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STRING 7--recent developments in the integration and prediction of protein interactions
2007
Nucleic Acids Research
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The database and online resource STRING generalizes access to protein interaction data, by integrating known and predicted interactions from a variety of sources. ...
As of release 7, STRING has almost doubled to 373 distinct organisms, and contains more than 1.5 million proteins for which associations have been pre-computed. ...
This work was supported in part by grants from the Bundesministerium für Forschung und Bildung, Germany, as well as through the ADIT Integrated Project, contract number LSHB-CT-2005-511065, and through ...
doi:10.1093/nar/gkl825
pmid:17098935
pmcid:PMC1669762
fatcat:tlao5nbbsvbl7i6wngzibx5j3y
STRING 7--recent developments in the integration and prediction of protein interactions
2007
Preserved Fulltext
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The database and online resource STRING generalizes access to protein interaction data, by integrating known and predicted interactions from a variety of sources. ...
The database and online resource STRING generalizes access to protein interaction data, by integrating known and predicted interactions from a variety of sources. ...
This work was supported in part by grants from the Bundesministerium für Forschung und Bildung, Germany, as well as through the ADIT Integrated Project, contract number LSHB-CT-2005-511065, and through ...
doi:10.5167/uzh-34526
fatcat:dybmvjkal5brxih7jkw2wfqa54
Crawling Cells Can Close Wounds without Purse Strings or Signaling
2011
PLoS Computational Biology
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However, wounds made in monolayers of Madin-Darby canine kidney (MDCK) cells still close even when a row of cells is deactivated at the periphery of the wound, and recent experiments show complex, highly-correlated ...
In some cases, such as in wounded embryonic chick wing buds, the movement of the cells is driven by cortical actin contraction (i.e., a purse string mechanism). ...
Cellular sheets lacking adherens junctions should have a reduced viscoelastic timescale, and therefore our model would also predict a more linear advance of the border. A recent paper by Mark et al. ...
doi:10.1371/journal.pcbi.1002007
pmid:21423710
pmcid:PMC3053312
fatcat:rxjgaea3ijf5xjrz4ecynbzc3u
Combining Hierarchical Inference in Ontologies with Heterogeneous Data Sources Improves Gene Function Prediction
2008
2008 IEEE International Conference on Bioinformatics and Biomedicine
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methods, and (ii) propose to use it in conjunction with an integrative protein-protein association network, STRING (Search Tool for the Retrieval of INteracting Genes/proteins), which combines information ...
Results show that our combined use of the proposed computational framework and the protein network from STRING offers substantial improvements in prediction. ...
In contrast, PHIPA integrates the protein interaction data with both the GO hierarchy and protein motif and localization data, and additionally utilizes STRING to encode protein interactions. ...
doi:10.1109/bibm.2008.37
dblp:conf/bibm/JiangNSKGK08
fatcat:ro5u76enmfazfjnf4xeimzbhhe
Compound Target Identification in Tissue-Specific Interaction Networks
2021
IEEE Access
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Recent network-based studies ameliorate the target identification problem by integrating protein-protein interaction (PPI) networks and transcriptome data. ...
Isik et al. developed a drug target prioritization approach by integrating compound induced gene expression signatures with the search tool for the retrieval of interacting genes/proteins (STRING) PPI ...
doi:10.1109/access.2021.3086051
fatcat:pdty2nzxufdfpprq4jnhruu6yq
InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes
2007
BMC Bioinformatics
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Although many genomic features have been used in the prediction of proteinprotein interactions (PPIs), frequently only one is used in a computational method. ...
in STRING. ...
Acknowledgements We thank Jill Opalesky and Emily Mitchell for critically reading the manuscript and three anonymous reviewers for valuable comments. ...
doi:10.1186/1471-2105-8-414
pmid:17963500
pmcid:PMC2238723
fatcat:zni4kfmycndmbek5ep6vaow7ra
The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible
2016
Nucleic Acids Research
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The STRING database aims to collect and integrate this information, by consolidating known and predicted protein-protein association data for a large number of organisms. ...
Apart from collecting and reassessing available experimental data on protein-protein interactions, and importing known pathways and protein complexes from curated databases, interaction predictions are ...
Thomas Rattei (University of Vienna) for producing and sharing systematic, allagainst-all protein-protein similarity data. ...
doi:10.1093/nar/gkw937
pmid:27924014
pmcid:PMC5210637
fatcat:3y6esccgnrc4tbzudtgsowov4a
Protein–Protein Interaction (PPI) Network of Zebrafish Oestrogen Receptors: A Bioinformatics Workflow
2022
Life
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Protein–protein interaction (PPI) is involved in every biological process that occurs within an organism. ...
However, the application of the PPI network in aquaculture is limited as compared to humans and plants. ...
