{"id":159,"date":"2021-12-19T00:03:48","date_gmt":"2021-12-18T23:03:48","guid":{"rendered":"http:\/\/metachemibio.webgazel.pl\/?page_id=159"},"modified":"2026-03-18T14:44:00","modified_gmt":"2026-03-18T13:44:00","slug":"protein-ligands","status":"publish","type":"page","link":"https:\/\/biochemia.uwm.edu.pl\/metachemibio\/protein-ligands\/","title":{"rendered":"Protein ligands"},"content":{"rendered":"\n

Protein ligands<\/h4>\n\n\n\n
2P2Idb<\/a><\/td>Basse M.-J., Betzi S., Morelli X., Roche P., 2P2Idb v2: update of a structural database dedicated to orthosteric modulation of protein\u2013protein interactions. Database, 2016, Article No baw007. Abstract<\/a><\/td><\/tr>
AffinDB<\/a><\/td>Block P., Sotriffer C. A., Dramburg I., Klebe G., AffinDB: a freely accessible database of affinities for protein\u2013ligand complexes from the PDB. Nucleic Acids Research, 2006, 34, D522-D526. Abstract<\/a><\/td><\/tr>
ASD<\/a><\/td>Huang Z., Zhu L., Cao Y., Wu G., Liu X., Chen Y., Wang Q., Shi T., Zhao Y., Wang Y., Li W., Li Y., Chen H., Chen G., Zhang J., ASD: a comprehensive database of allosteric proteins and modulators. Nucleic Acids Research, 2011, 39, D663\u2013D669. Abstract<\/a><\/td><\/tr>
BATMAN-TCM<\/a><\/td>Kong X., Liu C., Zhang Z., Cheng M., Mei Z., Li X., Liu P., Diao L., Ma Y., Jiang P., Kong X., Nie S., Guo Y., Wang Z., Zhang X., Wang Y., Tang L., Guo S., Liu Z., Li D., BATMAN-TCM 2.0: an enhanced integrative database for known and predicted interactions between traditional Chinese medicine ingredients and target proteins. Nucleic Acids Research, 2024, 52, D1110\u2013D1120. Abstract<\/a><\/td><\/tr>
Binding DB<\/a><\/td>Liu T., Hwang L., Burley S., Nitsche C. I., Southan C., Walters W. P., Gilson M. K., BindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding data. Nucleic Acids Research, 2025, 53, D1633\u2013D1644. Abstract<\/a><\/td><\/tr>
BioLiP<\/a><\/td>Zhang C., Zhang X., Freddolino P. L., Zhang Y., BioLiP2: an updated structure database for biologically relevant ligand\u2013protein interactions. Nucleic Acids Research, 2024, 52, D404\u2013D412. Abstract<\/a><\/td><\/tr>
cBinderDB<\/a><\/td>Du J., Yan X., Liu Z., Cui L., Ding P., Tan X., Li X., Zhou H., Gu Q., Xu J., cBinderDB: a covalent binding agent database. Bioinformatics, 2017, 33, 1258-1260. Abstract<\/a><\/td><\/tr>
ChemBioPort<\/a><\/td>Liu L., Rovers E., Schapira M., ChemBioPort: an online portal to navigate the structure, function and chemical inhibition of the human proteome. Database, 2022, Article No baac088. Abstract<\/a><\/td><\/tr>
Chemical Probes Portal<\/a><\/td>Sanfelice D., Antolin A. A., Crisp A., Chen Y., Bellenie B., Brennan P. E., Edwards A., M\u00fcller S., Al-Lazikani B., Workman P., The Chemical Probes Portal \u2013 2024: update on this public resource to support best-practice selection and use of small molecules in biomedical research. Nucleic Acids Research, 2025, 53, D1663\u2013D1669. Abstract<\/a><\/td><\/tr>
Chem(Pro)2<\/a><\/td>Fu S., Chen Z., Luo Z., Nie M., Fu T., Zhou Y., Yang Q., Zhu F., Ni F., Chem(Pro)2: the atlas of chemoproteomic probes labelling human proteins. Nucleic Acids Research, 2025, 53, D1651\u2013D1662. Abstract<\/a><\/td><\/tr>
ChemProt<\/a><\/td>Kringelum J., Kjaerulff S. K., Brunak S., Lund O., Oprea T. I., Taboureau T., ChemProt-3.0: a global chemical biology diseases mapping. Database, 2016, Article No bav123. Abstract<\/a><\/td><\/tr>
