Filters








69 Hits in 2.7 sec

The Negatome database: a reference set of non-interacting protein pairs

Pawel Smialowski, Philipp Pagel, Philip Wong, Barbara Brauner, Irmtraud Dunger, Gisela Fobo, Goar Frishman, Corinna Montrone, Thomas Rattei, Dmitrij Frishman, Andreas Ruepp
<span title="2009-11-17">2009</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
The Negatome is a collection of protein and domain pairs that are unlikely to be engaged in direct physical interactions.  ...  The database currently contains experimentally supported non-interacting protein pairs derived from two distinct sources: by manual curation of literature and by analyzing protein complexes with known  ...  Our time-course analysis of the Negatome and IntAct databases suggests that in spite of a growing fraction of contradicting pairs between both sets, the absolute number of non-interacting pairs in our  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkp1026">doi:10.1093/nar/gkp1026</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19920129">pmid:19920129</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2808923/">pmcid:PMC2808923</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zixan3uerzgwbiav2kfctz7xva">fatcat:zixan3uerzgwbiav2kfctz7xva</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180420034609/https://fedora.phaidra.univie.ac.at/fedora/get/o:244191/bdef:Content/download" 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/7e/ba/7ebacfc6c8ee7dcce0e5a21150c3ee8ddf8f607d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkp1026"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808923" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Negatome 2.0: a database of non-interacting proteins derived by literature mining, manual annotation and protein structure analysis

Philipp Blohm, Goar Frishman, Pawel Smialowski, Florian Goebels, Benedikt Wachinger, Andreas Ruepp, Dmitrij Frishman
<span title="2013-11-08">2013</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
We present the second version of Negatome, a database of proteins and protein domains that are unlikely to engage in physical interactions (available online at http://mips.helmholtz-muenchen.de/proj/ ppi  ...  Knowledge about non-interacting proteins (NIPs) is important for training the algorithms to predict protein-protein interactions (PPIs) and for assessing the false positive rates of PPI detection efforts  ...  To increase the precision of the analysis PAS were restricted to a narrower set of verbs specifically referring to interactions or binding (e.g.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkt1079">doi:10.1093/nar/gkt1079</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24214996">pmid:24214996</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3965096/">pmcid:PMC3965096</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/n4psp35bkfacppp5jfv3tkqgty">fatcat:n4psp35bkfacppp5jfv3tkqgty</a> </span>
<a target="_blank" rel="noopener" href="https://archive.org/download/pubmed-PMC3965096/PMC3965096-gkt1079.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> File Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f0/d3/f0d3164f7aeb581a391f3a2e8152a99ea4952b5c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkt1079"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965096" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

DIMA 3.0: Domain Interaction Map

Q. Luo, P. Pagel, B. Vilne, D. Frishman
<span title="2010-11-19">2010</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
Additionally predictions are filtered to exclude those domain pairs that are reported as non-interacting by the Negatome database.  ...  Domain Interaction MAp (DIMA, available at http:// webclu.bio.wzw.tum.de/dima) is a database of predicted and known interactions between protein domains.  ...  ACKNOWLEDGEMENTS The authors wish to thank Thomas Rattei, Patrick Tischler and Roland Arnold for their help with the SIMAP resource and Xing-Ming Zhao for assisting us with the DIPD approach.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkq1200">doi:10.1093/nar/gkq1200</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21097782">pmid:21097782</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3013740/">pmcid:PMC3013740</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5cs6hxryyfgipdlfneanw6b3qa">fatcat:5cs6hxryyfgipdlfneanw6b3qa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190303154826/http://pdfs.semanticscholar.org/b7fe/bf5b57eee4db49f72dc26d22522b6a00f49a.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/b7/fe/b7febf5b57eee4db49f72dc26d22522b6a00f49a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkq1200"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013740" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

KUPS: constructing datasets of interacting and non-interacting protein pairs with associated attributions