A recently developed database, the Integrated Interactions Database (IID) [45] , focuses on the tissue-specific PPIs that would facilitate the experimental studies in model organisms. ...
doi:10.3390/life12050650
fatcat:djnoah54gvgafg4bl2nepoxqhu
KiPho: malaria parasite kinome and phosphatome portal
2017
Database: The Journal of Biological Databases and Curation
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To develop KiPho, we have made use of search methods to retrieve, consolidate and integrate predicted as well as annotated information from several publically available web repositories. ...
In the current work, we have developed KiPho, a comprehensive and one step web-based information resource for Plasmodium kinases and phosphatases. ...
We used STRING, PlasmoMAP and BioGrid to predict interacting partners for the queried proteins. ...
doi:10.1093/database/bax063
pmid:29220464
pmcid:PMC5737071
fatcat:svl76ahoivd5vescvimp6nzkme
SMART: recent updates, new developments and status in 2015
2014
Nucleic Acids Research
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The underlying protein databases were synchronized with UniProt, Ensembl and STRING, bringing the total number of annotated domains and other protein features above 100 million. ...
Taxonomic tree displays in SMART have been significantly improved, and can be easily navigated using the integrated search engine. ...
EXPANDED BIOLOGICAL PATHWAY AND PROTEIN INTERACTION DATA With the update of the underlying protein databases, we have also synchronized our protein interaction data with the latest version of the STRING ...
doi:10.1093/nar/gku949
pmid:25300481
pmcid:PMC4384020
fatcat:yfkluv6fgvepzl6quev6z26cxq
A Review on Compound-Protein Interaction Prediction Methods: Data, Format, Representation and Model
2021
Computational and Structural Biotechnology Journal
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There has recently been a rapid progress in computational methods for determining protein targets of small molecule drugs, which will be termed as compound protein interaction (CPI). ...
Thus, recent successes in the improved quality of CPI prediction are due to use of both sophisticated computational techniques and higher quality information in the databases. ...
Table 7 Applications of the attention mechanism in CPI methods. a) molecular string, protein string
Study Description Karimi et al. ...
doi:10.1016/j.csbj.2021.03.004
pmid:33841755
pmcid:PMC8008185
fatcat:x3xk3b566vh6ljpeffojtusda4
Data integration through heterogeneous ensembles for protein function prediction
[article]
2020
bioRxiv
pre-print
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Several data integration strategies have been developed to leverage the inherent diversity and complementarity of multi-modal datasets to build comprehensive predictive models about the biomedical processes ...
Through the sample challenging problem of protein function prediction, we demonstrate that EI performs better for this task than some other forms of data integration. ...
We tested EI's effectiveness for the challenging problem of protein function prediction (PFP) 1-3 using diverse networks from the STRING database 29 , and compared its performance with data integration ...
doi:10.1101/2020.05.29.123497
fatcat:ckudl4wd3ncuhhgaszywcyztwy
deepNF: Deep network fusion for protein function prediction
[article]
2017
bioRxiv
pre-print
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We also show substantial improvement in the performance of our method in predicting GO terms of varying type and specificity. ...
We compare the cross-validation and temporal holdout predictive performance of our method with state-of-the-art methods, including the recently proposed method Mashup . ...
We thank Ian Fisk, Nicholas Carriero and Dylan Simon of the Simons Foundation for discussion and help with high performance computing. ...
doi:10.1101/223339
fatcat:fi6mhf6rajh2ble7nxs3fj332e
RAIN: RNA–protein Association and Interaction Networks
2017
Database: The Journal of Biological Databases and Curation
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Here, we present a database of ncRNA-RNA and ncRNA-protein interactions and its integration with the STRING database of protein-protein interactions. ...
We demonstrate that RAIN outperforms the underlying microRNA-target predictions in inferring ncRNA interactions. ...
RAIN is tightly integrated with the STRING database for protein-protein interactions and adds ncRNAs together with their interactions to the existing protein-protein interaction networks in STRING. ...
doi:10.1093/database/baw167
pmid:28077569
pmcid:PMC5225963
fatcat:e4kgyz6nojepjlycmn6sbv5yma
Fuzzy Integral Based Data Fusion for Protein Function Prediction
[chapter]
2011
Lecture Notes in Computer Science
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Data fusion using diverse biological data has been applied to predict the protein function in recent years. ...
In this paper, fuzzy integral fusion based on fuzzy measure is used to integrate the probabilistic outputs of different classifiers. ...
STRING is a database of known and predicted protein interactions of very high quality. For each protein pair, it has an interactive combined score S that ranges from 0 to 1. ...
doi:10.1007/978-3-642-21515-5_68
fatcat:v7jceunesranndcu6lmnb7zyqu
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