Extracellular Matrix Interaction Database
Names
More detailed information about this field from each metasource.
Extracellular Matrix Interaction Database
metasource: Fairsharing.org
version: FAIRsharing.org: MatrixDB; Extracellular Matrix Interaction Database; DOI: https://doi.org/10.25504/FAIRsharing.91yrz6; Last edited: Feb. 25, 2021, 10:24 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
MatrixDB
metasource: Fairsharing.org
version: FAIRsharing.org: MatrixDB; Extracellular Matrix Interaction Database; DOI: https://doi.org/10.25504/FAIRsharing.91yrz6; Last edited: Feb. 25, 2021, 10:24 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: MatrixDB; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3M03H last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:00.589480
Extracellular Matrix interactions DataBase
metasource: re3data.org
version: re3data.org: MatrixDB; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3M03H last accessed: 2022-11-04
matrixdb
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:00.589480
Names
More detailed information about this field from each metasource.
Extracellular Matrix Interaction Database
metasource: Fairsharing.orgversion: FAIRsharing.org: MatrixDB; Extracellular Matrix Interaction Database; DOI: https://doi.org/10.25504/FAIRsharing.91yrz6; Last edited: Feb. 25, 2021, 10:24 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
MatrixDB
metasource: Fairsharing.orgversion: FAIRsharing.org: MatrixDB; Extracellular Matrix Interaction Database; DOI: https://doi.org/10.25504/FAIRsharing.91yrz6; Last edited: Feb. 25, 2021, 10:24 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: MatrixDB; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3M03H last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:00.589480
Extracellular Matrix interactions DataBase
metasource: re3data.orgversion: re3data.org: MatrixDB; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3M03H last accessed: 2022-11-04
matrixdb
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:00.589480
Other names: MatrixDB, Extracellular Matrix interactions DataBase, matrixdb
Names
More detailed information about this field from each metasource.
Extracellular Matrix Interaction Database
metasource: Fairsharing.orgversion: FAIRsharing.org: MatrixDB; Extracellular Matrix Interaction Database; DOI: https://doi.org/10.25504/FAIRsharing.91yrz6; Last edited: Feb. 25, 2021, 10:24 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
MatrixDB
metasource: Fairsharing.orgversion: FAIRsharing.org: MatrixDB; Extracellular Matrix Interaction Database; DOI: https://doi.org/10.25504/FAIRsharing.91yrz6; Last edited: Feb. 25, 2021, 10:24 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: MatrixDB; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3M03H last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:00.589480
Extracellular Matrix interactions DataBase
metasource: re3data.orgversion: re3data.org: MatrixDB; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3M03H last accessed: 2022-11-04
matrixdb
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:00.589480
MatrixDB stores experimental data established by full-length proteins, matricryptins, glycosaminoglycans, lipids and cations. MatrixDB reports interactions with individual polypeptide chains or with multimers (e.g. collagens, laminins, thrombospondins) when appropriate. Multimers are treated as permanent complexes, referencing EBI identifiers when possible. Human interactions were inferred from non-human homologous interactions when available.
Description
More detailed information about this field from each metasource.
MatrixDB stores experimental data established by full-length proteins, matricryptins, glycosaminoglycans, lipids and cations. MatrixDB reports interactions with individual polypeptide chains or with multimers (e.g. collagens, laminins, thrombospondins) when appropriate. Multimers are treated as permanent complexes, referencing EBI identifiers when possible. Human interactions were inferred from non-human homologous interactions when available.
metasource: Fairsharing.orgversion: FAIRsharing.org: MatrixDB; Extracellular Matrix Interaction Database; DOI: https://doi.org/10.25504/FAIRsharing.91yrz6; Last edited: Feb. 25, 2021, 10:24 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
Extracellular matrix proteins and their interactions
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
MatrixDB is a freely available database focused on interactions established by extracellular proteins and polysaccharides. MatrixDB takes into account the multimetric nature of the extracellular proteins (e.g. collagens, laminins and thrombospondins are multimers). MatrixDB includes interaction data extracted from the literature by manual curation in our lab, and offers access to relevant data involving extracellular proteins provided by our IMEx partner databases through the PSICQUIC webservice, as well as data from the Human Protein Reference Database. MatrixDB is in charge of the curation of papers published in Matrix Biology since January 2009
metasource: re3data.orgversion: re3data.org: MatrixDB; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3M03H last accessed: 2022-11-04
It is a database focused on interactions established by extracellular proteins and polysaccharides. It takes into account the multimeric nature of several extracellular protein families for the curation of interactions, and reports interactions with individual polypeptide chains or with multimers, considered as permanent complexes.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:00.589480
Webpage:
http://matrixdb.univ-lyon1.frWebpage
More detailed information about this field from each metasource.
