TY - JOUR AU - Pándy-Szekeres, Gáspár AU - Taracena Herrera, Luis P AU - Caroli, Jimmy AU - Kermani, Ali A AU - Kulkarni, Yashraj AU - Keserű, György Miklós AU - Gloriam, David E TI - GproteinDb in 2024: new G protein-GPCR couplings, AlphaFold2-multimer models and interface interactions JF - NUCLEIC ACIDS RESEARCH J2 - NUCLEIC ACIDS RES VL - 52 PY - 2024 IS - D1 SP - D466 EP - D475 SN - 0305-1048 DO - 10.1093/nar/gkad1089 UR - https://m2.mtmt.hu/api/publication/34405999 ID - 34405999 AB - G proteins are the major signal proteins of ∼800 receptors for medicines, hormones, neurotransmitters, tastants and odorants. GproteinDb offers integrated genomic, structural, and pharmacological data and tools for analysis, visualization and experiment design. Here, we present the first major update of GproteinDb greatly expanding its coupling data and structural templates, adding AlphaFold2 structure models of GPCR–G protein complexes and advancing the interactive analysis tools for their interfaces underlying coupling selectivity. We present insights on coupling agreement across datasets and parameters, including constitutive activity, agonist-induced activity and kinetics. GproteinDb is accessible at https://gproteindb.org. LA - English DB - MTMT ER - TY - JOUR AU - Bajusz, Dávid AU - Pándy-Szekeres, Gáspár AU - Takács, Ágnes AU - de Araujo, Elvin D AU - Keserű, György Miklós TI - SH2db, an information system for the SH2 domain JF - NUCLEIC ACIDS RESEARCH J2 - NUCLEIC ACIDS RES VL - 51 PY - 2023 IS - W1 SP - W542 EP - W552 SN - 0305-1048 DO - 10.1093/nar/gkad420 UR - https://m2.mtmt.hu/api/publication/33845452 ID - 33845452 N1 - Funding Agency and Grant Number: MSCA ITN ALLODD [956314]; National Research Development and Innovation Office of Hungary [K135150, RRF-2.3.1-21-2022-00015]; Janos Bolyai Research Scholarship of the Hungarian Academy of Sciences; New National Excellence Program of the Ministry for Innovation and Technology [UNKP-22-5]; MSCA [956314, K135150] Funding text: MSCA ITN ALLODD [956314 to G.M.K.]; National Research Development and Innovation Office of Hungary [K135150, PharmaLab (RRF-2.3.1-21-2022-00015)]; the work of D.B. was supported by the Janos Bolyai Research Scholarship of the Hungarian Academy of Sciences and the 'UNKP-22-5 New National Excellence Program of the Ministry for Innovation and Technology. FUNDING for open access charge: MSCA-funded project 'ALLODD' [956314] and NRDIO grant [K135150]. AB - SH2 domains are key mediators of phosphotyrosine-based signalling, and therapeutic targets for diverse, mostly oncological, disease indications. They have a highly conserved structure with a central beta sheet that divides the binding surface of the protein into two main pockets, responsible for phosphotyrosine binding (pY pocket) and substrate specificity (pY + 3 pocket). In recent years, structural databases have proven to be invaluable resources for the drug discovery community, as they contain highly relevant and up-to-date information on important protein classes. Here, we present SH2db, a comprehensive structural database and webserver for SH2 domain structures. To organize these protein structures efficiently, we introduce (i) a generic residue numbering scheme to enhance the comparability of different SH2 domains, (ii) a structure-based multiple sequence alignment of all 120 human wild-type SH2 domain sequences and their PDB and AlphaFold structures. The aligned sequences and structures can be searched, browsed and downloaded from the online interface of SH2db (http://sh2db.ttk.hu), with functions to conveniently prepare multiple structures into a Pymol session, and to export simple charts on the contents of the database. Our hope is that SH2db can assist researchers in their day-to-day work by becoming a one-stop shop for SH2 domain related research. LA - English DB - MTMT ER - TY - JOUR AU - Pándy-Szekeres, Gáspár AU - Caroli, Jimmy AU - Mamyrbekov, Alibek AU - Kermani, Ali A. AU - Keserű, György Miklós AU - Kooistra, Albert J. AU - Gloriam, David E. TI - GPCRdb in 2023: state-specific structure models using AlphaFold2 and new ligand resources JF - NUCLEIC ACIDS RESEARCH J2 - NUCLEIC ACIDS RES VL - 51 PY - 2023 IS - D1 SP - D395 EP - D402 PG - 8 SN - 0305-1048 DO - 10.1093/nar/gkac1013 UR - https://m2.mtmt.hu/api/publication/33421768 ID - 33421768 AB - G protein-coupled receptors (GPCRs) are physiologically abundant signaling hubs routing hundreds of extracellular signal substances and drugs into intracellular pathways. The GPCR database, GPCRdb supports > 5000 interdisciplinary researchers every month with reference data, analysis, visualization, experiment design and dissemination. Here, we present our fifth major GPCRdb release setting out with an overview of the many resources for receptor sequences, structures, and ligands. This includes recently published additions of class