{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,22]],"date-time":"2025-11-22T11:25:47Z","timestamp":1763810747706,"version":"3.41.2"},"reference-count":56,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2022,3,2]],"date-time":"2022-03-02T00:00:00Z","timestamp":1646179200000},"content-version":"vor","delay-in-days":60,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010665","name":"H2020 Marie Sklodowska-Curie Actions","doi-asserted-by":"publisher","award":["842490"],"award-info":[{"award-number":["842490"]}],"id":[{"id":"10.13039\/100010665","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Thematic Excellence Programme","award":["TKP2020-NKA-11"],"award-info":[{"award-number":["TKP2020-NKA-11"]}]},{"DOI":"10.13039\/501100018818","name":"National Research, Development and Innovation Office","doi-asserted-by":"publisher","award":["NN124363"],"award-info":[{"award-number":["NN124363"]}],"id":[{"id":"10.13039\/501100018818","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The postsynaptic region is the receiving part of the synapse comprising thousands of proteins forming an elaborate and dynamically changing network indispensable for the molecular mechanisms behind fundamental phenomena such as learning and memory. Despite the growing amount of information about individual protein\u2013protein interactions (PPIs) in this network, these data are mostly scattered in the literature or stored in generic databases that are not designed to display aspects that are fundamental to the understanding of postsynaptic functions. To overcome these limitations, we collected postsynaptic PPIs complemented by a high amount of detailed structural and biological information and launched a freely available resource, the Postsynaptic Interaction Database (PSINDB), to make these data and annotations accessible. PSINDB includes tens of thousands of binding regions together with structural features, mediating and regulating the formation of PPIs, annotated with detailed experimental information about each interaction. PSINDB is expected to be useful for various aspects of molecular neurobiology research, from experimental design to network and systems biology-based modeling and analysis of changes in the protein network upon various stimuli.<\/jats:p>\n               <jats:p>Database URL<\/jats:p>\n               <jats:p>https:\/\/psindb.itk.ppke.hu\/<\/jats:p>","DOI":"10.1093\/database\/baac007","type":"journal-article","created":{"date-parts":[[2022,2,7]],"date-time":"2022-02-07T20:10:56Z","timestamp":1644264656000},"source":"Crossref","is-referenced-by-count":8,"title":["PSINDB: the postsynaptic protein\u2013protein interaction database"],"prefix":"10.1093","volume":"2022","author":[{"given":"Zsofia E","family":"Kalman","sequence":"first","affiliation":[{"name":"Faculty of Information Technology and Bionics, P\u00e1zm\u00e1ny P\u00e9ter Catholic University, Pr\u00e1ter u. 50\/A, Budapest 1083, Hungary"}]},{"given":"D\u00e1niel","family":"Dudola","sequence":"additional","affiliation":[{"name":"Faculty of Information Technology and Bionics, P\u00e1zm\u00e1ny P\u00e9ter Catholic University, Pr\u00e1ter u. 50\/A, Budapest 1083, Hungary"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0919-4449","authenticated-orcid":false,"given":"B\u00e1lint","family":"M\u00e9sz\u00e1ros","sequence":"additional","affiliation":[{"name":"Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstra\u00dfe 1, Heidelberg 69117, Germany"}]},{"given":"Zolt\u00e1n","family":"G\u00e1sp\u00e1ri","sequence":"additional","affiliation":[{"name":"Faculty of Information Technology and Bionics, P\u00e1zm\u00e1ny P\u00e9ter Catholic University, Pr\u00e1ter u. 50\/A, Budapest 1083, Hungary"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2765-3872","authenticated-orcid":false,"given":"Laszlo","family":"Dobson","sequence":"additional","affiliation":[{"name":"Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstra\u00dfe 1, Heidelberg 69117, Germany"},{"name":"Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tud\u00f3sok K\u00f6r\u00fatja 2, Budapest 1117, Hungary"}]}],"member":"286","published-online":{"date-parts":[[2022,3,2]]},"reference":[{"key":"2022031007350341700_R1","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1007\/s00441-006-0274-5","article-title":"The postsynaptic density","volume":"326","author":"Boeckers","year":"2006","journal-title":"Cell Tissue Res."