CLiBE<\/a><\/td>Chen X., Ji Z. L., Zhi D. G., Chen Y. Z., CLiBE: A database of computed ligand binding energy for ligand-receptor complexes and its potential use in the analysis of drug binding competitiveness. Computers & Chemistry, 2002, 26, 661-666. Abstract<\/a><\/td><\/tr>
ConsensusPathDB<\/a><\/td>Kamburov A., Stelzl U., Lehrach H., Herwig R., The ConsensusPathDB interaction database: 2013 update. Nucleic Acids Research, 2013, 41, D793-D800. Abstract<\/a><\/td><\/tr>
CovalentInDB<\/a><\/td>Du H., Zhang X., Wu Z., Zhang O., Gu S., Wang M., Zhu F., Li D., Hou T., Pan P., CovalentInDB 2.0: an updated comprehensive database for structure-based and ligand-based covalent inhibitor design and screening. Nucleic Acids Research, 2025, 53, D1322\u2013D1327. Abstract<\/a><\/td><\/tr>
CovPDB<\/a><\/td>Gao M., Moumbock A. F. A., Qaseem A., Xu Q., G\u00fcnther S., CovPDB: a high-resolution coverage of the covalent protein\u2013ligand interactome. Nucleic Acids Research, 2022, 50, D445\u2013D450. Abstract<\/a><\/td><\/tr>
CREDO<\/a><\/td>Schreyer A., Blundell T., CREDO: A protein\u2013ligand interaction database for drug discovery. Chemical Biology & Drug Design, 2009, 73, 157-167 Abstract<\/a><\/td><\/tr>
Cysteinome<\/a><\/td>Wu S., Luo (Howard) H., Wang H., Zhao W., Hu Q., Yang Y., Cysteinome: The first comprehensive database for proteins with targetable cysteine and their covalent inhibitors. Biochemical and Biophysical Research Communications, 2016, 478, 1268-1273. Abstract<\/a><\/td><\/tr>
DIONYSUS<\/a><\/td>Gheeraert A., Bailly T., Ren Y., Hamraoui A., Te J., Vander Meersche Y., Cretin G., Lin R. L. F., Gelly J.-C., P\u00e9rez S., Guyon F., Galochkina T., 2025, DIONYSUS: a database of protein\u2013carbohydrate interfaces. Nucleic Acids Research, 2025, 53, D387\u2013D395. Abstract<\/a><\/td><\/tr>
DiPPI<\/a><\/td>Cankara F., Senyuz S., Sayin A. Z., Gursoy A., Keskin O., DiPPI: A curated data set for drug-like molecules in protein\u2013protein interfaces. Journal of Chemical Information and Modeling, 2024, 64, 5041-5051. Abstract<\/a><\/td><\/tr>
DockNMine<\/a><\/td>Gheyouche E., Launay R., Lethiec J., Labeeuw A., Roze C., Amoss\u00e9 A., T\u00e9letch\u00e9a S., DockNmine, a web portal to assemble and analyse virtual and experimental interaction data. International Journal of Molecular Sciences, 2019, 20, Article No 5062. Abstract<\/a><\/td><\/tr>
Drug2Gene<\/a><\/td>Roider H. G., Pavlova N., Kirov I., Slavov S., Slavov T., Uzunov Z., Weiss B., Drug2Gene: an exhaustive resource to explore effectively the drug-target relation network. BMC Bioinformatics, 2014, 15, Article No 68. Abstract<\/a><\/td><\/tr>
DrugPort<\/a><\/td>Provider: European Bioinformatics Institute<\/td><\/tr>
Drug Target Commons<\/a><\/td>Tanoli Z. R., Alam Z., V\u00e4h\u00e4-Koskela M., Ravikumar B., Malyutina A., Jaiswal A., Tang J., Wennerberg K., Aittokallio T., Drug Target Commons 2.0: a community platform for systematic analysis of drug\u2013target interaction profiles. Database, 2018, Article No bay083. Abstract<\/a><\/td><\/tr>
DrumPID<\/a><\/td>Kunz M., Liang C., Nilla S., Cecil A., Dandekar T.,The drug-minded protein interaction database (DrumPID) for efficient target analysis and drug development. Database, 2016, Article No baw041. Abstract<\/a><\/td><\/tr>