X.-w. Chen, J. C. Jeong, P. Dermyer
<span title="2010-10-15">2010</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
users to construct ready-to-use data sets of interacting protein pairs (IPPs), non-interacting protein pairs (NIPs) and associated features.  ...  KUPS (The University of Kansas Proteomics Service) provides high-quality protein-protein interaction (PPI) data for researchers developing and evaluating computational models for predicting PPIs by allowing  ...  Conflict of interest statement. None declared.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkq943">doi:10.1093/nar/gkq943</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20952400">pmid:20952400</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3013794/">pmcid:PMC3013794</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/yjsdiwxqrrc6jbpgzcyb4afjzi">fatcat:yjsdiwxqrrc6jbpgzcyb4afjzi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180730015950/https://watermark.silverchair.com/gkq943.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAaowggGmBgkqhkiG9w0BBwagggGXMIIBkwIBADCCAYwGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMZ_hfnOYfqYfJ4V8WAgEQgIIBXS68ICUL3ey2sVih52FjiEvBhduFt8I6M0WUOd49XrU2508rS0o2ROyUMogoBeaZRspau82fJ1G4oqw2eCY0ca_7t-85OKAei5uf_idv4ILa4uLCoqkljAm9XboCBYgH-wJDWPFYc89zxHFlJVQsZhOqOdRg_5WCzNSh8qTCpuyhToxOvRabCtPm7mFNx5MlErmzl9SWbrFN0AWzd1ALADYpEi9phLrejvEDdZ7sQxaMzsXzIzuZxvoF2NoTqumdpg_6FTzG_xhhhHw27x-XTQrQSErIx-NwRj1HuuDVqLBXKK3s3PYRj_XcA9v055AmDXR-1qQ7twREhpnGyjUuBffQ3XDdZgWedfeNFkuUU8KmHerjIwab8dtQlcJ5C4VNwee7fHqO-cvdoYY3v0sLQNQtneZybWXxjg6bTDe_UrOlAHJCKU1DEtA2d9toFKiMFw4JPo78jwXGXwiTbi0" 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/d1/95/d195ac367ec0105c896c89d748efd3a9cba53236.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkq943"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013794" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study

J. M. Villaveces, R. C. Jimenez, P. Porras, N. del-Toro, M. Duesbury, M. Dumousseau, S. Orchard, H. Choi, P. Ping, N. C. Zong, M. Askenazi, B. H. Habermann (+1 others)
<span title="2015-02-04">2015</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ejkvir3kzbdojf5kygupkidsca" style="color: black;">Database: The Journal of Biological Databases and Curation</a> </i> &nbsp;
Experimental data is captured in multiple repositories, but there is no simple way to assess the evidence of an interaction occurring in a cellular environment.  ...  Merging and scoring of data are commonly required operations after querying for the details of specific molecular interactions, to remove redundancy and assess the strength of accompanying experimental  ...  Merging is performed by matching interacting molecule pairs using a predefined set of database identifiers and cross references.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/bau131">doi:10.1093/database/bau131</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25652942">pmid:25652942</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4316181/">pmcid:PMC4316181</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/n2oauiczgjgqtlgpkv6tuopexm">fatcat:n2oauiczgjgqtlgpkv6tuopexm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190308212136/http://pdfs.semanticscholar.org/eec3/3d57e6346e3c33dde5a04fcde6a8d0303d01.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/ee/c3/eec33d57e6346e3c33dde5a04fcde6a8d0303d01.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/bau131"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4316181" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

UniProt-Related Documents (UniReD): assisting wet lab biologists in their quest on finding novel counterparts in a protein network