http://matrixdb.univ-lyon1.fr
metasource: Fairsharing.orgversion: FAIRsharing.org: MatrixDB; Extracellular Matrix Interaction Database; DOI: https://doi.org/10.25504/FAIRsharing.91yrz6; Last edited: Feb. 25, 2021, 10:24 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
http://matrixdb.ibcp.fr
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
http://matrixdb.univ-lyon1.fr/
metasource: re3data.orgversion: re3data.org: MatrixDB; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3M03H last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:00.589480
Licence:
Name: Creative Commons Attribution 4.0 International (CC BY 4.0)Licence name
More detailed information about this field from each metasource.
Creative Commons Attribution 4.0 International (CC BY 4.0)
metasource: Fairsharing.orgversion: FAIRsharing.org: MatrixDB; Extracellular Matrix Interaction Database; DOI: https://doi.org/10.25504/FAIRsharing.91yrz6; Last edited: Feb. 25, 2021, 10:24 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
CC
metasource: re3data.orgversion: re3data.org: MatrixDB; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3M03H last accessed: 2022-11-04
Licence URL
More detailed information about this field from each metasource.
https://creativecommons.org/licenses/by/4.0/
metasource: Fairsharing.orgversion: FAIRsharing.org: MatrixDB; Extracellular Matrix Interaction Database; DOI: https://doi.org/10.25504/FAIRsharing.91yrz6; Last edited: Feb. 25, 2021, 10:24 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
https://creativecommons.org/licenses/by/2.5/
metasource: re3data.orgversion: re3data.org: MatrixDB; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3M03H last accessed: 2022-11-04
Publications:
Publications
More detailed information about this field from each metasource.
MatrixDB, the extracellular matrix interaction database
PMID: 20852260
metasource: Fairsharing.org
version: FAIRsharing.org: MatrixDB; Extracellular Matrix Interaction Database; DOI: https://doi.org/10.25504/FAIRsharing.91yrz6; Last edited: Feb. 25, 2021, 10:24 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:00.589480
MatrixDB, the extracellular matrix interaction database: updated content, a new navigator and expanded functionalities
PMID: 25378329
metasource: Fairsharing.org
version: FAIRsharing.org: MatrixDB; Extracellular Matrix Interaction Database; DOI: https://doi.org/10.25504/FAIRsharing.91yrz6; Last edited: Feb. 25, 2021, 10:24 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:00.589480
MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate interactions
PMID: 19147664
metasource: Fairsharing.org
version: FAIRsharing.org: MatrixDB; Extracellular Matrix Interaction Database; DOI: https://doi.org/10.25504/FAIRsharing.91yrz6; Last edited: Feb. 25, 2021, 10:24 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
MatrixDB: integration of new data with a focus on glycosaminoglycan interactions
PMID: 30371822
metasource: Fairsharing.org
version: FAIRsharing.org: MatrixDB; Extracellular Matrix Interaction Database; DOI: https://doi.org/10.25504/FAIRsharing.91yrz6; Last edited: Feb. 25, 2021, 10:24 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:00.589480
http://dx.doi.org/10.1093/nar/gku1091
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
MatrixDB, the extracellular matrix interaction database
PMID: 20852260
metasource: Fairsharing.org
version: FAIRsharing.org: MatrixDB; Extracellular Matrix Interaction Database; DOI: https://doi.org/10.25504/FAIRsharing.91yrz6; Last edited: Feb. 25, 2021, 10:24 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:00.589480
MatrixDB, the extracellular matrix interaction database: updated content, a new navigator and expanded functionalities
PMID: 25378329
metasource: Fairsharing.org
version: FAIRsharing.org: MatrixDB; Extracellular Matrix Interaction Database; DOI: https://doi.org/10.25504/FAIRsharing.91yrz6; Last edited: Feb. 25, 2021, 10:24 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:00.589480
MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate interactions
PMID: 19147664
metasource: Fairsharing.org
version: FAIRsharing.org: MatrixDB; Extracellular Matrix Interaction Database; DOI: https://doi.org/10.25504/FAIRsharing.91yrz6; Last edited: Feb. 25, 2021, 10:24 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
MatrixDB: integration of new data with a focus on glycosaminoglycan interactions
PMID: 30371822
metasource: Fairsharing.org
version: FAIRsharing.org: MatrixDB; Extracellular Matrix Interaction Database; DOI: https://doi.org/10.25504/FAIRsharing.91yrz6; Last edited: Feb. 25, 2021, 10:24 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:00.589480
http://dx.doi.org/10.1093/nar/gku1091
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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MatrixDB, the extracellular matrix interaction database
PubMed citations: 55.