EGFRIndb<\/a><\/td>Yadav I. S., Singh H., Khan I., Chaudhury A., Raghava G. P. S., Agarwal S. M., EGFRIndb: Epidermal Growth Factor Receptor Inhibitor Database. Anti-Cancer Agents in Medicinal Chemistry, 2014, 14, 928-935. Abstract<\/a><\/td><\/tr>
EpiDBase<\/a><\/td>Loharch S., Bhutani I., Jain K., Gupta P., Sahoo D. K., Parkesh R., EpiDBase: a manually curated database for small molecule modulators of epigenetic landscape. Database, 2015, Article No bav013. Abstract<\/a><\/td><\/tr>
ExCAPE-DB<\/a><\/td>Sun J., Jeliazkova N., Chupakin V., Golib-Dzib J.-F., Engkvist O., Carlsson L., Wegner J., Ceulemans H., Georgiev I., Jeliazkov V., Kochev N., Ashby T. J., Chen H., ExCAPE-DB: an integrated large scale dataset facilitating Big Data analysis in chemogenomics. Journal of Cheminformatics, 2017, 9, Article No 17. Abstract<\/a><\/td><\/tr>
FGDB<\/a><\/td>Toti D., Macari G., Barbierato E., Polticelli F., FGDB: a comprehensive graph database of ligand fragments from the Protein Data Bank. Database, 2022, Article No baac044. Abstract<\/a><\/td><\/tr>
FireDB<\/a><\/td>Maietta P., Lopez G., Carro A., Pingilley B. J., Leon L. G., Valencia A., Tress M. L., FireDB: a compendium of biological and pharmacologically relevant ligands. Nucleic Acids Research, 2014, 42, D267\u2013D272. Abstract<\/a><\/td><\/tr>
GLIDA<\/a><\/td>Okuno Y., Tamon A., Yabuuchi H., Niijima S., Minowa Y., Tonomura K., Kunimoto R., Feng C., GLIDA: GPCR\u2014ligand database for chemical genomics drug discovery\u2014database and tools update. Nucleic Acids Research, 2008, 36, D907-D912. Abstract<\/a><\/td><\/tr>
GPCRdb<\/a><\/td>Taracena Herrera L. P., Andreassen S. N., Caroli J., Rodr\u00edguez-Espigares I., Kermani A. A., Keser\u0171 G., Kooistra A. J., P\u00e1ndy-Szekeres G., Gloriam D. E., GPCRdb in 2025: adding odorant receptors, data mapper, structure similarity search and models of physiological ligand complexes. Nucleic Acids Research, 2025, 53, D425\u2013D435. Abstract<\/a><\/td><\/tr>
HDACiDB<\/a><\/td>Murugan K., Sangeetha S., Ranjitha S., Vimala A., Al-Sohaibani S., Rameshkumar G., HDACiDB: a database for histone deacetylase inhibitors. Drug Design, Development and Therapy, 2015, 9, 2257\u20132264. Abstract<\/a><\/td><\/tr>
Hic-Up<\/a><\/td>Kleywegt G. J., Henrick K., Dodson E. J., van Aalten D. M. F., Pound-wise but penny-foolish – How well do micromolecules fare in macromolecular refinement? Structure, 2003, 11, 1051-1059. Request<\/a><\/td><\/tr>
HIT<\/a><\/td>Yan D., Zheng G., Wang C., Chen Z., Mao T., Gao J., Yan Y., Chen X., Ji X., Yu J., Mo S., Wen H., Han W., Zhou M., Wang Y., Wang J., Tang K., Cao Z., HIT 2.0: an enhanced platform for Herbal Ingredients\u2019 Targets. Nucleic Acids Research, 2022, 50, D1238\u2013D1243. Abstract<\/a><\/td><\/tr>
HProteome-BSite<\/a><\/td>Sim J., Kwon S., Seok C., HProteome-BSite: predicted binding sites and ligands in human 3D proteome. Nucleic Acids Research, 2023, 51, D403\u2013D408. Abstract<\/a><\/td><\/tr>
HSPMdb<\/a><\/td>Singh P., Unik B., Puri A., Nagpal G., Singh B., Gautam A., Sharma D., HSPMdb: a computational repository of heat shock protein modulators. Database, 2020, Article No baaa003. Abstract<\/a><\/td><\/tr>