},{"key":"2022031007350341700_R2","doi-asserted-by":"publisher","DOI":"10.1101\/cshperspect.a005678","article-title":"The postsynaptic organization of synapses","volume":"3","author":"Sheng","year":"2011","journal-title":"Cold Spring Harb. Perspect. Biol."},{"key":"2022031007350341700_R3","doi-asserted-by":"crossref","first-page":"1899","DOI":"10.1021\/pr060393m","article-title":"Functional anthology of intrinsic disorder. 2. Cellular components, domains, technical terms, developmental processes, and coding sequence diversities correlated with long disordered regions","volume":"6","author":"Vucetic","year":"2007","journal-title":"J. Proteome Res."},{"key":"2022031007350341700_R4","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1126\/science.aai8355","article-title":"Homer1a drives homeostatic scaling-down of excitatory synapses during sleep","volume":"355","author":"Diering","year":"2017","journal-title":"Science"},{"key":"2022031007350341700_R5","doi-asserted-by":"crossref","first-page":"7003","DOI":"10.1523\/JNEUROSCI.1964-20.2021","article-title":"Rapid ultrastructural changes in the PSD and surrounding membrane after induction of structural LTP in single dendritic spines","volume":"41","author":"Sun","year":"2021","journal-title":"J. Neurosci."},{"key":"2022031007350341700_R6","doi-asserted-by":"crossref","first-page":"447","DOI":"10.1093\/jb\/mvy022","article-title":"Postsynaptic density proteins and their involvement in neurodevelopmental disorders","volume":"163","author":"Kaizuka","year":"2018","journal-title":"J. Biochem."},{"key":"2022031007350341700_R7","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1038\/nm.4071","article-title":"Advancing the understanding of autism disease mechanisms through genetics","volume":"22","author":"de la Torre-Ubieta","year":"2016","journal-title":"Nat. Med."},{"key":"2022031007350341700_R8","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1016\/j.bbrc.2014.08.108","article-title":"Genomic and genetic aspects of autism spectrum disorder","volume":"452","author":"Liu","year":"2014","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"2022031007350341700_R9","doi-asserted-by":"publisher","DOI":"10.3390\/e21080761","article-title":"Occurrence of ordered and disordered structural elements in postsynaptic proteins supports optimization for interaction diversity","volume":"21","author":"Kiss-T\u00f3th","year":"2019","journal-title":"Entropy"},{"key":"2022031007350341700_R10","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1016\/j.pbiomolbio.2008.05.007","article-title":"Intrinsic disorder in scaffold proteins: getting more from less","volume":"98","author":"Cortese","year":"2008","journal-title":"Prog. Biophys. Mol. Biol."},{"key":"2022031007350341700_R11","doi-asserted-by":"crossref","first-page":"4636","DOI":"10.1016\/j.jmb.2018.08.005","article-title":"Multiple modes of protein-protein interactions promote RNP granule assembly","volume":"430","author":"Mittag","year":"2018","journal-title":"J. Mol. Biol."},{"key":"2022031007350341700_R12","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1038\/nn1013","article-title":"Activity level controls postsynaptic composition and signaling via the ubiquitin-proteasome system","volume":"6","author":"Ehlers","year":"2003","journal-title":"Nat. Neurosci."