A., Martin H. G., Keasling J. D., Backman T. W. H., ClusterCAD 2.0: an updated computational platform for chimeric type I polyketide synthase and nonribosomal peptide synthetase design. Nucleic Acids Research, 2023, 51, D532–D538. 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
EnzyMineSun D., Cheng X., Tian Y., Ding S., Zhang D., Cai P., Hu Q., EnzyMine: a comprehensive database for enzyme function annotation with enzymatic reaction chemical feature. Database, 2020, Article No baaa065. 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
GotEnzymesLi F., Chen Y., Anton M., Nielsen J., GotEnzymes: an extensive database of enzyme parameter predictions. Nucleic Acids Research, 2023, 51, D583–D586. 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
iCAZyGFADBFu C., Yang Y., iCAZyGFADB: an insect CAZyme and gene function annotation database. Database, 2023, Article No baad086. Abstract
INTEDEZhang Y., Liu X., Li F., Yin J., Yang H., Li X., Liu X., Chai X., Niu T., Zeng S., Jia Q., Zhu F., INTEDE 2.0: the metabolic roadmap of drugs. Nucleic Acids Research, 2024, 52, D1355–D1364. 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., Kawashima M., Ishiguro-Watanabe M., KEGG for taxonomy-based analysis of pathways and genomes. Nucleic Acids Research, 2023, 51, D587–D592. Abstract
KinScanBrahma R., Shin J.-M., Cho K.-H., KinScan: AI-based rapid profiling of activity across the kinome. Briefings in Bioinformatics, 2023, 24, Article No bbad396. Abstract
LabWorm EnzymesAuthors: Yoav Bauman, Roy Granit, Alon 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
MeDBAYu J.-L., Wu S., Zhou C., Dai Q.-Q., Schofield C. J., Li G.-B., MeDBA: the Metalloenzyme Data Bank and Analysis platform. Nucleic Acids Research, 2023, 51, D593–D602. 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., Baker J., Malangone C., Lopez I., Miranda A., Cruz-Castillo C., Fumis L., Bernal-Llinares M., Tsukanov K., Cornu H., Tsirigos K., Razuvayevskaya O., Buniello A., Schwartzentruber J., Karim M., Ariano B., Martinez Osorio R. E., Ferrer J., Ge X., Machlitt-Northen S., Gonzalez-Uriarte A., Saha S., Tirunagari S., Mehta C., Roldán-Romero J. M., Horswell S., Young S., Ghoussaini M., Hulcoop D. G., Dunham I., McDonagh E. M., The next-generation Open Targets Platform: reimagined, redesigned, rebuilt. Nucleic Acids Research, 2023, 51, D1353–D1359. 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
PlasticDBGambarini V., Pantos O., Kingsbury J. M., Weaver L., Handley K. M., Lear G., PlasticDB: a database of microorganisms and proteins linked to plastic biodegradation. Database, 2022, Article No baac008. Abstract
PLBDLingė D., Gedgaudas M., Merkys A., Petrauskas V., Vaitkus A., Grybauskas A., Paketurytė V., Zubrienė A., Zakšauskas A., Mickevicǐūtė A., Smirnovienė J., Baranauskienė L., Čapkauskaitė E., Dudutienė V., Urniezǐus E., Konovalovas A., Kazlauskas E., Shubin K., Schiöth H. P., Chen W.-Y., Ladbury J. E., Grazǔlis S., Matulis D., PLBD: protein–ligand binding database of thermodynamic and kinetic intrinsic parameters. Database, 2023, Article No baad040. Abstract
RetroBioCatFinnigan W., Hepworth L. J., Flitsch S. L., Turner N. J., RetroBioCat as a computer-aided synthesis planning tool for biocatalytic reactions and cascades. Nature Catalysis, 2021, 4, 98–104. 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
RibocentreDeng J., Shi Y., Peng X., He Y., Chen X., Li1 M., Lin X., Liao W., Huang Y., Jiang T., Lilley D. M. J., Miao Z., Huang L., Ribocentre: a database of ribozymes. Nucleic Acids Research, 2023, 51, D262–D268. Abstract
SABIO-RKDudaš D., Wittig U., Rey M., Weidemann A., Müller W., Improved insights into the SABIO-RK database via visualization. Database, 2023, Article No baad011. 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
SulfAtlasStam M., Lelièvre P., Hoebeke M., Corre E., Barbeyron T., Michel G., SulfAtlas, the sulfatase database: state of the art and new developments. Nucleic Acids Research, 2023, 51, D647–D653. 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

Last Updated on 19-04-2024 by Piotr Minkiewicz