IMID<\/a><\/td>Balaji S., Mcclendon C., Chowdhary R., Liu J. S., Zhang J., IMID: integrated molecular interaction database. Bioinformatics, 2012, 28, 747-749. Abstract<\/a><\/td><\/tr>
IPAD-DB<\/a><\/td>Peng C., Liu X., Meng X., Chen C., Wu X., Bai L., Lu F., Liu F., IPAD-DB: a manually curated database for experimentally verified inhibitors of proteins associated with Alzheimer\u2019s disease. Database, 2024, Article No baae048. Abstract<\/a><\/td><\/tr>
iPPI-DB<\/a><\/td>Labb\u00e9 C. M., Kuenemann M., Zarzycka B., Vriend G., Nicolaes G. A. F., Lagorce D., Miteva M. A., Villoutreix B. O., Sperandio O., iPPI-DB: an online database of modulators of protein\u2013protein interactions. Nucleic Acids Research, 2016, 44, D542\u2013D547. Abstract<\/a><\/td><\/tr>
ISTransbase<\/a><\/td>Peng J., Yi J., Yang G., Huang Z., Cao D., ISTransbase: an online database for inhibitor and substrate of drug transporters. Database, 2024, Article No baae053. Abstract<\/a><\/td><\/tr>
Ki Database<\/a><\/td>Roth B. L., Lopez E., Patel S., Kroeze W. L., The multiplicity of serotonin receptors: uselessly diverse molecules or an embarrassment of riches? Neuroscientist, 2000, 6, 252-262. Abstract<\/a><\/td><\/tr>
KOFFI<\/a><\/td>Norval L. W., Kr\u00e4mer S. D., Gao M., Herz T., Li J., Rath C., W\u00f6hrle J., G\u00fcnther S., Roth G., KOFFI and Anabel 2.0-a new binding kinetics database and its integration in an open-source binding analysis software. Database, 2019, Article No baz101. Abstract<\/a><\/td><\/tr>
LabWorm Receptor Ligands<\/a><\/td>Authors: Yoav Bauman<\/a>, Roy Granit<\/a>, Alon Vitenshtein<\/a><\/td><\/tr>
LIGAND<\/a><\/td>Goto S., Okuno Y., Hattori M., Nishioka T., Kanehisa M., LIGAND: Database of chemical compounds and reactions in biological pathways. Nucleic Acids Research, 2002, 30, 402-404. Abstract<\/a><\/td><\/tr>
Ligand Expo<\/a><\/td>Feng Z., Chen L., Maddula H., Akcan O., Oughtred R., Berman H. M., Westbrook J., Ligand Depot: a data warehouse for ligands bound to macromolecules. Bioinformatics, 2004, 20, 2153\u20132155. Abstract<\/a><\/td><\/tr>
LSD<\/a><\/td>Hall B. W., Tummino T. A., Tang K., Mailhot O., Castanon M., Irwin J. J., Shoichet B. K., A Database for large-scale docking and experimental results. Journal of Chemical Information and Modeling, 2025, 65, 4458\u20134467. Abstract<\/a><\/td><\/tr>
MATADOR<\/a><\/td>G\u00fcnther S., Kuhn M., Dunkel M., Campillos M., Senger C., Petsalaki E., Ahmed J., Garcia Urdiales E., Gewiess A, Juhl Jensen L., Schneider R., Skoblo R., Russell R. B., Bourne P. E., Bork P., Preissner R., SuperTarget and Matador: resources for exploring drug-target relationships. Nucleic Acids Research, 2008, 36, D919\u2013D922. Abstract<\/a><\/td><\/tr>
Metrabase<\/a><\/td>Mak L., Marcus D., Howlett1 A., Yarova G., Duchateau G., Klaffke W., Bender A., Glen R. C., Metrabase: a cheminformatics and bioinformatics database for small molecule transporter data analysis and (Q)SAR modeling. Journal of Cheminformatics, 2015, 7, Article No 31. Abstract<\/a><\/td><\/tr>
MGDB<\/a><\/td>Li C., Luo H., Pang Y., Liu Y., Luo Y., Liang X., Li H., Li W., Wang L., MGDB: a curated database for molecular glues. Nucleic Acids Research, 2026, 54, D1488\u2013D1499. Abstract<\/a><\/td><\/tr>
MGTbind<\/a><\/td>Zhu J., Liao Y., Lin H., Xie J., Deng Z., Han J., Zhang Z., Xiao J., Wang Z., Zhang S., Lai L., Pei J., MGTbind: a comprehensive database of molecular glue ternary interactome. Nucleic Acids Research, 2026, 54, D1500\u2013D1509. Abstract<\/a><\/td><\/tr>