55 articles citing: MatrixDB, the extracellular matrix interaction database
The Landscape of Virus-Host Protein-Protein Interaction Databases. PMID:35910656
GlycoGrip: Cell Surface-Inspired Universal Sensor for Betacoronaviruses. PMID:35106370
Navigating Multi-Scale Cancer Systems Biology Towards Model-Driven Clinical Oncology and Its Applications in Personalized Therapeutics. PMID:34900668
A Layered View on Focal Adhesions. PMID:34827182
Global effects of RAB3GAP1 dysexpression on the proteome of mouse cortical neurons. PMID:34363538
Databases for Protein-Protein Interactions. PMID:34236665
The Interactome of Cancer-Related Lysyl Oxidase and Lysyl Oxidase-Like Proteins. PMID:33383846
Three-Dimensional Structures of Carbohydrates and Where to Find Them. PMID:33081008
Databases and Bioinformatic Tools for Glycobiology and Glycoproteomics. PMID:32937895
Glycosaminoglycan-Protein Interactions: The First Draft of the Glycosaminoglycan Interactome. PMID:32757871
Topological features of integrin adhesion complexes revealed by multiplexed proximity biotinylation. PMID:32585685
Proteomics, Glycomics, and Glycoproteomics of Matrisome Molecules. PMID:31471497
Prediction of Self-Interacting Proteins from Protein Sequence Information Based on Random Projection Model and Fast Fourier Transform. PMID:30795499
MatrixDB: integration of new data with a focus on glycosaminoglycan interactions. PMID:30371822
Evolution of In Silico Strategies for Protein-Protein Interaction Drug Discovery. PMID:30082644
Extracellular matrix scaffold and hydrogel derived from decellularized and delipidized human pancreas. PMID:29993013
Glycosaminoglycanomics: where we are. PMID:27900575
Extracting a low-dimensional description of multiple gene expression datasets reveals a potential driver for tumor-associated stroma in ovarian cancer. PMID:27287041
Comparing Alzheimer's and Parkinson's diseases networks using graph communities structure. PMID:26935435
Novel Neuroprotective Multicomponent Therapy for Amyotrophic Lateral Sclerosis Designed by Networked Systems. PMID:26807587
Fundamentals of protein interaction network mapping. PMID:26681426
Meta-Analysis of Large-Scale Toxicogenomic Data Finds Neuronal Regeneration Related Protein and Cathepsin D to Be Novel Biomarkers of Drug-Induced Toxicity. PMID:26335687
Integrated inference and evaluation of host-fungi interaction networks. PMID:26300851
Network-based proteomic approaches reveal the neurodegenerative, neuroprotective and pain-related mechanisms involved after retrograde axonal damage. PMID:25784190
Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study. PMID:25652942
A visual review of the interactome of LRRK2: Using deep-curated molecular interaction data to represent biology. PMID:25648416
MatrixDB, the extracellular matrix interaction database: updated content, a new navigator and expanded functionalities. PMID:25378329
New tricks for "old" domains: how novel architectures and promiscuous hubs contributed to the organization and evolution of the ECM. PMID:25323955
The complex portal--an encyclopaedia of macromolecular complexes. PMID:25313161
VirusMentha: a new resource for virus-host protein interactions. PMID:25217587
Protein-protein interactions and genetic diseases: The interactome. PMID:24892209
Building and exploring an integrated human kinase network: global organization and medical entry points. PMID:24704859
Large-scale investigation of Leishmania interaction networks with host extracellular matrix by surface plasmon resonance imaging. PMID:24478075
The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases. PMID:24234451
DBATE: database of alternative transcripts expression. PMID:23842462
Complementing the Eukaryotic Protein Interactome. PMID:23825550
Optimization criteria and biological process enrichment in homologous multiprotein modules. PMID:23757502
Defining the extracellular matrix using proteomics. PMID:23419153
Interactome3D: adding structural details to protein networks. PMID:23399932
A survey of protein interaction data and multigenic inherited disorders. PMID:23398688
The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies. PMID:23398680