Theodosios Theodosiou, Nikolaos Papanikolaou, Maria Savvaki, Giulia Bonetto, Stella Maxouri, Eirini Fakoureli, Aristides G Eliopoulos, Nektarios Tavernarakis, Grigoris D Amoutzias, Georgios A Pavlopoulos, Michalis Aivaliotis, Vasiliki Nikoletopoulou (+3 others)
<span title="2020-02-11">2020</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dhm4lwu4tvbf5dklpg7zonzosa" style="color: black;">NAR Genomics and Bioinformatics</a> </i> &nbsp;
The in-depth study of proteinprotein interactions (PPIs) is of key importance for understanding how cells operate.  ...  As a proof of concept, we demonstrate its usefulness by experimentally validating six predicted interactions and by benchmarking it against public databases of experimentally validated PPIs succeeding  ...  We also thank several experimental biologists from the University of Crete, Massachusetts Institute of Technology and Icahn School of Medicine at Mount Sinai (NY) for testing UniReD and providing us with  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nargab/lqaa005">doi:10.1093/nargab/lqaa005</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33575553">pmid:33575553</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7671407/">pmcid:PMC7671407</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kyojpa7jkvcobpwiqlasfgqcau">fatcat:kyojpa7jkvcobpwiqlasfgqcau</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200722235341/https://watermark.silverchair.com/lqaa005.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAq4wggKqBgkqhkiG9w0BBwagggKbMIIClwIBADCCApAGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMQ4G7IIYI6YDy5yKYAgEQgIICYT-tIyuhOlzZfgtzP5_N5VwiHyCN5oElAYWbpKw5_XMsKQ5M_K0TeCeDQf0QEa6hLzOe43v6_kFzCLSVIrLRapkz_n0DaSAFWj-4-7aS5UwjUknhWJssxPrTRY1007Gmcv-2V90Xbh48Sa1P2wQgbbFWu8yFPWCqAYgYuANt8hAcAjMS2CWdKXCrxxQYjZkTpRGoafyLmbs8JnTX6_ph4IcN5NiTA5mUCrMyCFxrUbXOnPClMM7EiXo6yJzc101yTZVvObTYv8bZLNQGoIZn0oradlNe7YZwXC3Gweg9nRuURDJ0b28qQuV-1wsxW4I-eftRDDH2UkmvAH0llZB9D4FpZi8Qu5NkQ_yRdzcye5My4x88y5Z8Kbdxay673wxHs4vyNOkRYKI6-wIyD7Vgd3WIF26Jli-I6_OD9O8cIlxmClRAblbMkWXgHEuzV8V6ek-leIanBnSDYZolXTS7Ur7kHtlycP3icfp1gq5zVutPj_thzMPkWlaxujdGGgavXtOKySHfajt2ga1XghooZyyXYmLRTQYvhoA2tzjLRKclfD-u1mdNkHc_GfAmAtN9kA1Ae4VqCjePiy_ufjGXahXSE1okQF0qI2YU4sKM27ukbllPW0A7E5SwWwwa7gNpfYY06GKqJVoWDXCcZ0Ci3Fl0_VIIT7TiHyXp84SJ5GJZ7RVovk12j1pyRt1xdMvrIYcr60p5E1ZUKZkf1WGuRnK7JDxeMftplIlXg_upduwHhJGhZ7-HhxefWapIZkVdCja4af1zxV-wNuFlbsXVP9VdDvJ6CteXsIeZ09mROEkIMQ" 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/3b/e4/3be4cdf112dc13c1a2a52cbe55cbfad7359648f2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nargab/lqaa005"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7671407" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

INBIA: a boosting methodology for proteomic network inference

Davide S. Sardina, Giovanni Micale, Alfredo Ferro, Alfredo Pulvirenti, Rosalba Giugno
<span title="">2018</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
The first, Negatome, takes into account likely non-interacting proteins by combining both structure properties and literature mining.  ...  The Pan-cancer proteomic project, in The Cancer Genome Atlas, collects protein expressions in human cancers and it is a reference resource for the functional study of cancers.  ...  We decided to focus only on non-induced motifs because the number of non-induced occurrences of a motif is less sensitive to the presence of false positive interactions in a network, so the non-induced  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-018-2183-5">doi:10.1186/s12859-018-2183-5</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30066650">pmid:30066650</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6069689/">pmcid:PMC6069689</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/slcdeza2pjfpdl7znbcdeemy4q">fatcat:slcdeza2pjfpdl7znbcdeemy4q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190427003643/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2183-5" 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/47/42/4742b38b3a1631a2088e977cfd89e4a6061158c3.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-018-2183-5"> <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/PMC6069689" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

AutoCoEv—A High-Throughput In Silico Pipeline for Predicting Inter-Protein Coevolution

