Bajusz, Dávid and Pándy-Szekeres, Gáspár and Takács, Ágnes and de Araujo, Elvin D. and Keserű, György Miklós (2023) SH2db, an information system for the SH2 domain. NUCLEIC ACIDS RESEARCH, 51 (W1). W542-W552. ISSN 0305-1048
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Bajuszetal.-2023-SH2dbaninformationsystemfortheSH2domain.pdf Available under License Creative Commons Attribution. Download (1MB) | Preview |
Abstract
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.
Item Type: | Article |
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Additional Information: | 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]. |
Subjects: | Q Science / természettudomány > QD Chemistry / kémia |
SWORD Depositor: | MTMT SWORD |
Depositing User: | MTMT SWORD |
Date Deposited: | 15 Sep 2023 07:45 |
Last Modified: | 15 Sep 2023 07:45 |
URI: | http://real.mtak.hu/id/eprint/173634 |
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