Proteomics-based methods for discovery, quantification, and validation of protein-protein interactions. PMID:23157382
Effects of protein interaction data integration, representation and reliability on the use of network properties for drug target prediction. PMID:23146171
The ConsensusPathDB interaction database: 2013 update. PMID:23143270
Knowledge building insights on biomarkers of arsenic toxicity to keratinocytes and melanocytes. PMID:23115478
Relationships between the amyloid precursor protein and its various proteolytic fragments and neuronal systems. PMID:22498202
Integrated inference and analysis of regulatory networks from multi-level measurements. PMID:22482944
Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. PMID:22453911
How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience. PMID:22438567
Identifying gene interaction networks. PMID:22307715
TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks. PMID:22292669
Benchmarking of the 2010 BioCreative Challenge III text-mining competition by the BioGRID and MINT interaction databases. PMID:22151178
MINT, the molecular interaction database: 2012 update. PMID:22096227
Overview of the matrisome--an inventory of extracellular matrix constituents and functions. PMID:21937732
Reactome pathway analysis to enrich biological discovery in proteomics data sets. PMID:21751369 -
MatrixDB, the extracellular matrix interaction database: updated content, a new navigator and expanded functionalities
PubMed citations: 54.
54 articles citing: MatrixDB, the extracellular matrix interaction database: updated content, a new navigator and expanded functionalities
SIPGCN: A Novel Deep Learning Model for Predicting Self-Interacting Proteins from Sequence Information Using Graph Convolutional Networks. PMID:35884848
ImitateDB: A database for domain and motif mimicry incorporating host and pathogen protein interactions. PMID:35487995
GlycoGrip: Cell Surface-Inspired Universal Sensor for Betacoronaviruses. PMID:35106370
Network analysis of host-pathogen protein interactions in microbe induced cardiovascular diseases. PMID:35001887
Computational repurposing of therapeutic small molecules from cancer to pulmonary hypertension. PMID:34669463
Peptide Location Fingerprinting Reveals Tissue Region-Specific Differences in Protein Structures in an Ageing Human Organ. PMID:34638745
Applications and analytical tools of cell communication based on ligand-receptor interactions at single cell level. PMID:34217372
Peptide location fingerprinting reveals modification-associated biomarker candidates of ageing in human tissue proteomes. PMID:33830638
NLPEI: A Novel Self-Interacting Protein Prediction Model Based on Natural Language Processing and Evolutionary Information. PMID:33488064
The Interactome of Cancer-Related Lysyl Oxidase and Lysyl Oxidase-Like Proteins. PMID:33383846
Towards a unified open access dataset of molecular interactions. PMID:33262342
Three-Dimensional Structures of Carbohydrates and Where to Find Them. PMID:33081008
Databases and Bioinformatic Tools for Glycobiology and Glycoproteomics. PMID:32937895
Glycosaminoglycan-Protein Interactions: The First Draft of the Glycosaminoglycan Interactome. PMID:32757871
Predicting Self-Interacting Proteins Using a Recurrent Neural Network and Protein Evolutionary Information. PMID:32550764
Dynamic rewiring of the human interactome by interferon signaling. PMID:32539747
MicrobioLink: An Integrated Computational Pipeline to Infer Functional Effects of Microbiome-Host Interactions. PMID:32455748
Machine learning approaches and databases for prediction of drug-target interaction: a survey paper. PMID:31950972
Identification of self-interacting proteins by integrating random projection classifier and finite impulse response filter. PMID:31881833
Sequence-Derived Markers of Drug Targets and Potentially Druggable Human Proteins. PMID:31803227
A Survey of Gene Prioritization Tools for Mendelian and Complex Human Diseases. PMID:31494632
Integrated analysis identified core signal pathways and hypoxic characteristics of human glioblastoma. PMID:31282108
Structural and Computational Characterization of Disease-Related Mutations Involved in Protein-Protein Interfaces. PMID:30934865
