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STITCH 4: integration of protein–chemical interactions with user data

Michael Kuhn, Damian Szklarczyk, Sune Pletscher-Frankild, Thomas H. Blicher, Christian von Mering, Lars J. Jensen, Peer Bork
2013 Nucleic Acids Research  
STITCH is a database of protein-chemical interactions that integrates many sources of experimental and manually curated evidence with text-mining information and interaction predictions.  ...  STITCH can be accessed with a web-interface, an API and downloadable files ABSTRACT STITCH is a database of protein-chemical interactions that integrates many sources of experimental and manually curated  ...  Yuan (EMBL) for his outstanding support with the STITCH servers. Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkt1207 pmid:24293645 pmcid:PMC3964996 fatcat:pn3selqejnelve5rx2cl32dce4

STITCH 4: integration of protein–chemical interactions with user data

Michael Kuhn, Damian Szklarczyk, Sune Pletscher-Frankild, Thomas H Blicher, Christian Von Mering, Lars J Jensen, Peer Bork
2014
STITCH is a database of protein-chemical interactions that integrates many sources of experimental and manually curated evidence with text-mining information and interaction predictions.  ...  STITCH can be accessed with a web-interface, an API and downloadable files ABSTRACT STITCH is a database of protein-chemical interactions that integrates many sources of experimental and manually curated  ...  Yuan (EMBL) for his outstanding support with the STITCH servers. Conflict of interest statement. None declared.  ... 
doi:10.5167/uzh-155269 fatcat:dfkyfpljprhfzf7i4uai5cjpgi

STITCH: interaction networks of chemicals and proteins

M. Kuhn, C. von Mering, M. Campillos, L. J. Jensen, P. Bork
2007 Nucleic Acids Research  
STITCH further allows exploring the network of chemical relations, also in the context of associated binding proteins. Each proposed interaction can be traced back to the original data sources.  ...  To facilitate access to this data, STITCH ('search tool for interactions of chemicals') integrates information about interactions from metabolic pathways, crystal structures, binding experiments and drug-target  ...  ACKNOWLEDGEMENTS The authors thank members of the Bork and von Mering groups for comments on the STITCH web interface. This work was funded by the BMBF QuantPro grant (0313831D).  ... 
doi:10.1093/nar/gkm795 pmid:18084021 pmcid:PMC2238848 fatcat:uplvdvv2wzcjfntakzns7ctgki

STITCH 3: zooming in on protein-chemical interactions

M. Kuhn, D. Szklarczyk, A. Franceschini, C. von Mering, L. J. Jensen, P. Bork
2011 Nucleic Acids Research  
To facilitate the study of interactions between proteins and chemicals, we have created STITCH, an aggregated database of interactions connecting over 300 000 chemicals and 2.6 million proteins from 1133  ...  Compared to the previous version, the number of chemicals with interactions and the number of high-confidence interactions both increase 4-fold.  ...  STITCH enables the user to query the database for chemical or protein names, for InChIKeys and for SMILES strings.  ... 
doi:10.1093/nar/gkr1011 pmid:22075997 pmcid:PMC3245073 fatcat:dkri4srxl5egbn7ou4wikebg6i

STITCH 5: augmenting protein–chemical interaction networks with tissue and affinity data

Damian Szklarczyk, Alberto Santos, Christian von Mering, Lars Juhl Jensen, Peer Bork, Michael Kuhn
2015 Nucleic Acids Research  
To address this, we have developed STITCH ('Search Tool for Interacting Chemicals') that integrates these disparate data sources for 430 000 chemicals into a single, easy-to-use resource.  ...  In the new, fifth release of STITCH, we have implemented functionality to filter out the proteins and chemicals not associated with a given tissue.  ...  Yuan (EMBL) for his outstanding support with the STITCH servers and Rebeca Quiñones (NNF Center for Protein Research) for help with migrating the text-mining pipeline to a high-performance compute centre  ... 
doi:10.1093/nar/gkv1277 pmid:26590256 pmcid:PMC4702904 fatcat:ofgnm7c3t5eizpqshlb7unurle

