{"id":95,"date":"2021-12-16T21:56:33","date_gmt":"2021-12-16T20:56:33","guid":{"rendered":"http:\/\/metachemibio.webgazel.pl\/?page_id=95"},"modified":"2026-04-15T10:26:00","modified_gmt":"2026-04-15T08:26:00","slug":"biochemical-reactions","status":"publish","type":"page","link":"https:\/\/biochemia.uwm.edu.pl\/metachemibio\/biochemical-reactions\/","title":{"rendered":"Biochemical reactions"},"content":{"rendered":"\n

Biochemical reactions<\/strong><\/p>\n\n\n\n

BiGG<\/a><\/td>King Z. A., Lu J., Dr\u00e4ger 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\u2013D522. Abstract<\/a><\/td><\/tr>
BRENDA<\/a><\/td>Hauenstein J., Jeske L., J\u00e4de A., Krull M., D\u00fcmmer K., Koblitz J., Tietz A., Jahn D., Reimer L. C., Bunk B., BRENDA in 2026: a Global Core Biodata Resource for functional enzyme and metabolic data within the DSMZ Digital Diversity. Nucleic Acids Research, 2026, 54, D527\u2013D534. Abstract<\/a><\/td><\/tr>
CAZy<\/a><\/td>Lombard V., Henrissat B., Garron M.-L., CAZac: an activity descriptor for carbohydrate-active enzymes. Nucleic Acids Research, 2025, 53, D625\u2013D633. Abstract<\/a><\/td><\/tr>
ClusterCAD<\/a><\/td>Tao 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\u2013D538. Abstract<\/a><\/td><\/tr>
ClusterMine360<\/a><\/td>Conway K. R., Boddy C. N., ClusterMine360: A database of microbial PKS\/NRPS biosynthesis. Nucleic Acids Research, 2013, 41, D402-D407. Abstract<\/a><\/td><\/tr>
CSDB_GT<\/a><\/td>Egorova K. S., Toukach P. V., CSDB_GT: a new curated database on glycosyltransferases. Glycobiology, 2017, 27, 285-290. Abstract<\/a><\/td><\/tr>
db-CAN-seq<\/a><\/td>Huang 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\u2013D521. Abstract<\/a><\/td><\/tr>
EnzEngDB<\/a><\/td>Long Y., Abbasinejad F., Li F.-Z., Reinprecht P., Wittmann B., Kennemur J. L., Carder H., Yang J., Lambert T., O\u2019Meara R., Radtke L., Qin Z., Brinkmann-Chen S., Arnold F., Mora A., Enzyme Engineering Database (EnzEngDB): a platform for sharing and interpreting sequence\u2013function relationships across protein engineering campaigns. Nucleic Acids Research, 2026, 54, D564\u2013D571. Abstract<\/a><\/td><\/tr>
ENZYME<\/a><\/td>Bairoch A., The ENZYME database in 2000. Nucleic Acids Research, 2000, 28, 304-305. Abstract<\/a><\/td><\/tr>
Enzyme Portal<\/a><\/td>Alc\u00e1ntara 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., L\u00f3pez R., Overington J. P., Kleywegt G. J., Hermjakob H., O\u2019Donovan C., Mart\u00edn M. J., Thornton J. M., Steinbeck C., The EBI enzyme portal. Nucleic Acids Research, 2013, 41, D773\u2013D780. Abstract<\/a><\/td><\/tr>
EnzyMine<\/a><\/td>Sun 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<\/a><\/td><\/tr>
eQuilibrator<\/a><\/td>Beber 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\u2013D609. Abstract<\/a><\/td><\/tr>
ExplorEnz<\/a><\/td>McDonald A. G., Boyce S., Tipton K. F., ExplorEnz: the primary source of the IUBMB enzyme list. Nucleic Acids Research, 2009, 37, D593-D597. Abstract<\/a><\/td><\/tr>
EzCatDB<\/a><\/td>Nagano 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\u2013D458. Abstract<\/a><\/td><\/tr>
FEDA<\/a><\/td>Deckers 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<\/a><\/td><\/tr>
GotEnzymes<\/a><\/td>Lyu B., Wu K., Huang Y., Anton M., Li X., Viknander S., Anwer D., Yang Y., Lu D., Kerkhoven E., Zelezniak A., Gao D., Chen Y., Li F., GotEnzymes2: expanding coverage of enzyme kinetics and thermal properties. Nucleic Acids Research, 2026, 54, D583\u2013D592. Abstract<\/a><\/td><\/tr>
GTD<\/a><\/td>Goldberg R. N., Tewari Y. B., Bhat T. N., Thermodynamics of enzyme-catalyzed reactions-a database for quantitative biochemistry. Bioinformatics, 2004, 20, 2874-2877. Abstract<\/a><\/td><\/tr>
GTDB<\/a><\/td>Zhou 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<\/a><\/td><\/tr>
iCAZyGFADB<\/a><\/td>Fu C., Yang Y., iCAZyGFADB: an insect CAZyme and gene function annotation database. Database, 2023, Article No baad086. Abstract<\/a><\/td><\/tr>
