Filters








7 Hits in 2.0 sec

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
<span title="">2007</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
to calculate an integrated score for each protein pair predicted by the four genomic context based methods.  ...  Conclusion: This study evaluated the PPI prediction by four genomic context based methods, and presents an integrated evaluation method that shows better performance in E. coli.  ...  Acknowledgements We thank Jill Opalesky and Emily Mitchell for critically reading the manuscript and three anonymous reviewers for valuable comments.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-8-414">doi:10.1186/1471-2105-8-414</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17963500">pmid:17963500</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2238723/">pmcid:PMC2238723</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zni4kfmycndmbek5ep6vaow7ra">fatcat:zni4kfmycndmbek5ep6vaow7ra</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190427121311/https://scholarscompass.vcu.edu/cgi/viewcontent.cgi?article=1007&amp;context=psych_pubs" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/db/de/dbde06f0f0fe3a1d5678fcea2082b2dd95a675db.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-8-414"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238723" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Protein-Protein Interaction Detection: Methods and Analysis

V. Srinivasa Rao, K. Srinivas, G. N. Sujini, G. N. Sunand Kumar
<span title="">2014</span> <i title="Hindawi Limited"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/uzojk7p2kbhxnhqrrphigusdpm" style="color: black;">International Journal of Proteomics</a> </i> &nbsp;
Protein-protein interaction plays key role in predicting the protein function of target protein and drug ability of molecules.  ...  Recent developments have also led to the construction of networks having all the protein-protein interactions using computational methods for signaling pathways and protein complex identification in specific  ...  Acknowledgment The authors wish to thank the University Grants Commission (UGC) for extending financial support for this study.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2014/147648">doi:10.1155/2014/147648</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24693427">pmid:24693427</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3947875/">pmcid:PMC3947875</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/q3lzrbo25jexln6wkta4uwsmzi">fatcat:q3lzrbo25jexln6wkta4uwsmzi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190224145609/http://pdfs.semanticscholar.org/5997/71e06e3cc957cd1cae90e2e40d049de8c581.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/59/97/599771e06e3cc957cd1cae90e2e40d049de8c581.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2014/147648"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> hindawi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3947875" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Genome-wide prediction of prokaryotic two-component system networks using a sequence-based meta-predictor

Altan Kara, Martin Vickers, Martin Swain, David E. Whitworth, Narcis Fernandez-Fuentes
<span title="2015-09-18">2015</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Conclusion: We have developed MetaPred2CS, a support vector machine-based metapredictor for prokaryotic TCS protein pairings.  ...  MetaPred2CS integrates six sequence-based prediction methods: in-silico two-hybrid, mirror-tree, gene fusion, phylogenetic profiling, gene neighbourhood, and gene operon.  ...  We also thank all the authors of the methods and data used in this work for making them freely available to the scientific community.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-015-0741-7">doi:10.1186/s12859-015-0741-7</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26384938">pmid:26384938</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4575426/">pmcid:PMC4575426</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rwxdu52irjggbkesdkhr6zxzru">fatcat:rwxdu52irjggbkesdkhr6zxzru</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171001004218/https://core.ac.uk/download/pdf/30717575.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/68/a7/68a7662954c649b51cf7a72b5b456ce920c8e50c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-015-0741-7"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4575426" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Bioinformatics: A Way Forward to Explore "Plant Omics" [chapter]

Mehboob-ur Rahman, Tayyaba Shaheen, Mahmood-ur Rahman, Muhammad Atif Iqbal, Yusuf Zafar
<span title="2016-07-27">2016</span> <i title="InTech"> Bioinformatics - Updated Features and Applications </i> &nbsp;
Synergism of "plant omics" and bioinformatics set a firm foundation for deducing ancestral karyotype of multiple plant families, predicting genes, etc.  ...  This science has progressed parallel to the evolution of genome-sequencing tools, for example, the next-generation sequencing technologies, that resulted in arranging and analyzing the genome-sequencing  ...  InPrePPI InPrePPI predicts protein interactions in prokaryotes based on genomic context http://inpreppi.biosino.org/InPrePPI/ index.jsp 11.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5772/64043">doi:10.5772/64043</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/w3cwexdezvf27e5adz3gfos4v4">fatcat:w3cwexdezvf27e5adz3gfos4v4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190426215717/https://cdn.intechopen.com/pdfs/51698.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/87/e2/87e2b6dce37c000d51ee9cf21c7492320ee4ca17.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5772/64043"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Prediction of Protein–Protein Interactions by Evidence Combining Methods

