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STRING 7--recent developments in the integration and prediction of protein interactions

C. von Mering, L. J. Jensen, M. Kuhn, S. Chaffron, T. Doerks, B. Kruger, B. Snel, P. Bork
2007 Nucleic Acids Research  
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

C Von Mering, L J Jensen, M Kuhn, S Chaffron, T Doerks, B Krüger, B Snel, P Bork
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

Pilhwa Lee, Charles W. Wolgemuth, Andrew D. McCulloch
2011 PLoS Computational Biology  
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

Xiaoyu Jiang, Naoki Nariai, Martin Steffen, Simon Kasif, David Gold, Eric D. Kolaczyk
2008 2008 IEEE International Conference on Bioinformatics and Biomedicine  
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

Feristah Dalkilic, Zerrin Isik
2021 IEEE Access  
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

Jingchun Sun, Yan Sun, Guohui Ding, Qi Liu, Chuan Wang, Youyu He, Tieliu Shi, Yixue Li, Zhongming Zhao
2007 BMC Bioinformatics  
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

Damian Szklarczyk, John H Morris, Helen Cook, Michael Kuhn, Stefan Wyder, Milan Simonovic, Alberto Santos, Nadezhda T Doncheva, Alexander Roth, Peer Bork, Lars J. Jensen, Christian von Mering
2016 Nucleic Acids Research  
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

Rabiatul-Adawiah Zainal-Abidin, Nor Afiqah-Aleng, Muhammad-Redha Abdullah-Zawawi, Sarahani Harun, Zeti-Azura Mohamed-Hussein
2022 Life  
Proteinprotein 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

Rajan Pandey, Pawan Kumar, Dinesh Gupta
2017 Database: The Journal of Biological Databases and Curation  
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

Ivica Letunic, Tobias Doerks, Peer Bork
2014 Nucleic Acids Research  
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

Sangsoo Lim, Yijingxiu Lu, Chang Yun Cho, Inyoung Sung, Jungwoo Kim, Youngkuk Kim, Sungjoon Park, Sun Kim
2021 Computational and Structural Biotechnology Journal  
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]

Linhua Wang, Jeffrey Law, T M N Murali, Gaurav Pandey
2020 bioRxiv   pre-print
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]

Vladimir Gligorijević, Meet Barot, Richard Bonneau
2017 bioRxiv   pre-print
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

Alexander Junge, Jan C. Refsgaard, Christian Garde, Xiaoyong Pan, Alberto Santos, Ferhat Alkan, Christian Anthon, Christian von Mering, Christopher T. Workman, Lars Juhl Jensen, Jan Gorodkin
2017 Database: The Journal of Biological Databases and Curation  
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]

Yinan Lu, Yan Zhao, Xiaoni Liu, Yong Quan
2011 Lecture Notes in Computer Science  
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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