STITCH 2: an interaction network database for small molecules and proteins

Michael Kuhn, Damian Szklarczyk, Andrea Franceschini, Monica Campillos, Christian von Mering, Lars Juhl Jensen, Andreas Beyer, Peer Bork
2009 Nucleic Acids Research  
To create a network of interactions, STITCH aims to integrate the data dispersed over the literature and various databases of biological pathways, drug-target relationships and binding affinities.  ...  To facilitate links to other chemical databases, we adopt InChIKeys that allow identification of chemicals with a short, checksum-like string.  ...  USER INTERFACE IMPROVEMENTS Many proteins, especially drug targets, have a large number of high-scoring interactions with small molecules in the STITCH network.  ... 
doi:10.1093/nar/gkp937 pmid:19897548 pmcid:PMC2808890 fatcat:vxqn3s5gu5gl7jdgnzwjj3bkju

Stitching the synapse: Cross-linking mass spectrometry into resolving synaptic protein interactions

M. A. Gonzalez-Lozano, F. Koopmans, P. F. Sullivan, J. Protze, G. Krause, M. Verhage, K. W. Li, F. Liu, A. B. Smit
2020 Science Advances  
Here, we made use of recent advances in cross-linking mass spectrometry (XL-MS) in combination with biochemical and computational approaches to reveal the architecture and assembly of synaptic protein  ...  Using XL-MS, we generated a protein interaction resource that we made easily accessible via a web-based platform (http://xlink.cncr.nl) to provide new entries into exploration of all protein interactions  ...  Data and materials availability: All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials.  ... 
doi:10.1126/sciadv.aax5783 pmid:32128395 pmcid:PMC7030922 fatcat:ydm7bdudine7de5zdkcereezy4

A stitch in time: narrative review of interventions to reduce preterm births in Malawi

2019 International Health  
The rising rate of preterm births (PTBs) is a global concern, and Malawi has a high rate of PTBs (10.5%).  ...  health of girls and women as well as focus on improving the delivery of antenatal services in the community.  ...  despite the evidence of causality. 54, 55 Antenatal treatment of specific infections in early pregnancy with appropriate antibiotics may reduce the chemical trigger for preterm labour 42, 56 to modify  ... 
doi:10.1093/inthealth/ihz101 pmid:31867622 pmcid:PMC7320425 fatcat:vesarlhkqjftrf3lslw5zbexe4

ChemDIS: a chemical–disease inference system based on chemical–protein interactions

Chun-Wei Tung
2015 Journal of Cheminformatics  
The chemical-protein interactions from a large database STITCH and protein-disease relationship from disease ontology and disease ontology lite were utilized for chemical-protein-disease inferences.  ...  However, we lack the toxicological data for a large portion of chemicals due to the high cost of experiments for a huge number of chemicals.  ...  Compliance with ethical guidelines  ... 
doi:10.1186/s13321-015-0077-3 pmid:26078786 pmcid:PMC4466364 fatcat:yjgrrmhskrefnnyuklgmnybytq

OnTheFly 2.0: A tool for automatic annotation of files and biological information extraction

Evangelos Pafilis, Georgios A. Pavlopoulos, Venkata P. Satagopam, Nikolas Papanikolaou, Heiko Horn, Christos Arvanitidis, Lars Juhl Jensen, Reinhard Schneider, Ioannis Iliopoulos
2013 13th IEEE International Conference on BioInformatics and BioEngineering  
With a simple drag-and-drop motion, the text of a document is extensively parsed for bioentities such as protein/gene names and chemical compound names.  ...  Utilizing high quality data integration platforms, OnTheFly allows the generation of informative summaries, interaction networks and at-a-glance popup windows containing knowledge related to the bioentities  ...  Network option: a protein-protein, protein-chemical or chemical-chemical interaction network is generated according to the information available in the STITCH [16] database.  ... 
doi:10.1109/bibe.2013.6701679 dblp:conf/bibe/PafilisPSPHAJ0I13 fatcat:g6ygv23dkjc5bpqjb433lku2sa