D generic residue numbers, a comparative structure analysis tool to identify functional determinants, trees clustering GPCR structures by 3D conformation, and mutations stabilizing inactive/active states. We provide new state-specific structure models of all human non-olfactory GPCRs built using AlphaFold2-MultiState. We also provide a new resource of endogenous ligands along with a larger number of surrogate ligands with bioactivity, vendor, and physiochemical descriptor data. The one-stop-shop ligand resources integrate ligands/data from the ChEMBL, Guide to Pharmacology, PDSP Ki and PubChem database. The GPCRdb is available athttps://gpcrdb.org. LA - English DB - MTMT ER - TY - CHAP AU - Kiss, Dóra Judit AU - Pándy-Szekeres, Gáspár AU - Keserű, György Miklós ED - Kenakin, Terry TI - Computational Medicinal Chemistry to Target GPCRs T2 - Comprehensive Pharmacology PB - Elsevier Inc. CY - Online kiadás SN - 9780128208762 PY - 2022 SP - 84 EP - 114 PG - 31 DO - 10.1016/B978-0-12-820472-6.00208-5 UR - https://m2.mtmt.hu/api/publication/32832459 ID - 32832459 LA - English DB - MTMT ER - TY - JOUR AU - Pándy-Szekeres, Gáspár AU - Esguerra, Mauricio AU - Hauser, Alexander S AU - Caroli, Jimmy AU - Munk, Christian AU - Pilger, Steven AU - Keserű, György Miklós AU - Kooistra, Albert J AU - Gloriam, David E TI - The G protein database, GproteinDb JF - NUCLEIC ACIDS RESEARCH J2 - NUCLEIC ACIDS RES VL - 50 PY - 2022 IS - D1 SP - 518 EP - 525 PG - 8 SN - 0305-1048 DO - 10.1093/nar/gkab852 UR - https://m2.mtmt.hu/api/publication/32544494 ID - 32544494 LA - English DB - MTMT ER - TY - JOUR AU - Kooistra, Albert J AU - Mordalski, Stefan AU - Pándy-Szekeres, Gáspár AU - Esguerra, Mauricio AU - Mamyrbekov, Alibek AU - Munk, Christian AU - Keserű, György Miklós AU - Gloriam, David E TI - GPCRdb in 2021: integrating GPCR sequence, structure and function JF - NUCLEIC ACIDS RESEARCH J2 - NUCLEIC ACIDS RES VL - 49 PY - 2021 IS - D1 SP - D335 EP - D343 SN - 0305-1048 DO - 10.1093/nar/gkaa1080 UR - https://m2.mtmt.hu/api/publication/31817126 ID - 31817126 N1 - Funding Agency and Grant Number: Lundbeck FoundationLundbeckfonden [R218-2016-1266, R163-2013-16327]; EU Horizon 2020, Innovative Training Network SAFER [765657]; Independent Research Fund Denmark | Natural Sciences [8021-00173B]; Novo Nordisk FoundationNovo Nordisk FoundationNovocure Limited [NNF18OC0031226]; Alfred Benzon Foundation [ABF-0-0-312]; Polish National Science Center [HARMONIA 2015/18/M/NZ2/00423]; National Research, Development and Innovation Office, Hungary [National Brain Research Program]National Research, Development & Innovation Office (NRDIO) - Hungary [2017-1.2.1-NKP-201700002] Funding text: Lundbeck Foundation [R218-2016-1266] to C.M.; EU Horizon 2020, Innovative Training Network SAFER [765657], Independent Research Fund Denmark | Natural Sciences [8021-00173B], Lundbeck Foundation [R163-2013-16327], Novo Nordisk Foundation [NNF18OC0031226] to D.E.G.; Alfred Benzon Foundation [ABF-0-0-312], Polish National Science Center [HARMONIA 2015/18/M/NZ2/00423] to S.M.; National Research, Development and Innovation Office, Hungary [National Brain Research Program, 2017-1.2.1-NKP-201700002 to G.M.K.]. Funding for open access charge: the Novo Nordisk Foundation [NNF18OC0031226]. LA - English DB - MTMT ER - TY - JOUR AU - Egyed, Attila AU - Domány-Kovács, Katalin AU - Koványi, Bence AU - Horti, Ferenc AU - Kurko, Dalma AU - Kiss, Dóra Judit AU - Pándy-Szekeres, Gáspár AU - Greiner, István AU - Keserű, György Miklós TI - Controlling receptor function from the extracellular vestibule of G-protein coupled receptors JF - CHEMICAL COMMUNICATIONS J2 - CHEM COMMUN VL - 56 PY - 2020 IS - 91 SP - 14167 EP - 14170 PG - 4 SN - 1359-7345 DO - 10.1039/D0CC05532H UR - https://m2.mtmt.hu/api/publication/31799297 ID - 31799297 N1 - Cited By :11 Export Date: 7 April 2024 CODEN: CHCOF LA - English DB - MTMT ER - TY - JOUR AU - Jójárt, Balázs AU - Orgován, Zoltán AU - Márki, Árpád AU - Pándy-Szekeres, Gáspár AU - Ferenczy, György AU - Keserű, György Miklós TI - Allosteric activation of metabotropic glutamate receptor 5 JF - JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS J2 - J BIOMOL STRUCT DYN VL - 38 PY - 2020 IS - 9 SP - 2624 EP - 2632 PG - 10 SN - 0739-1102 DO - 10.1080/07391102.2019.1638302 UR - https://m2.mtmt.hu/api/publication/30834454 ID - 30834454 LA - English DB - MTMT ER - TY - JOUR AU - Pándy-Szekeres, Gáspár AU - Munk, Christian AU - Tsonkov, Tsonko M AU - Mordalski, Stefan AU - Harpsøe, Kasper AU - Hauser, Alexander S AU - Bojarski, Andrzej J AU - Gloriam, David E TI - GPCRdb in 2018: adding GPCR structure models and ligands JF - NUCLEIC ACIDS RESEARCH J2 - NUCLEIC ACIDS RES VL - 46 PY - 2018 IS - D1 SP - D440 EP - D446 SN - 0305-1048 DO - 10.1093/nar/gkx1109 UR - https://m2.mtmt.hu/api/publication/31163292 ID - 31163292 LA - English DB - MTMT ER -