},{"key":"2022031007350341700_R13","doi-asserted-by":"crossref","first-page":"D330","DOI":"10.1093\/nar\/gky1055","article-title":"The gene ontology resource: 20 years and still GOing strong","volume":"47","author":"The Gene Ontology Consortium","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2022031007350341700_R14","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1016\/j.neuron.2019.05.002","article-title":"SynGO: an evidence-based, expert-curated knowledge base for the synapse","volume":"103","author":"Koopmans","year":"2019","journal-title":"Neuron"},{"key":"2022031007350341700_R15","doi-asserted-by":"crossref","first-page":"897","DOI":"10.1093\/bioinformatics\/bts040","article-title":"SynaptomeDB: an ontology-based knowledgebase for synaptic genes","volume":"28","author":"Pirooznia","year":"2012","journal-title":"Bioinformatics"},{"key":"2022031007350341700_R16","doi-asserted-by":"crossref","first-page":"D846","DOI":"10.1093\/nar\/gkn700","article-title":"G2Cdb: the Genes to Cognition database","volume":"37","author":"Croning","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2022031007350341700_R17","doi-asserted-by":"crossref","first-page":"D841","DOI":"10.1093\/nar\/gkr1088","article-title":"The IntAct molecular interaction database in 2012","volume":"40","author":"Kerrien","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2022031007350341700_R18","doi-asserted-by":"crossref","first-page":"D529","DOI":"10.1093\/nar\/gky1079","article-title":"The BioGRID interaction database: 2019 update","volume":"47","author":"Oughtred","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2022031007350341700_R19","doi-asserted-by":"crossref","first-page":"D437","DOI":"10.1093\/nar\/gkaa1038","article-title":"RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences","volume":"49","author":"Burley","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2022031007350341700_R20","doi-asserted-by":"crossref","first-page":"D605","DOI":"10.1093\/nar\/gkaa1074","article-title":"The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene\/measurement sets","volume":"49","author":"Szklarczyk","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2022031007350341700_R21","doi-asserted-by":"crossref","first-page":"D480","DOI":"10.1093\/nar\/gkaa1100","article-title":"UniProt: the universal protein knowledgebase in 2021","volume":"49","author":"UniProt Consortium","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2022031007350341700_R22","doi-asserted-by":"crossref","first-page":"D1038","DOI":"10.1093\/nar\/gky1151","article-title":"OMIM.org: leveraging knowledge across phenotype-gene relationships","volume":"47","author":"Amberger","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2022031007350341700_R23","doi-asserted-by":"crossref","first-page":"3779","DOI":"10.1093\/bioinformatics\/btz132","article-title":"CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination","volume":"35","author":"Perfetto","year":"2019","journal-title":"Bioinformatics"},{"key":"2022031007350341700_R24","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1016\/j.sbi.2019.01.007","article-title":"Shanks - multidomain molecular scaffolds of the postsynaptic density","volume":"54","author":"Kursula","year":"2019","journal-title":"Curr. Opin. Struct. Biol."},{"key":"2022031007350341700_R25","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1126\/science.1118995","article-title":"An architectural framework that may lie at the core of the postsynaptic density","volume":"311","author":"Baron","year":"2006","journal-title":"Science"},{"key":"2022031007350341700_R26","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1016\/j.cell.2009.01.050","article-title":"The postsynaptic density proteins Homer and Shank form a polymeric network structure","volume":"137","author":"Hayashi","year":"2009","journal-title":"Cell"},{"key":"2022031007350341700_R27","doi-asserted-by":"crossref","first-page":"849","DOI":"10.1111\/jnc.13232","article-title":"Shank synaptic scaffold proteins: keys to understanding the pathogenesis of autism and other synaptic disorders","volume":"135","author":"Sala","year":"2015","journal-title":"J. Neurochem."},{"key":"2022031007350341700_R28","doi-asserted-by":"crossref","DOI":"10.3389\/fnmol.2020.00011","article-title":"Editorial: shankopathies: shank protein deficiency-induced synaptic diseases","volume":"13","author":"Ey","year":"2020","journal-title":"Front. Mol. Neurosci."},{"key":"2022031007350341700_R29","doi-asserted-by":"crossref","DOI":"10.1126\/scitranslmed.3002166","article-title":"Protein interactome reveals converging molecular pathways among autism disorders","volume":"3","author":"Sakai","year":"2011","journal-title":"Sci. Transl. Med."