Petar B. Petrov, Luqman O. Awoniyi, Vid Šuštar, M. Özge Balci, Pieta K. Mattila
<span title="2022-03-20">2022</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;
However, an evolutionary analysis of large arrays of proteins in silico is a highly time-consuming effort that has limited the usage of this method for protein pairs or small protein groups.  ...  Here, we developed AutoCoEv, a user-friendly, open source, computational pipeline for the search of coevolution between a large number of proteins.  ...  The authors would like to thank Martti Tolvanen for discussions on the theoretical basis of the analysis, Akseli Mantila for help with the C++ code of CAPS2, and Dian Dimitrov for advising on mathematics  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/ijms23063351">doi:10.3390/ijms23063351</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/35328772">pmid:35328772</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8952222/">pmcid:PMC8952222</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jwjd42rx2fblrpsb22wolf5adq">fatcat:jwjd42rx2fblrpsb22wolf5adq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220620210039/https://mdpi-res.com/d_attachment/ijms/ijms-23-03351/article_deploy/ijms-23-03351.pdf?version=1647769047" 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/37/b2/37b2e3a79210fd1d161f4ee015c7ed3c610e1849.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/ijms23063351"> <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/PMC8952222" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Large-scale extraction of gene interactions from full-text literature using DeepDive

Emily K. Mallory, Ce Zhang, Christopher Ré, Russ B. Altman
<span title="2015-09-03">2015</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
We evaluated this system against the Database of Interacting Proteins and against randomly curated extractions.  ...  These gene-gene interactions include both proteinprotein interactions and transcription factor interactions. The majority of known interactions are found in the biomedical literature.  ...  Conflict of Interest: none declared.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btv476">doi:10.1093/bioinformatics/btv476</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26338771">pmid:26338771</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4681986/">pmcid:PMC4681986</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/oe33airyhvbxroebiwm2mnbon4">fatcat:oe33airyhvbxroebiwm2mnbon4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200209201531/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC4681986&amp;blobtype=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/47/55/47557161b9fd8a5208509fc63b91719b034e3d3b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btv476"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4681986" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A yeast BiFC-seq method for genome-wide interactome mapping [article]

Limin Shang, Yaohui Zhang, Yuchen Liu, Chaozhi Jin, Yanzhi Yuan, Chunyan Tian, Ming Ni, Xiaochen Bo, Li Zhang, Dong Li, Fuchu He, Jian Wang
<span title="2020-06-17">2020</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Two-thirds (9/13) of known interactions of EBOV were recaptured and five novel interactions were discovered. Next, we used BiFC-seq method to map the interactome of the tumor protein p53.  ...  Genome-wide physical protein-protein interaction (PPI) mapping remains a major challenge for current technologies.  ...  Towards a proteome-scale map of the human protein-protein interaction network. Negatome database: a reference set of non-interacting protein pairs.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.06.16.154146">doi:10.1101/2020.06.16.154146</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/j35vfqpsmvhd5nud6xeybtqbei">fatcat:j35vfqpsmvhd5nud6xeybtqbei</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201108135146/https://www.biorxiv.org/content/biorxiv/early/2020/06/17/2020.06.16.154146.full.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/cc/80/cc803308303fe06b9700af6bc827aa4995818359.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.06.16.154146"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

A Sequence-Based Mesh Classifier for the Prediction of Protein-Protein Interactions [article]

Edgar D. Coelho, Igor N. Cruz, André Santiago, José Luis Oliveira, António Dourado, Joel P. Arrais
<span title="2017-11-12">2017</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
The study of Protein-Protein Interactions (PPIs) has been a cornerstone in the clarification of complex physiological and pathogenic processes, thus being a priority for the identification of vital components  ...  Despite the advances of laboratorial techniques, computational models allow the screening of protein interactions between entire proteomes in a fast and inexpensive manner.  ...  Acknowledgments The work leading to these results has received funding from the European Union Sev  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1711.04294v1">arXiv:1711.04294v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/b6te7qq3jzegfpoyon4monn4sa">fatcat:b6te7qq3jzegfpoyon4monn4sa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191026181005/https://arxiv.org/pdf/1711.04294v1.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/fb/4a/fb4a5e50583f549c9777f2c29618c1b18b820d1c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1711.04294v1" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

Prediction of host - pathogen protein interactions between Mycobacterium tuberculosis and Homo sapiens using sequence motifs