MolBiC<\/a><\/td>Ge Y., Yang M., Yu X., Zhou Y., Zhang Y., Mou M., Chen Z., Sun X., Ni F., Fu T., Liu S., Han L., Zhu F., MolBiC: the cell-based landscape illustrating molecular bioactivities. Nucleic Acids Research, 2025, 53, D1683\u2013D1691. Abstract<\/a><\/td><\/tr>
Molecular Libraries Program<\/a><\/a><\/td>Publications<\/a><\/td><\/tr>
MolGlueDB<\/a><\/td>Wang X., Zhuang Z., Zhang C., Zhang B., Zhan W., Wang Y., Liu Z., Yuan S., Niu W., He Q., Tian Y., Xu X., Fang S., Qin C., MolGlueDB: an online database of molecular glues. Nucleic Acids Research, 2026, 54, D1510\u2013D1518. Abstract<\/a><\/td><\/tr>
MTLD<\/a><\/td>Chen C., Wu M., Cen S., Wu J., Zhou J., MTLD, a Database of Multiple Target Ligands, the updated version. Molecules, 2017, 22, Article No 1375. Abstract<\/a><\/td><\/tr>
NRLiSt BDB<\/a><\/td>Lagarde N., Ben Nasr N., J\u00e9r\u00e9mie A., Guillemain H., Laville V., Labib T., Zagury J.-F., Montes M., NRLiSt BDB, the manually curated nuclear receptors ligands and structures benchmarking database. Journal of Medicinal Chemistry, 2014, 57, 3117\u20133125. Abstract<\/a><\/td><\/tr>
PathGuide<\/a><\/td>Bader G. D., Cary M. P., Sander C., Pathguide: a pathway resource list. Nucleic Acids Research, 2006, 34, D504-D506. Abstract<\/a><\/td><\/tr>
PDBeChem<\/a><\/td>Provider: European Bioinformatics Institute<\/td><\/tr>
PGxDB<\/a><\/td>Nguyen T. T. D., Tanoli Z., Hassan S., \u00d6zcan U. O., Caroli J., Kooistra A. J., Gloriam D. E., Hauser A. S., PGxDB: an interactive web-platform for pharmacogenomics research. Nucleic Acids Research, 2025, 53, D1486\u2013D1497. Abstract<\/a><\/td><\/tr>
PHAROS<\/a><\/td>Nguyen D.-T., Mathias S., Bologa C., Brunak S., Fernandez N., Gaulton A., Hersey A., Holmes J., Jensen L. J., Karlsson A., Liu G., Ma’ayan A., Mandava G., Mani S., Mehta S., Overington J., Patel J., Rouillard A. D., Sch\u00fcrer S., Sheils T., Simeonov A., Sklar L. A., Southall N., Ursu O., Vidovic D., Waller A., Yang J., Jadhav A., Oprea T. I., Guha R., Pharos: Collating protein information to shed light on the druggable genome. Nucleic Acids Research, 2017, 45, D995-D1002. Abstract<\/a><\/td><\/tr>
PLBD<\/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>
PLIC<\/a><\/td>Anand P., Nagarajan D., Mukherjee S., Chandra N., PLIC: protein\u2013ligand interaction clusters. Database, 2014, Article No bau029. Abstract<\/a><\/td><\/tr>
PMADS<\/a><\/td>Zheng J., Chen S., Zhang Y., Zhang B., Qiao K., Xu J., Fan Y., Feng M., Feng Z., Wang Z., Wang H., PMADS: an integrated database of cur at ed and proteomics-inferred associations between protein post-translational modifications and drug sensitivity. Nucleic Acids Research, 2026, 54, D1569\u2013D1578. Abstract<\/a><\/td><\/tr>
PMI-DB<\/a><\/td>Zhao T., Liu J., Zeng X., Wang W., Li S., Zang T., Peng J., Yang Y., Prediction and collection of protein\u2013metabolite interactions. Briefings in Bioinformatics, 2021, 22, Article No bbab014. Abstract<\/a><\/td><\/tr>
PoSSuMds<\/a><\/td>Ito J., Ikeda K., Yamada K., Mizuguchi K., Tomii K., PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs. Nucleic Acids Research, 2015, 43, D392-D398. Abstract<\/a><\/td><\/tr>