An Improved Deep Forest Model for Predicting Self-Interacting Proteins From Protein Sequence Using Wavelet Transformation. PMID:30881376
MorCVD: A Unified Database for Host-Pathogen Protein-Protein Interactions of Cardiovascular Diseases Related to Microbes. PMID:30858555
Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set. PMID:30602777
Prediction of protein self-interactions using stacked long short-term memory from protein sequences information. PMID:30577794
MatrixDB: integration of new data with a focus on glycosaminoglycan interactions. PMID:30371822
Genomic data integration systematically biases interactome mapping. PMID:30332399
Glycomics@ExPASy: Bridging the Gap. PMID:30097532
Insights into the structure and dynamics of lysyl oxidase propeptide, a flexible protein with numerous partners. PMID:30082873
Evolution of In Silico Strategies for Protein-Protein Interaction Drug Discovery. PMID:30082644
Factors Associated with Heritable Pulmonary Arterial Hypertension Exert Convergent Actions on the miR-130/301-Vascular Matrix Feedback Loop. PMID:30081553
Improving Prediction of Self-interacting Proteins Using Stacked Sparse Auto-Encoder with PSSM profiles. PMID:29989064
Identification of Central Regulators of Calcium Signaling and ECM-Receptor Interaction Genetically Associated With the Progression and Recurrence of Atrial Fibrillation. PMID:29868113
Phrase mining of textual data to analyze extracellular matrix protein patterns across cardiovascular disease. PMID:29775406
Conditional deletion of RB1 in the Tie2 lineage leads to aortic valve regurgitation. PMID:29304157
Functional Analysis of Human Hub Proteins and Their Interactors Involved in the Intrinsic Disorder-Enriched Interactions. PMID:29257115
The UCSC Genome Browser database: 2018 update. PMID:29106570
Simple and Efficient Purification of Recombinant Proteins Using the Heparin-Binding Affinity Tag. PMID:29091276
Computational methods using weighed-extreme learning machine to predict protein self-interactions with protein evolutionary information. PMID:29086182
Rapamycin-induced miR-21 promotes mitochondrial homeostasis and adaptation in mTORC1 activated cells. PMID:29029388
In-depth proteomic analysis of tissue interstitial fluid for hepatocellular carcinoma serum biomarker discovery. PMID:29024941
Protein-Protein Interactions in Virus-Host Systems. PMID:28861068
Glycosaminoglycanomics: where we are. PMID:27900575
A scored human protein-protein interaction network to catalyze genomic interpretation. PMID:27892958
Proteoglycan neofunctions: regulation of inflammation and autophagy in cancer biology. PMID:27860287
Identification of self-interacting proteins by exploring evolutionary information embedded in PSI-BLAST-constructed position specific scoring matrix. PMID:27732957
Decorin interacting network: A comprehensive analysis of decorin-binding partners and their versatile functions. PMID:27693454
HPIDB 2.0: a curated database for host-pathogen interactions. PMID:27374121
Matricellular TSP-1 as a target of interest for impeding melanoma spreading: towards a therapeutic use for TAX2 peptide. PMID:27349907
Reconstruction and Application of Protein-Protein Interaction Network. PMID:27338356
Matrix metalloproteinases as input and output signals for post-myocardial infarction remodeling. PMID:26721597
The extracellular matrix: Tools and insights for the "omics" era. PMID:26163349 -
MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate interactions
PubMed citations: 48.
48 articles citing: MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate interactions
GlycoGrip: Cell Surface-Inspired Universal Sensor for Betacoronaviruses. PMID:35106370
The Interactome of Cancer-Related Lysyl Oxidase and Lysyl Oxidase-Like Proteins. PMID:33383846
Databases and Bioinformatic Tools for Glycobiology and Glycoproteomics. PMID:32937895
Basement membrane ligands initiate distinct signalling networks to direct cell shape. PMID:32147508
Proteomics, Glycomics, and Glycoproteomics of Matrisome Molecules. PMID:31471497
PIMKL: Pathway-Induced Multiple Kernel Learning. PMID:30854223
MatrixDB: integration of new data with a focus on glycosaminoglycan interactions. PMID:30371822