INTEDE<\/a><\/td>Zhang 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\u2013D1364. Abstract<\/a><\/td><\/tr>
IntEnz<\/a><\/td>Fleischmann 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<\/a><\/td><\/tr>
KEGG reaction<\/a><\/td>Kanehisa M., Furumichi M., Sato Y., Matsuura Y., Ishiguro-Watanabe M., KEGG: biological systems database as a model of the real world. Nucleic Acids Research, 2025, 53, D672\u2013D677. Abstract<\/a><\/td><\/tr>
Kin<\/a>Scan<\/a><\/td>Brahma 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<\/a><\/td><\/tr>
LabWorm Enzymes<\/a><\/td>Authors: Yoav Bauman<\/a>, Roy Granit<\/a>, Alon Vitenshtein<\/a><\/td><\/tr>
LICEDB<\/a><\/td>Gong L., Liu F., Zhang C., Ming Y. Mou Y., Yuan Z., Jiang H., Gao B., Lu F., Zhang L., LICEDB: light industrial core enzyme database for industrial applications and AI enzyme design. Database, 2025, Article No baaf001. Abstract<\/a><\/td><\/tr>
MACiE<\/a><\/td>Holliday 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<\/a><\/td><\/tr>
M-CSA<\/a><\/td>Ribeiro 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\u2013D623. Abstract<\/a><\/td><\/tr>
MeDBA<\/a><\/td>Yu 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\u2013D602. Abstract<\/a><\/td><\/tr>
MeLAD<\/a><\/td>Li 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<\/a><\/td><\/tr>
MEROPS<\/a><\/td>Rawlings 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\u2013D632. Abstract<\/a><\/td><\/tr>
MetabFlow<\/a><\/td>Zhu S., Chen L., Li X., Xu H., Lu W., Zhou C., Hu Y., Tao L., MetabFlow: a comprehensive metabolic map for exogenous natural products. Nucleic Acids Research, 2026, 54, D607\u2013D616. Abstract<\/a><\/td><\/tr>
MITE<\/a><\/td>Rutz A., Probst D., Aguilar C., Akiyama D. Y., Alberti F., Augustijn H. E., Avalon N. E., Beemelmanns C., Bertoletti Barbieri H., Biermann F., Bridge A. J., Charria Gir\u00f3n E., Cox R., Cr\u00fcsemann M., D\u2019Agostino P. M., Feuermann M., Gerke J., Guti\u00e9rrez Garc\u00eda K., Holme J. E., Hwang J.-Y., Iacovelli R., Barbosa J. C. J., Kaur N., Klapper M., K\u00f6hler A. M., Korenskaia A., Kubach N., Lee B. T., Loureiro C., Mantri S., Narula S., Meijer D., Navarro-Mu\u00f1oz J. C., Nguyen G.-S., Paliyal S., Panghal M., Rao L., Sieber S., Sokolova N., Sowa S., Szenei J., Terlouw B. R., Weddeling H. G., Yu J., Ziemert N., Weber T., Blin K., van der Hooft J. J. J., Medema M. H., Zdouc M. M., MITE: the Minimum Information about a Tailoring Enzyme database for capturing specialized metabolite biosynthesis. Nucleic Acids Research, 2026, 54, D635\u2013D642. Abstract<\/a><\/td><\/tr>
Open Enzyme Database<\/a><\/td>Yuan L., Bianchi D. M., Arneson K., Guo B., Lambert S., Stephens C., Wasnik Y. H., Pond C., Berry M. J., Zhao H., Open Enzyme Database: a community-wide repository for sharing enzyme data. Nucleic Acids Research, 2026, 54, D643\u2013D651. Abstract<\/a><\/td><\/tr>
Open Targets<\/a><\/td>Buniello A., Suveges D., Cruz-Castillo C., Bernal Llinares M., Cornu H., Lopez I., Tsukanov K., Rold\u00e1n-Romero J. M., Mehta C., Fumis L., McNeill G., Hayhurst J. D., Martinez Osorio R. E., Barkhordari E., Ferrer J., Carmona M., Uniyal P., Falaguera M. J., Rusina P., Smit I., Schwartzentruber J., Alegbe T., Ho V. W., Considine D., Ge X., Szyszkowski S., Tsepilov Y., Ghoussaini M., Dunham I., Hulcoop D. G., McDonagh E. M., Ochoa D., Open Targets Platform: facilitating therapeutic hypotheses building in drug discovery. Nucleic Acids Research, 2025, 53, D1467\u2013D1475. Abstract<\/a><\/td><\/tr>
OxDBase<\/a><\/td>Arora 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<\/a><\/td><\/tr>
PlantCAZyme<\/a><\/td>Ekstrom A., Taujale R., McGinn N., Yin Y., PlantCAZyme: a database for plant carbohydrate-active enzymes, Database, 2014, Article no bau079. Abstract<\/a><\/td><\/tr>