ChemProt-2.0: visual navigation in a disease chemical biology database

Sonny Kim Kjærulff, Louis Wich, Jens Kringelum, Ulrik P. Jacobsen, Irene Kouskoumvekaki, Karine Audouze, Ole Lund, Søren Brunak, Tudor I. Oprea, Olivier Taboureau
2012 Nucleic Acids Research  
ChemProt-2.0 (http://www.cbs.dtu.dk/services/ ChemProt-2.0) is a public available compilation of multiple chemical-protein annotation resources integrated with diseases and clinical outcomes information  ...  Each protein is linked to quality-scored human protein-protein interactions data based on more than half a million interactions, for studying diseases and biological outcomes (diseases, pathways and GO  ...  Compared with other approaches, ChemProt-1.0 offered a high level of integration of chemical and biological data, including internally curated disease-associated proteinprotein interactions (PPIs) (15  ... 
doi:10.1093/nar/gks1166 pmid:23185041 pmcid:PMC3531079 fatcat:gqa6fa2r3naqxlfaumbym2q664

ChemDIS 2: an update of chemical-disease inference system

Chun-Wei Tung, Shan-Shan Wang
2018 Database: The Journal of Biological Databases and Curation  
Previously, we have developed a ChemDIS system utilizing information of interacting targets for chemical-disease inference.  ...  analysis function for joint analysis of multi-omics data; (iii) mixture analysis function for the identification of interaction and overall effects; (iv) web application programming interface (API) for  ...  Instead of relying on chemical-protein interaction data from STITCH database, the custom analysis function accepts user inputs of a custom set of differentially expressed genes, proteins, miRNAs or metabolites  ... 
doi:10.1093/database/bay077 pmid:30053236 pmcid:PMC6057493 fatcat:bbd2b7jhprb3fmijjr7hri2vbi

ChemProt [chapter]

Olivier Taboureau, Tudor Oprea
2013 Computational Chemogenomics  
We gathered over 2-million chemical-protein interactions, which were integrated in a quality scored human PPI network of 428 429 interactions.  ...  There is a critical need to develop network-based approaches to integrate the growing body of chemical biology knowledge with network biology.  ...  However, several other proteins are retrieved from CTD and STITCH based on association data with this chemical.  ... 
doi:10.1201/b15631-8 fatcat:nx2zmj2kgndezjbpjr6fdubzxy

ChemProt: a disease chemical biology database

O. Taboureau, S. K. Nielsen, K. Audouze, N. Weinhold, D. Edsgard, F. S. Roque, I. Kouskoumvekaki, A. Bora, R. Curpan, T. S. Jensen, S. Brunak, T. I. Oprea
2010 Nucleic Acids Research  
We gathered over 2-million chemical-protein interactions, which were integrated in a quality scored human PPI network of 428 429 interactions.  ...  There is a critical need to develop network-based approaches to integrate the growing body of chemical biology knowledge with network biology.  ...  However, several other proteins are retrieved from CTD and STITCH based on association data with this chemical.  ... 
doi:10.1093/nar/gkq906 pmid:20935044 pmcid:PMC3013776 fatcat:onpzqrlqajdndlyaryk3ll7azq

GPCRs, G-proteins, effectors and their interactions: human-gpDB, a database employing visualization tools and data integration techniques

V. P. Satagopam, M. C. Theodoropoulou, C. K. Stampolakis, G. A. Pavlopoulos, N. C. Papandreou, P. G. Bagos, R. Schneider, S. J. Hamodrakas
2010 Database: The Journal of Biological Databases and Curation  
Acknowledgements The authors thank the reviewers of this article for their useful criticism. M.C.T. collected the data, V.P.S. developed the web application and data integration, G.A.P.  ...  Conflict of interest. None declared.  ...  Together with the variety of information that STITCH database holds, this is the main reason why this tool was selected to provide to the user the relevant protein-protein and protein-chemical interaction  ... 
doi:10.1093/database/baq019 pmid:20689020 pmcid:PMC2931634 fatcat:xz6tridda5fwdipuivdwjutmsu
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