PPDMs<\/a><\/td>Kruger F. A., Gaulton A., Nowotka M., Overington J. P., PPDMs\u2014a resource for mapping small molecule bioactivities from ChEMBL to Pfam-A protein domains. Bioinformatics, 2015, 31, 776-778. Abstract<\/a><\/td><\/tr>
PrePCI<\/a><\/td>Trudeau S. J., Hwang H., Mathur D., Begum K., Petrey D., Murray D., Honig B., PrePCI: A structure- and chemical similarity-informed database of predicted protein compound interactions. Protein Science, 2023, 32, Article No e4594. Abstract<\/a><\/td><\/tr>
ProBiS-Dock Database<\/a><\/td>Konc J., Le\u0161nik S., \u0160krlj B., Jane\u017ei\u010d D., 2021, ProBiS-Dock Database: A web server and interactive web repository of small ligand\u2013protein binding sites for drug design. Journal of Chemical Information and Modeling, 2021, 61, 4097\u20134107. Abstract<\/a><\/td><\/tr>
ProtChemSI<\/a><\/td>Kalinina O. V., Wichmann O., Apic G., Russell R. B., ProtChemSI: a network of protein\u2013chemical structural interactions. Nucleic Acids Research, 2012, 40, D549\u2013D553. Abstract<\/a><\/td><\/tr>
PTS<\/a><\/td>Ding P., Yan X., Liu z., Du J., Du Y., Lu Y., Wu D., Xu Y., Zhou H., Gu Q., Xu J., PTS: a pharmaceutical target seeker. Database, 2017, Article No bax095. Abstract<\/a><\/td><\/tr>
S2RSLDB<\/a><\/td>Nastasi G., Miceli C., Pittal\u00e0 V., Modica M. N., Prezzavento O., Romeo G., Rescifina A., Marrazzo A., Amata E., S2RSLDB: a comprehensive manually curated, internet-accessible database of the sigma-2 receptor selective ligands. Journal of Cheminformatics, 2017, 9, Article No 3. Abstract<\/a><\/td><\/tr>
sc-PDB-Frag<\/a><\/td>Desaphy J., Rognan D., sc-PDB-Frag: a database of protein\u2013ligand interaction patterns for bioisosteric replacements. Journal of Chemical Information and Modeling, 2014, 54, 1908\u20131918. Abstract<\/a><\/td><\/tr>
SMMDB<\/a><\/td>Mishra S. K., Jain N., Shankar U., Tawani A., Mishra A., Kumar A., SMMDB: a web-accessible database for small molecule modulators and their targets involved in neurological diseases. Database, 2018, Article No bay082. Abstract<\/a><\/td><\/tr>
STITCH<\/a><\/td>Szklarczyk D., Santos A., von Mering C., Jensen L. J., Bork P., Kuhn M., STITCH 5: augmenting protein\u2013chemical interaction networks with tissue and affinity data. Nucleic Acids Research, 2016, 44, D380\u2013D384. Abstract<\/a><\/td><\/tr>
SuperLigands<\/a><\/td>Michalsky E., Dunkel M., Goede A., Preissner R., SuperLigands \u2013 a database of ligand structures derived from the Protein Data Bank. BMC Bioinformatics, 2005, 6, Article No 122. Abstract<\/a><\/td><\/tr>
SuperTarget<\/a><\/td>Hecker N., Ahmed J., von Eichborn J., Dunkel M., Macha K., Eckert A., Gilson M. K., Bourne P. E., Preissner R., SuperTarget goes quantitative: update on drug\u2013target interactions.  Nucleic Acids Research, 2012, 40, D1113-D1117. Abstract<\/a><\/td><\/tr>
SwissBioisostere<\/a><\/td>Cuozzo A., Daina A., Perez M. A. S., Michielin O., Zoete V., SwissBioisostere 2021: updated structural, bioactivity and physicochemical data delivered by a reshaped web interface. Nucleic Acids Research, 2022, 50, D1382\u2013D1390. Abstract<\/a><\/td><\/tr>
SynPharm<\/a><\/td>Ireland S. M., Southan C., Dominguez-Monedero A., Harding S. D., Sharman J. L., Davies J. A., SynPharm: A Guide to PHARMACOLOGY database tool for designing drug control into engineered proteins. ACS Omega, 2018, 3, 7993-8002. Abstract<\/a><\/td><\/tr>