Evolution of In Silico Strategies for Protein-Protein Interaction Drug Discovery. PMID:30082644
Tumor endothelial marker 8 promotes cancer progression and metastasis. PMID:30046396
Mesoscopic Rigid Body Modelling of the Extracellular Matrix Self-Assembly. PMID:29886454
A large-scale expression strategy for multimeric extracellular protein complexes using Drosophila S2 cells and its application to the recombinant expression of heterodimeric ligand-binding domains of taste receptor. PMID:28833672
Glycosaminoglycanomics: where we are. PMID:27900575
The integrin adhesome network at a glance. PMID:27799358
Modulation of FAK and Src adhesion signaling occurs independently of adhesion complex composition. PMID:26833789
BioGRID: A Resource for Studying Biological Interactions in Yeast. PMID:26729913
Identification of the Glycosaminoglycan Binding Site of Interleukin-10 by NMR Spectroscopy. PMID:26677224
The extracellular matrix: Tools and insights for the "omics" era. PMID:26163349
PrOnto database : GO term functional dissimilarity inferred from biological data. PMID:26089836
Extreme multifunctional proteins identified from a human protein interaction network. PMID:26054620
The hierarchical organization of natural protein interaction networks confers self-organization properties on pseudocells. PMID:26050708
Coinheritance of COL4A5 and MYO1E mutations accentuate the severity of kidney disease. PMID:25739341
A proteomic approach reveals integrin activation state-dependent control of microtubule cortical targeting. PMID:25609142
Microtubule-dependent modulation of adhesion complex composition. PMID:25526367
MatrixDB, the extracellular matrix interaction database: updated content, a new navigator and expanded functionalities. PMID:25378329
ComPPI: a cellular compartment-specific database for protein-protein interaction network analysis. PMID:25348397
Linear motif-mediated interactions have contributed to the evolution of modularity in complex protein interaction networks. PMID:25299147
Plant systems biology: insights, advances and challenges. PMID:24671625
Capturing cooperative interactions with the PSI-MI format. PMID:24067240
Comparative proteomic analysis of supportive and unsupportive extracellular matrix substrates for human embryonic stem cell maintenance. PMID:23658023
Defining the extracellular matrix using proteomics. PMID:23419153
Proteomic analysis of extracellular matrix from the hepatic stellate cell line LX-2 identifies CYR61 and Wnt-5a as novel constituents of fibrotic liver. PMID:22694338
NetAligner--a network alignment server to compare complexes, pathways and whole interactomes. PMID:22618871
A framework for mapping, visualisation and automatic model creation of signal-transduction networks. PMID:22531118
The role of structural disorder in the rewiring of protein interactions through evolution. PMID:22389433
Systems pharmacology: network analysis to identify multiscale mechanisms of drug action. PMID:22235860
Overview of the matrisome--an inventory of extracellular matrix constituents and functions. PMID:21937732
Bio::Homology::InterologWalk--a Perl module to build putative protein-protein interaction networks through interolog mapping. PMID:21767381
Reactome pathway analysis to enrich biological discovery in proteomics data sets. PMID:21751369
The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods. PMID:21472436
A systems biology approach for the investigation of the heparin/heparan sulfate interactome. PMID:21454685
The collagen family. PMID:21421911
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. PMID:21045058
The impact of gene expression regulation on evolution of extracellular signaling pathways. PMID:20935258
Human protein reference database and human proteinpedia as discovery resources for molecular biotechnology. PMID:20927658
MatrixDB, the extracellular matrix interaction database. PMID:20852260
MINT, the molecular interaction database: 2009 update. PMID:19897547
The IntAct molecular interaction database in 2010. PMID:19850723
The first draft of the endostatin interaction network. PMID:19542224 -
MatrixDB: integration of new data with a focus on glycosaminoglycan interactions
PubMed citations: 39.