Ji-Wei Chang, Yan-Qing Zhou, Muhammad Ul Qamar, Ling-Ling Chen, Yu-Duan Ding
<span title="2016-11-22">2016</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/3loumxx7kzamnlu4h6x3xoz6ay" style="color: black;">International Journal of Molecular Sciences</a> </i> &nbsp;
Most cellular functions involve proteins' features based on their physical interactions with other partner proteins.  ...  These methods are developed for integration of multi-dimensional evidence, for designing the strategies to predict novel interactions, and for making the results consistent with the increase of prediction  ...  Case 2: InPrePPI (an integrated evaluation method based on genomic context for predicting proteinprotein interactions in prokaryotic genomes) [21] uses AC value (an integrated value of the accuracy  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/ijms17111946">doi:10.3390/ijms17111946</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27879651">pmid:27879651</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5133940/">pmcid:PMC5133940</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kttovj6jsnhhhenyjmksj6wffa">fatcat:kttovj6jsnhhhenyjmksj6wffa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180728004106/https://res.mdpi.com/def502000d89c11c8119ece3cc507fefd63c4a1e9307cb59d2d83c613a069fc1884b5818f6f4f132a59794b5cf19dc3a589d9de7571f2929a79fdb3d98e638cbd3b0d2812446475dc9e7f6a6f939fa187a6f842d682b99b8058327462a5f21711de4478ad051a67d31b0a71641c704f99e14d055bd74f41100b0cd209062c457368021eb4603cc?filename=&amp;attachment=1" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/70/d5/70d5e21cf8d6edfdca13777b0bcb45a90f565391.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/ijms17111946"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5133940" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Genome-wide protein-protein interactions and protein function exploration in cyanobacteria

Qi Lv, Weimin Ma, Hui Liu, Jiang Li, Huan Wang, Fang Lu, Chen Zhao, Tieliu Shi
<span title="2015-10-22">2015</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tnqhc2x2aneavcd3gx5h7mswhm" style="color: black;">Scientific Reports</a> </i> &nbsp;
Here, we effectively explored protein functions and the biological mechanism based on inferred high confident protein-protein interaction (PPI) network in cyanobacteria.  ...  We integrated data from seven different sources and predicted 1,997 PPIs, which were evaluated by experiments in molecular mechanism, text mining of literatures in proved direct/indirect evidences, and  ...  The genome context methods (gene fusion, gene neighborhood, phylogenetic profile and gene cluster) were analyzed by InPrePPI 28 .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/srep15519">doi:10.1038/srep15519</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26490033">pmid:26490033</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4614683/">pmcid:PMC4614683</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tuqftmwe5fb4rlecwdr7uywgtm">fatcat:tuqftmwe5fb4rlecwdr7uywgtm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190304060251/http://pdfs.semanticscholar.org/c1ec/d58386b5389acabccad6e432b303855fc9cb.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c1/ec/c1ecd58386b5389acabccad6e432b303855fc9cb.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/srep15519"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4614683" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Approaches for network based drug discovery

<span title="2021-06-30">2021</span> <i title="Bioscience Research Institute Pte. Ltd."> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tmyaeuy3n5e35p5rehim2siiua" style="color: black;">Frontiers in bioscience (Scholar edition)</a> </i> &nbsp;
Molecular network-based studies have gained tremendous importance in biomedical research.  ...  In the present scenario, an enormous amount of molecular network databases are available which can be accessed freely by the public. This is the central focus of this article.  ...  InPrePPI It is based on genomic content for predicting PPIs especially in prokaryotes. 4 TSEMA It predicts the interaction between two protein families. 5 G-NEST It uses chromosomal closeness/gene neighborhood  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.52586/s551">doi:10.52586/s551</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/34256528">pmid:34256528</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/g4qb44catbfwddkq7436zvgn54">fatcat:g4qb44catbfwddkq7436zvgn54</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210716090759/https://www.fbscience.com/Scholar/articles/pdf/Scholar551.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ef/50/ef50f26201b4ea3622e3762a50b4e1d3111d9b49.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.52586/s551"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>