{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,14]],"date-time":"2026-05-14T23:57:10Z","timestamp":1778803030642,"version":"3.51.4"},"reference-count":42,"publisher":"Wiley","issue":"8","license":[{"start":{"date-parts":[[2024,4,15]],"date-time":"2024-04-15T00:00:00Z","timestamp":1713139200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Molecular Informatics"],"published-print":{"date-parts":[[2024,8]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>The important role that the neurotrophin tyrosine kinase receptor \u2010 TrkB has in the pathogenesis of several neurodegenerative conditions such are Alzheimer's disease, Parkinson's disease, Huntington's disease, has been well described. This shouldn't be a surprise, since in the physiological conditions, once activated by brain\u2010derived neurotrophic factor (BDNF) and neurotrophin\u20104\/5 (NT\u20104\/5), the TrkB receptor promotes neuronal survival, differentiation and synaptic function. Considering that the natural ligands for TrkB receptor are large proteins, it is a challenge to discover small molecule capable to mimic their effects.<\/jats:p><jats:p>Even though, the surface of receptor that is interacting with BDNF or NT\u20104\/5 is known, there was always a question which pocket and interaction is responsible for activation of it. In order to answer this challenging question, we have used molecular dynamic (MD) simulations and Pocketron algorithm which enabled us to detect, for the first time, a pocket network existing in the interacting domain (d5) of the receptor; to describe them and to see how they are communicating with each other. This new discovery gave us potential new areas on receptor that can be targeted and used for structure\u2010based drug design approach in the development of the new ligands.<\/jats:p>","DOI":"10.1002\/minf.202400043","type":"journal-article","created":{"date-parts":[[2024,4,15]],"date-time":"2024-04-15T13:22:58Z","timestamp":1713187378000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Discovery of a pocket network on the domain 5 of the TrkB receptor \u2013 A potential new target in the quest for the new ligands"],"prefix":"10.1002","volume":"43","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4722-0903","authenticated-orcid":false,"given":"Mirjana","family":"Antonijevic","sequence":"first","affiliation":[{"name":"Normandie Univ. UNICAEN CERMN  14000 Caen France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jana","family":"Sopkova\u2010de Oliveira Santos","sequence":"additional","affiliation":[{"name":"Normandie Univ. UNICAEN CERMN  14000 Caen France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Patrick","family":"Dallemagne","sequence":"additional","affiliation":[{"name":"Normandie Univ. UNICAEN CERMN  14000 Caen France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7996-2082","authenticated-orcid":false,"given":"Christophe","family":"Rochais","sequence":"additional","affiliation":[{"name":"Normandie Univ. UNICAEN CERMN  14000 Caen France"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2024,4,15]]},"reference":[{"key":"e_1_2_9_2_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.phrs.2017.04.024"},{"key":"e_1_2_9_3_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.biochem.72.121801.161629"},{"key":"e_1_2_9_4_1","first-page":"83","volume-title":"Hormonal Signaling in Biology and Medicine","author":"Vilar M.","year":"2020"},{"key":"e_1_2_9_5_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1460-9568.2007.05625.x"},{"key":"e_1_2_9_6_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.mcn.2008.07.017"},{"key":"e_1_2_9_7_1","doi-asserted-by":"publisher","DOI":"10.3389\/fnins.2016.00026"},{"key":"e_1_2_9_8_1","first-page":"1","volume":"12","author":"Ferreira F. F.","year":"2018","journal-title":"Front. Cell. Neurosci."