39 articles citing: MatrixDB: integration of new data with a focus on glycosaminoglycan interactions
An approach to cellular tropism of SARS-CoV-2 through protein-protein interaction and enrichment analysis. PMID:35672403
The Non-pregnant and Pregnant Human Cervix: a Systematic Proteomic Analysis. PMID:35266109
GlycoGrip: Cell Surface-Inspired Universal Sensor for Betacoronaviruses. PMID:35106370
How Far Are We from the Completion of the Human Protein Interactome Reconstruction? PMID:35053288
Pyranose Ring Puckering Thermodynamics for Glycan Monosaccharides Associated with Vertebrate Proteins. PMID:35008898
Potential Molecular Mechanisms and Remdesivir Treatment for Acute Respiratory Syndrome Corona Virus 2 Infection/COVID 19 Through RNA Sequencing and Bioinformatics Analysis. PMID:34992355
ConsensusPathDB 2022: molecular interactions update as a resource for network biology. PMID:34850110
Preface for the Special Issue on the Exploration of the Multifaceted Roles of Glycosaminoglycans: GAGs. PMID:34827628
The IntAct database: efficient access to fine-grained molecular interaction data. PMID:34761267
IID 2021: towards context-specific protein interaction analyses by increased coverage, enhanced annotation and enrichment analysis. PMID:34755877
Analytical challenges of glycosaminoglycans at biological interfaces. PMID:34647134
Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review. PMID:34439912
Enhancing the interoperability of glycan data flow between ChEBI, PubChem and GlyGen. PMID:34314492
mPPI: a database extension to visualize structural interactome in a one-to-many manner. PMID:34156447
DGLinker: flexible knowledge-graph prediction of disease-gene associations. PMID:34125897
Sulfation and Calcium Favor Compact Conformations of Chondroitin in Aqueous Solutions. PMID:34056470
KEA3: improved kinase enrichment analysis via data integration. PMID:34019655
Prognostic impact of the glypican family of heparan sulfate proteoglycans on the survival of breast cancer patients. PMID:33742285
Analysing the yeast complexome-the Complex Portal rising to the challenge. PMID:33677561
The matrix in cancer. PMID:33589810
Development of Decellularized Oviductal Hydrogels as a Support for Rabbit Embryo Culture. PMID:33511539
Heparan Sulfate Glycosaminoglycans: (Un)Expected Allies in Cancer Clinical Management. PMID:33494442
Multiscale Regulation of the Intervertebral Disc: Achievements in Experimental, In Silico, and Regenerative Research. PMID:33445782
The Interactome of Cancer-Related Lysyl Oxidase and Lysyl Oxidase-Like Proteins. PMID:33383846
Big-Data Glycomics: Tools to Connect Glycan Biosynthesis to Extracellular Communication. PMID:33349503
GAG-DB, the New Interface of the Three-Dimensional Landscape of Glycosaminoglycans. PMID:33322545
Towards a unified open access dataset of molecular interactions. PMID:33262342
The IMEx coronavirus interactome: an evolving map of Coronaviridae-host molecular interactions. PMID:33206959
Three-Dimensional Structures of Carbohydrates and Where to Find Them. PMID:33081008
Constructing 3-Dimensional Atomic-Resolution Models of Nonsulfated Glycosaminoglycans with Arbitrary Lengths Using Conformations from Molecular Dynamics. PMID:33080973
Databases and Bioinformatic Tools for Glycobiology and Glycoproteomics. PMID:32937895
Glycosaminoglycan-Protein Interactions: The First Draft of the Glycosaminoglycan Interactome. PMID:32757871
The IMEx Coronavirus interactome: an evolving map of Coronaviridae-Host molecular interactions. PMID:32587962
ECMPride: prediction of human extracellular matrix proteins based on the ideal dataset using hybrid features with domain evidence. PMID:32377454
Efficient Construction of Atomic-Resolution Models of Non-Sulfated Chondroitin Glycosaminoglycan Using Molecular Dynamics Data. PMID:32252422
Analysis of Differentially Expressed Genes in Coronary Artery Disease by Integrated Microarray Analysis. PMID:31881747
Global Vectors Representation of Protein Sequences and Its Application for Predicting Self-Interacting Proteins with Multi-Grained Cascade Forest Model. PMID:31726752
Updates to the Symbol Nomenclature for Glycans guidelines. PMID:31184695
A Bioinformatics View of Glycan⁻Virus Interactions. PMID:31018588 - http://dx.doi.org/10.1093/nar/gku1091
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carbohydrate
metasource: Fairsharing.org
version: FAIRsharing.org: MatrixDB; Extracellular Matrix Interaction Database; DOI: https://doi.org/10.25504/FAIRsharing.91yrz6; Last edited: Feb. 25, 2021, 10:24 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
lipid
metasource: Fairsharing.org
version: FAIRsharing.org: MatrixDB; Extracellular Matrix Interaction Database; DOI: https://doi.org/10.25504/FAIRsharing.91yrz6; Last edited: Feb. 25, 2021, 10:24 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
molecular interaction
metasource: Fairsharing.org
version: FAIRsharing.org: MatrixDB; Extracellular Matrix Interaction Database; DOI: https://doi.org/10.25504/FAIRsharing.91yrz6; Last edited: Feb. 25, 2021, 10:24 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
protein
metasource: Fairsharing.org
version: FAIRsharing.org: MatrixDB; Extracellular Matrix Interaction Database; DOI: https://doi.org/10.25504/FAIRsharing.91yrz6; Last edited: Feb. 25, 2021, 10:24 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
protein interaction
metasource: Fairsharing.org