},{"key":"2022031007350341700_R30","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.66165","article-title":"Autism-associated missense point mutations impact conformational fluctuations and protein turnover at synapses","volume":"10","author":"Bucher","year":"2021","journal-title":"Elife"},{"key":"2022031007350341700_R31","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1009758","article-title":"Diversity of synaptic protein complexes as a function of the abundance of their constituent proteins: a modeling approach","volume":"18","author":"Miski","year":"2022","journal-title":"PLoS Comput. Biol."},{"key":"2022031007350341700_R32","doi-asserted-by":"crossref","first-page":"16959","DOI":"10.1523\/JNEUROSCI.1807-10.2010","article-title":"LRRK2 kinase regulates synaptic morphology through distinct substrates at the presynaptic and postsynaptic compartments of the Drosophila neuromuscular junction","volume":"30","author":"Lee","year":"2010","journal-title":"J. Neurosci."},{"key":"2022031007350341700_R33","doi-asserted-by":"crossref","first-page":"2157","DOI":"10.1016\/j.celrep.2019.04.060","article-title":"PLEKHA4\/kramer attenuates dishevelled ubiquitination to modulate Wnt and planar cell polarity signaling","volume":"27","author":"Shami Shah","year":"2019","journal-title":"Cell Rep."},{"key":"2022031007350341700_R34","doi-asserted-by":"publisher","DOI":"10.1101\/cshperspect.a008045","article-title":"Wnt signaling in neuromuscular junction development","volume":"4","author":"Koles","year":"2012","journal-title":"Cold Spring Harb. Perspect. Biol."},{"key":"2022031007350341700_R35","doi-asserted-by":"crossref","first-page":"15857","DOI":"10.1074\/jbc.M808986200","article-title":"Wnt-5a\/JNK signaling promotes the clustering of PSD-95 in hippocampal neurons","volume":"284","author":"Far\u00edas","year":"2009","journal-title":"J. Biol. Chem."},{"key":"2022031007350341700_R36","doi-asserted-by":"crossref","first-page":"8411","DOI":"10.1523\/JNEUROSCI.5736-09.2010","article-title":"Wnt-5a modulates recycling of functional GABAA receptors on hippocampal neurons","volume":"30","author":"Cuitino","year":"2010","journal-title":"J. Neurosci."},{"key":"2022031007350341700_R37","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1016\/j.canlet.2005.07.043","article-title":"Oncogenic rearrangements of the NTRK1\/NGF receptor","volume":"232","author":"Pierotti","year":"2006","journal-title":"Cancer Lett."},{"key":"2022031007350341700_R38","doi-asserted-by":"crossref","first-page":"627","DOI":"10.1016\/j.biopsych.2020.09.010","article-title":"Delineating the genetic component of gene expression in major depression","volume":"89","author":"Dall\u2019Aglio","year":"2021","journal-title":"Biol. Psychiatry"},{"key":"2022031007350341700_R39","doi-asserted-by":"crossref","first-page":"891","DOI":"10.2353\/ajpath.2009.080583","article-title":"The neuronal expression of MYC causes a neurodegenerative phenotype in a novel transgenic mouse","volume":"174","author":"Lee","year":"2009","journal-title":"Am. J. Pathol."},{"key":"2022031007350341700_R40","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1002\/pro.3987","article-title":"The Human Protein Atlas\u2014Spatial localization of the human proteome in health and disease. The Human Protein Atlas\u2014Spatial localization of the human proteome in health and disease","volume":"30","author":"Digre","year":"2021","journal-title":"Protein Sci."},{"key":"2022031007350341700_R41","article-title":"A unified resource and configurable model of the synapse proteome and its role in disease","volume":"11","author":"Sorokina","year":"2021","journal-title":"Sci. Rep."