T-ARDIS<\/a><\/td>Galletti C., Bota P. M., Oliva B., Fernandez-Fuentes N., Mining drug\u2013target and drug\u2013adverse drug reaction databases to identify target\u2013adverse drug reaction relationships. Database, 2021, Article No baab068. Abstract<\/a><\/td><\/tr>
TIBLE<\/a><\/td>Malhotra S., Mugumbate G., Blundell T. L., Higueruelo A. P., TIBLE: a web-based, freely accessible resource for small-molecule binding data for mycobacterial species. Database, 2017, Article No bax041. Abstract<\/a><\/td><\/tr>
TIMBAL<\/a><\/td>Higueruelo A. P., Jubb H., Blundell T. L., TIMBAL v2: update of a database holding small molecules modulating protein\u2013protein interactions. Database, 2013, Article No bat039. Abstract<\/a><\/td><\/tr>
TPDdb<\/a><\/td>Qin X., Zhang Y., Wang Y., Zhang Y., Jing J., Zhang Y., Xu G., Teng H., Wang T., Fu L., Zhou Y., Liu X., Zhu F., TPDdb: the comprehensive database of targeted protein degrader. Nucleic Acids Research, 2026, 54, D1683\u2013D1691. Abstract<\/a><\/td><\/tr>
tracerDB<\/a><\/td>Dopfer J., Vasta J. D., M\u00fcller S., Knapp S., Robers M. B., Schwalm M. P., tracerDB: a crowdsourced fluorescent tracer database for target engagement analysis. Nature Communications, 2024, 15, 5646. Abstract<\/a><\/td><\/tr>
ValidatorDB<\/a><\/td>Sehnal D., Svobodov\u00e1 V\u0103rekov\u00e1 R., Pravda L., Ionescu C.-M., Geidl S., Horsk\u00fd V., Jaiswal D., Wimmerov\u00e1 M., K\u014fca J., ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank. Nucleic Acids Research, 2015, 43, D369-D375. Abstract<\/a><\/td><\/tr>
Yeastpmi<\/a><\/td>Luzarowski M., Vicente R., Kiselev A., Wagner M., Schlossarek D., Erban A., Perez de Souza L., Childs D., Wojciechowska I., Luzarowska U., G\u00f3rka M., Soko\u0142owska E. M., Kosmacz M., Moreno J. C., Brzezi\u0144ska A., Vegesna B., Kopka J., Fernie A. R., Willmitzer L., Ewald J. C., Skirycz A., Global mapping of protein\u2013metabolite interactions in Saccharomyces cerevisiae reveals that Ser-Leu dipeptide regulates phosphoglycerate kinase activity. Communications Biology, 2021, 4, 181. Abstract<\/a><\/td><\/tr><\/tbody><\/table><\/figure>\n","protected":false},"excerpt":{"rendered":"

Protein ligands 2P2Idb Basse M.-J., Betzi S., Morelli X., Roche P., 2P2Idb v2: update of a structural database dedicated to orthosteric modulation of protein\u2013protein interactions. Database, 2016, Article No baw007. Abstract AffinDB Block P., Sotriffer C. A., Dramburg I., Klebe G., AffinDB: a freely accessible database of affinities for protein\u2013ligand complexes from the PDB. Nucleic Acids…<\/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":"","_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-159","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/biochemia.uwm.edu.pl\/metachemibio\/wp-json\/wp\/v2\/pages\/159","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=159"}],"version-history":[{"count":41,"href":"https:\/\/biochemia.uwm.edu.pl\/metachemibio\/wp-json\/wp\/v2\/pages\/159\/revisions"}],"predecessor-version":[{"id":522265,"href":"https:\/\/biochemia.uwm.edu.pl\/metachemibio\/wp-json\/wp\/v2\/pages\/159\/revisions\/522265"}],"wp:attachment":[{"href":"https:\/\/biochemia.uwm.edu.pl\/metachemibio\/wp-json\/wp\/v2\/media?parent=159"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}