version: FAIRsharing.org: MatrixDB; Extracellular Matrix Interaction Database; DOI: https://doi.org/10.25504/FAIRsharing.91yrz6; Last edited: Feb. 25, 2021, 10:24 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
small molecule
metasource: Fairsharing.org
version: FAIRsharing.org: MatrixDB; Extracellular Matrix Interaction Database; DOI: https://doi.org/10.25504/FAIRsharing.91yrz6; Last edited: Feb. 25, 2021, 10:24 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
protein sequence databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
protein localization and targeting
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
polysaccharides
metasource: re3data.org
version: re3data.org: MatrixDB; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3M03H last accessed: 2022-11-04
biomolecules
metasource: re3data.org
version: re3data.org: MatrixDB; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3M03H last accessed: 2022-11-04
collagens
metasource: re3data.org
version: re3data.org: MatrixDB; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3M03H last accessed: 2022-11-04
glycosamoglycan
metasource: re3data.org
version: re3data.org: MatrixDB; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3M03H last accessed: 2022-11-04
laminins
metasource: re3data.org
version: re3data.org: MatrixDB; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3M03H last accessed: 2022-11-04
proteins
metasource: re3data.org
version: re3data.org: MatrixDB; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3M03H last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:00.589480
thrombospondins
metasource: re3data.org
version: re3data.org: MatrixDB; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3M03H last accessed: 2022-11-04
molecular interactions, pathways and networks
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:00.589480
protein interactions
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:00.589480
gene and protein families
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:00.589480
Tags
More detailed information about this field from each metasource.
carbohydrate
metasource: Fairsharing.orgversion: FAIRsharing.org: MatrixDB; Extracellular Matrix Interaction Database; DOI: https://doi.org/10.25504/FAIRsharing.91yrz6; Last edited: Feb. 25, 2021, 10:24 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
lipid
metasource: Fairsharing.orgversion: FAIRsharing.org: MatrixDB; Extracellular Matrix Interaction Database; DOI: https://doi.org/10.25504/FAIRsharing.91yrz6; Last edited: Feb. 25, 2021, 10:24 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
molecular interaction
metasource: Fairsharing.orgversion: FAIRsharing.org: MatrixDB; Extracellular Matrix Interaction Database; DOI: https://doi.org/10.25504/FAIRsharing.91yrz6; Last edited: Feb. 25, 2021, 10:24 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
protein
metasource: Fairsharing.orgversion: FAIRsharing.org: MatrixDB; Extracellular Matrix Interaction Database; DOI: https://doi.org/10.25504/FAIRsharing.91yrz6; Last edited: Feb. 25, 2021, 10:24 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
protein interaction
metasource: Fairsharing.orgversion: FAIRsharing.org: MatrixDB; Extracellular Matrix Interaction Database; DOI: https://doi.org/10.25504/FAIRsharing.91yrz6; Last edited: Feb. 25, 2021, 10:24 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
small molecule
metasource: Fairsharing.orgversion: FAIRsharing.org: MatrixDB; Extracellular Matrix Interaction Database; DOI: https://doi.org/10.25504/FAIRsharing.91yrz6; Last edited: Feb. 25, 2021, 10:24 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
protein sequence databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
protein localization and targeting
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
polysaccharides
metasource: re3data.orgversion: re3data.org: MatrixDB; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3M03H last accessed: 2022-11-04
biomolecules
metasource: re3data.orgversion: re3data.org: MatrixDB; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3M03H last accessed: 2022-11-04
collagens
metasource: re3data.orgversion: re3data.org: MatrixDB; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3M03H last accessed: 2022-11-04
glycosamoglycan
metasource: re3data.orgversion: re3data.org: MatrixDB; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3M03H last accessed: 2022-11-04
laminins
metasource: re3data.orgversion: re3data.org: MatrixDB; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3M03H last accessed: 2022-11-04
proteins
metasource: re3data.orgversion: re3data.org: MatrixDB; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3M03H last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:00.589480
thrombospondins
metasource: re3data.orgversion: re3data.org: MatrixDB; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3M03H last accessed: 2022-11-04
molecular interactions, pathways and networks
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:00.589480
protein interactions
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:00.589480
gene and protein families
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:00.589480
carbohydrate lipid molecular interaction protein protein interaction small molecule protein sequence protein localization and targeting polysaccharides biomolecules collagens glycosamoglycan laminins proteins thrombospondins molecular interactions, pathways and networks protein interaction gene and protein families
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