},{"key":"e_1_2_9_9_1","doi-asserted-by":"publisher","DOI":"10.1093\/cercor\/bhu105"},{"key":"e_1_2_9_10_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2006.06.046"},{"key":"e_1_2_9_11_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.neurobiolaging.2009.05.012"},{"key":"e_1_2_9_12_1","doi-asserted-by":"crossref","unstructured":"X. Ye W. Tai D. Zhang Neurobiol. Aging2012 33 1122.e1\u20131122.e10.","DOI":"10.1016\/j.neurobiolaging.2011.11.004"},{"key":"e_1_2_9_13_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10735-013-9562-z"},{"key":"e_1_2_9_14_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-016-0028-x"},{"key":"e_1_2_9_15_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1460-9568.2005.04576.x"},{"key":"e_1_2_9_16_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1460-9568.2005.04290.x"},{"key":"e_1_2_9_17_1","doi-asserted-by":"publisher","DOI":"10.3390\/ijms21031170"},{"key":"e_1_2_9_18_1","doi-asserted-by":"publisher","DOI":"10.1016\/0169-328X(95)00250-V"},{"key":"e_1_2_9_19_1","doi-asserted-by":"publisher","DOI":"10.1113\/jphysiol.2008.152439"},{"key":"e_1_2_9_20_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ejmech.2023.115111"},{"key":"e_1_2_9_21_1","doi-asserted-by":"publisher","DOI":"10.3390\/molecules29020515"},{"key":"e_1_2_9_22_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0969-2126(01)00681-5"},{"key":"e_1_2_9_23_1","doi-asserted-by":"publisher","DOI":"10.1038\/43705"},{"key":"e_1_2_9_24_1","doi-asserted-by":"publisher","DOI":"10.1124\/jpet.117.240184"},{"key":"e_1_2_9_25_1","unstructured":"Schr\u00f6dinger Release 2018\u20134: Schr\u00f6dinger Suite 2018\u20133 Protein Preparation Wizard; Epik Schr\u00f6dinger LLC New York NY 2018; Impact Schr\u00f6dinger LLC New York NY 2018; Prime Schr\u00f6dinger LLC New York NY 2018."},{"key":"e_1_2_9_26_1","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.20289"},{"key":"e_1_2_9_27_1","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.23354"},{"key":"e_1_2_9_28_1","doi-asserted-by":"publisher","DOI":"10.1021\/jp003020w"},{"key":"e_1_2_9_29_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.5b00935"},{"key":"e_1_2_9_30_1","doi-asserted-by":"publisher","DOI":"10.1063\/1.464397"},{"key":"e_1_2_9_31_1","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1096-987X(19980115)19:1<102::AID-JCC9>3.0.CO;2-T"},{"key":"e_1_2_9_32_1","doi-asserted-by":"publisher","DOI":"10.1063\/1.470648"},{"key":"e_1_2_9_33_1","doi-asserted-by":"publisher","DOI":"10.1016\/0263-7855(96)00018-5"},{"key":"e_1_2_9_34_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.7b00680"},{"key":"e_1_2_9_35_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty761"},{"key":"e_1_2_9_36_1","doi-asserted-by":"publisher","DOI":"10.1021\/ct1006696"},{"key":"e_1_2_9_37_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.chembiol.2008.09.007"},{"key":"e_1_2_9_38_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cub.2010.12.048"},{"key":"e_1_2_9_39_1","doi-asserted-by":"publisher","DOI":"10.1172\/JCI43992"},{"key":"e_1_2_9_40_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.accounts.5b00516"},{"key":"e_1_2_9_41_1","doi-asserted-by":"publisher","DOI":"10.1172\/JCI41356"},{"key":"e_1_2_9_42_1","doi-asserted-by":"publisher","DOI":"10.1126\/scisignal.aal1670"},{"key":"e_1_2_9_43_1","doi-asserted-by":"publisher","DOI":"10.3389\/fnmol.2019.00205"}],"container-title":["Molecular Informatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/minf.202400043","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,8,12]],"date-time":"2024-08-12T09:32:28Z","timestamp":1723455148000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/minf.202400043"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,4,15]]},"references-count":42,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2024,8]]}},"alternative-id":["10.1002\/minf.202400043"],"URL":"https:\/\/doi.org\/10.1002\/minf.202400043","archive":["Portico"],"relation":{},"ISSN":["1868-1743","1868-1751"],"issn-type":[{"value":"1868-1743","type":"print"},{"value":"1868-1751","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,4,15]]},"assertion":[{"value":"2024-02-01","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-03-26","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-04-15","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e202400043"}}