},{"key":"2022031007350341700_R42","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly accurate protein structure prediction with AlphaFold","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"author":"Akdel","key":"2022031007350341700_R43","article-title":"A structural biology community assessment of AlphaFold 2 applications. A structural biology community assessment of AlphaFold 2 applications"},{"key":"2022031007350341700_R44","doi-asserted-by":"crossref","first-page":"966","DOI":"10.1038\/nmeth.4077","article-title":"OmniPath: guidelines and gateway for literature-curated signaling pathway resources","volume":"13","author":"T\u00fcrei","year":"2016","journal-title":"Nat. Methods"},{"key":"2022031007350341700_R45","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res."},{"key":"2022031007350341700_R46","doi-asserted-by":"crossref","DOI":"10.12688\/f1000research.21508.1","article-title":"Identifying orthologs with OMA: a primer","volume":"9","author":"Zahn-Zabal","year":"2020","journal-title":"F1000Research"},{"key":"2022031007350341700_R47","doi-asserted-by":"crossref","first-page":"894","DOI":"10.1038\/nbt1324","article-title":"The minimum information required for reporting a molecular interaction experiment (MIMIx)","volume":"25","author":"Orchard","year":"2007","journal-title":"Nat. Biotechnol."},{"key":"2022031007350341700_R48","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btab448","article-title":"VoroContacts: a tool for the analysis of interatomic contacts in macromolecular structures","volume":"37","author":"Olechnovi\u010d","year":"2021","journal-title":"Bioinformatics"},{"key":"2022031007350341700_R49","doi-asserted-by":"crossref","DOI":"10.1186\/s13062-015-0061-x","article-title":"The human transmembrane proteome","volume":"10","author":"Dobson","year":"2015","journal-title":"Biol. Direct"},{"key":"2022031007350341700_R50","first-page":"D360","article-title":"PhaSePro: the database of proteins driving liquid-liquid phase separation","volume":"48","author":"M\u00e9sz\u00e1ros","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"2022031007350341700_R51","doi-asserted-by":"crossref","first-page":"D497","DOI":"10.1093\/nar\/gkab975","article-title":"The Eukaryotic Linear Motif resource: 2022 release","volume":"50","author":"Kumar","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"2022031007350341700_R52","doi-asserted-by":"crossref","first-page":"D427","DOI":"10.1093\/nar\/gky995","article-title":"The Pfam protein families database in 2019","volume":"47","author":"El-Gebali","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2022031007350341700_R53","doi-asserted-by":"crossref","first-page":"2790","DOI":"10.1093\/bioinformatics\/bty1062","article-title":"DeepCoil-a fast and accurate prediction of coiled-coil domains in protein sequences","volume":"35","author":"Ludwiczak","year":"2019","journal-title":"Bioinformatics"},{"key":"2022031007350341700_R54","doi-asserted-by":"crossref","first-page":"W329","DOI":"10.1093\/nar\/gky384","article-title":"IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding","volume":"46","author":"M\u00e9sz\u00e1ros","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2022031007350341700_R55","doi-asserted-by":"crossref","first-page":"D940","DOI":"10.1093\/nar\/gkr972","article-title":"Disease ontology: a backbone for disease semantic integration","volume":"40","author":"Schriml","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2022031007350341700_R56","doi-asserted-by":"crossref","DOI":"10.1038\/msb.2011.75","article-title":"Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega","volume":"7","author":"Sievers","year":"2011","journal-title":"Mol. Syst. Biol."}],"container-title":["Database"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baac007\/42793438\/baac007.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baac007\/42793438\/baac007.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,3,10]],"date-time":"2022-03-10T07:35:54Z","timestamp":1646897754000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/baac007\/6541046"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,1,1]]},"references-count":56,"URL":"https:\/\/doi.org\/10.1093\/database\/baac007","relation":{},"ISSN":["1758-0463"],"issn-type":[{"type":"electronic","value":"1758-0463"}],"subject":[],"published-other":{"date-parts":[[2022,1,1]]},"published":{"date-parts":[[2022,1,1]]},"article-number":"baac007"}}