Tong Huo, Wei Liu, Yu Guo, Cheng Yang, Jianping Lin, Zihe Rao
<span title="2015-03-26">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;
Finally, a web accessible database named PATH (Protein interactions of M. tuberculosis and Human) was constructed to store these predicted interactions and proteins.  ...  A biological interaction network between M. tuberculosis and Homo sapiens was then constructed using the predicted inter-and intra-species interactions based on the 118 pairs of HPIs.  ...  Acknowledgements We would like to thank staff members of TJAB for their technical support.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-015-0535-y">doi:10.1186/s12859-015-0535-y</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25887594">pmid:25887594</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4456996/">pmcid:PMC4456996</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ktwa4aoceza7nfojdii4qyk63m">fatcat:ktwa4aoceza7nfojdii4qyk63m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170830114650/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-015-0535-y?site=http://bmcbioinformatics.biomedcentral.com" 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/e6/00/e6005cb9a9c6c332a3a117aaabb4314880f78504.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-015-0535-y"> <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/PMC4456996" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Modeling of negative protein-protein interactions: methods and experiments [article]

Andrea Moscatelli
<span title="2019-10-10">2019</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
These systems have to face two main problems: the high incompleteness of the human interactome and the lack of high-quality negative protein-protein interactions (i.e. proteins that are known to not interact  ...  Protein-protein interactions (PPIs) are of fundamental importance for the human body, and the knowledge of their existence can facilitate very important tasks like drug target developing and therapy design  ...  Negatome 2.0 One of the few negative datasets that have been generated is the Negatome 2.0 [7] , which is a database of proteins and protein domains that are unlikely to engage in physical interactions  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1910.04709v1">arXiv:1910.04709v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rqqcz5qmivdkhnj2tamsh2vrzm">fatcat:rqqcz5qmivdkhnj2tamsh2vrzm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200906214214/https://arxiv.org/pdf/1910.04709v1.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/ae/96/ae963677263c08eeec904061854b57d7194ff3bd.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1910.04709v1" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins

Pablo Minguez, Ivica Letunic, Luca Parca, Luz Garcia-Alonso, Joaquin Dopazo, Jaime Huerta-Cepas, Peer Bork
<span title="2014-10-31">2014</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
Several databases focus on the prediction and compilation of protein-protein interactions (PPIs) and no less on the collection and analysis of protein posttranslational modifications (PTMs), however, there  ...  We developed several methods based on residue co-evolution and proximity to predict the functional associations of pairs of PTMs that we apply to modifications in the same protein and between two interacting  ...  from pairs of PTMs placed on experimentally proved non-interacting proteins extracted from the Negatome database (49).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gku1081">doi:10.1093/nar/gku1081</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25361965">pmid:25361965</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4383916/">pmcid:PMC4383916</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/43c5ecunjrb5lnztwjyqeqcglm">fatcat:43c5ecunjrb5lnztwjyqeqcglm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190222230820/http://pdfs.semanticscholar.org/3e11/77598c76675b83b23b932f5e080cd7c342d0.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/3e/11/3e1177598c76675b83b23b932f5e080cd7c342d0.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gku1081"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383916" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

HAPPI-2: a Comprehensive and High-quality Map of Human Annotated and Predicted Protein Interactions

Jake Y. Chen, Ragini Pandey, Thanh M. Nguyen
<span title="2017-02-17">2017</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4srzxifvfrdlhjhg3dimznkp7m" style="color: black;">BMC Genomics</a> </i> &nbsp;
Results: The database of Human Annotated and Predicted Protein Interactions (HAPPI) version 2.0 is a major update to the original HAPPI 1.0 database.  ...  Compared with the HAPPI 1.0 database release, HAPPI database version 2.0 (HAPPI-2) represents a 485% of human PPI data coverage increase and a 73% protein coverage increase.  ...  RP integrated the data sets from various data sources, designed and implemented the database schema, developed the web site application, and drafted the manuscript under the supervision of JYC.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12864-017-3512-1">doi:10.1186/s12864-017-3512-1</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28212602">pmid:28212602</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5314692/">pmcid:PMC5314692</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5vv4bc7w7jeebgmp2pm7qgyguy">fatcat:5vv4bc7w7jeebgmp2pm7qgyguy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180722050031/https://scholarworks.iupui.edu/bitstream/handle/1805/13321/12864_2017_Article_3512.pdf;jsessionid=8BADD4708721452C0076DA8370E68044?sequence=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/dc/14/dc14ebf7984cb0d5c7603437d9dfdac176de2e11.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12864-017-3512-1"> <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/PMC5314692" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
&laquo; Previous Showing results 1 &mdash; 15 out of 69 results