Plant Metabolic Network<\/a><\/td>Hawkins C., Xue B., Yasmin F., Wyatt G., Zerbe P., Rhee S. Y., Plant Metabolic Network 16: expansion of underrepresented plant groups and experimentally supported enzyme data. Nucleic Acids Research, 2025, 53, D1606\u2013D1613. Abstract<\/a><\/td><\/tr>
PlasticDB<\/a><\/td>Gambarini 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<\/a><\/td><\/tr>
PLB<\/a>D<\/a><\/td>Linge\u0307 D., Gedgaudas M., Merkys A., Petrauskas V., Vaitkus A., Grybauskas A., Paketuryte\u0307 V., Zubriene\u0307 A., Zak\u0161auskas A., Mickevici\u030cu\u0304te\u0307 A., Smirnoviene\u0307 J., Baranauskiene\u0307 L., C\u030capkauskaite\u0307 E., Dudutiene\u0307 V., Urniezi\u030cus E., Konovalovas A., Kazlauskas E., Shubin K., Schio\u0308th H. P., Chen W.-Y., Ladbury J. E., Grazu\u030clis S., Matulis D., PLBD: protein\u2013ligand binding database of thermodynamic and kinetic intrinsic parameters. Database, 2023, Article No baad040. Abstract<\/a><\/td><\/tr>
RetroBioCat<\/a><\/td>Finnigan 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\u2013104. Abstract<\/a><\/td><\/tr>
Rhea<\/a><\/td>Bansal 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\u2013D700. Abstract<\/a><\/td><\/tr>
Ribocentre<\/a><\/td>Deng 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\u2013D268. Abstract<\/a><\/td><\/tr>
SABIO-RK<\/a><\/td>Duda\u0161 D., Wittig U., Rey M., Weidemann A., M\u00fcller W., Improved insights into the SABIO-RK database via visualization. Database, 2023, Article No baad011. Abstract<\/a><\/td><\/tr>
SFLD<\/a><\/td>Holliday 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<\/a><\/td><\/tr>
STRENDA<\/a><\/td>Provider: Beilstein Institute<\/td><\/tr>
SulfAtlas<\/a><\/td>Stam M., Leli\u00e8vre 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\u2013D653. Abstract<\/a><\/td><\/tr>
TECR<\/a><\/td>Goldberg R. N., Tewari Y. B., Bhat T. N., Thermodynamics of Enzyme-Catalyzed Reactions – a database for quantitative biochemistry. Bioinformatics, 2004, 20, 2874-2877. Abstract<\/a><\/td><\/tr>
Transformer<\/a><\/td>Hoffmann 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\u2013D1117. Abstract<\/a><\/td><\/tr>
XMetDB<\/a><\/td>Spjuth 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<\/a><\/td><\/tr><\/tbody><\/table><\/figure>\n","protected":false},"excerpt":{"rendered":"

Biochemical reactions BiGG King Z. A., Lu J., Dr\u00e4ger 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\u2013D522. Abstract BRENDA Hauenstein J., Jeske L., J\u00e4de A., Krull M., D\u00fcmmer K., Koblitz J.,…<\/p>\n","protected":false},"author":3,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_lmt_disableupdate":"no","_lmt_disable":"no","_kad_post_transparent":"","_kad_post_title":"default","_kad_post_layout":"left","_kad_post_sidebar_id":"sidebar-primary","_kad_post_content_style":"boxed","_kad_post_vertical_padding":"","_kad_post_feature":"","_kad_post_feature_position":"","_kad_post_header":false,"_kad_post_footer":false,"footnotes":""},"class_list":["post-95","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/biochemia.uwm.edu.pl\/metachemibio\/wp-json\/wp\/v2\/pages\/95","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/biochemia.uwm.edu.pl\/metachemibio\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/biochemia.uwm.edu.pl\/metachemibio\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/biochemia.uwm.edu.pl\/metachemibio\/wp-json\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/biochemia.uwm.edu.pl\/metachemibio\/wp-json\/wp\/v2\/comments?post=95"}],"version-history":[{"count":41,"href":"https:\/\/biochemia.uwm.edu.pl\/metachemibio\/wp-json\/wp\/v2\/pages\/95\/revisions"}],"predecessor-version":[{"id":522267,"href":"https:\/\/biochemia.uwm.edu.pl\/metachemibio\/wp-json\/wp\/v2\/pages\/95\/revisions\/522267"}],"wp:attachment":[{"href":"https:\/\/biochemia.uwm.edu.pl\/metachemibio\/wp-json\/wp\/v2\/media?parent=95"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}