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DRNApred, fast sequence-based method that accurately predicts and discriminates DNA- and RNA-binding residues

Jing Yan, Lukasz Kurgan
<span title="2017-01-27">2017</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;
Therefore, we focus on the computational prediction of DNA-and RNA-binding residues from protein chains.  ...  There are two types of sequence-based methods: those that predict DNA-or RNA-binding proteins versus DNA-or RNA-binding residues in protein sequences.  ...  ACKNOWLEDGEMENTS We thank Chen Wang for his contribution to setup the webserver and to perform assessment based on the protein structures.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkx059">doi:10.1093/nar/gkx059</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28132027">pmid:28132027</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5449545/">pmcid:PMC5449545</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/znlsl7jm2jgurjaphsspnduali">fatcat:znlsl7jm2jgurjaphsspnduali</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190222171514/http://pdfs.semanticscholar.org/3aa1/769f73b5639fd90502f18ab535fa8daaa630.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/3a/a1/3aa1769f73b5639fd90502f18ab535fa8daaa630.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkx059"> <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/PMC5449545" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Identification of hub genes in key hallmarks of ovarian cancer via bioinformatics analysis

Rongjia Su, Chengjuan Jin, Chengwen Jin, Menghua Kuang, Jiangdong Xiang
<span title="">2021</span> <i title="AME Publishing Company"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/7qfgvhekxvasbh2mducvro7c4y" style="color: black;">Translational Cancer Research</a> </i> &nbsp;
Hub genes were confirmed to have higher mRNA and protein expression levels in ovarian cancer tissues than in normal tissues through public databases [Gene Expression Profiling Interactive Analysis (GEPIA  ...  We aimed to identify critical hallmarks of the surface epithelium between normal ovaries and serous ovarian carcinomas and then obtain the hub genes associated with these critical hallmarks.  ...  Acknowledgments Funding: The present study was supported by the National Natural Science Foundation of China (No. 81802590 to Jiangdong Xiang).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.21037/tcr-20-2604">doi:10.21037/tcr-20-2604</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/35116413">pmid:35116413</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8797326/">pmcid:PMC8797326</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/weot42rgp5emxamwm6cnaaq6fi">fatcat:weot42rgp5emxamwm6cnaaq6fi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210308025025/https://tcr.amegroups.com/article/download/48396/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/c1/65/c16515400e06698488e1bc98a1a9d755c5bcef2a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.21037/tcr-20-2604"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8797326" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Cooperativity Principles in Self-Assembled Nanomedicine

Yang Li, Yiguang Wang, Gang Huang, Jinming Gao
<span title="2018-04-25">2018</span> <i title="American Chemical Society (ACS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/3jiv5gamdrch7lswaebpzyrjmi" style="color: black;">Chemical Reviews</a> </i> &nbsp;
In this review, we provide a comprehensive analysis of the cooperativity principles in multiple self-assembled nanostructures.  ...  In both natural and synthetic self-assembled nanostructures, molecular cooperativity is emerging as an important hallmark.  ...  Self-Organization of Protein and RNA 2.1.1. Protein Folding.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/acs.chemrev.8b00195">doi:10.1021/acs.chemrev.8b00195</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29693377">pmid:29693377</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6524957/">pmcid:PMC6524957</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/66y4ymzwfvd63j3jvnvln3hyhy">fatcat:66y4ymzwfvd63j3jvnvln3hyhy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200429105942/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC6524957&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/88/41/88413090fd9a4d48963c7c5c05a3717b761302e1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/acs.chemrev.8b00195"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> acs.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6524957" 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 Multi-Layered Study on Harmonic Oscillations in Mammalian Genomics and Proteomics

Nikolai Genov, Stefano Castellana, Felix Scholkmann, Daniele Capocefalo, Mauro Truglio, Jessica Rosati, Elisa Maria Turco, Tommaso Biagini, Annalucia Carbone, Tommaso Mazza, Angela Relógio, Gianluigi Mazzoccoli
<span title="2019-09-17">2019</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;
We found hallmarks of the three oscillating gene subsets, including different (i) functional annotation, (ii) proteomic and electrochemical features, and (iii) transcription factor binding motifs in upstream  ...  Our multifaceted bioinformatics analysis of circadian and ultradian genes suggests that the different rhythmicity of gene expression impacts physiological outcomes and may be related to transcriptional  ...  Hogenesch from the Division of Human Genetics and Immunobiology, Center for Chronobiology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, for critical comments and discussion.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/ijms20184585">doi:10.3390/ijms20184585</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31533246">pmid:31533246</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6770795/">pmcid:PMC6770795</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vkzqa3lyjbd7zpfxhpc4r7stka">fatcat:vkzqa3lyjbd7zpfxhpc4r7stka</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200506204552/https://refubium.fu-berlin.de/bitstream/handle/fub188/26456/2019_Genov_etal.pdf;jsessionid=CBCFAC49664649B1AD2C5E09EF68C7C9?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/53/3a/533a1844fad03d38491a69b5414a95ff4a7eadb5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/ijms20184585"> <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/PMC6770795" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

In silico whole-genome scanning of cancer-associated nonsynonymous SNPs and molecular characterization of a dynein light chain tumour variant

Abdel Aouacheria, Vincent Navratil, Wenyu Wen, Ming Jiang, Dominique Mouchiroud, Christian Gautier, Manolo Gouy, Mingjie Zhang
<span title="2005-05-16">2005</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/3xwigx3kbzej7bhsigycvwxwiq" style="color: black;">Oncogene</a> </i> &nbsp;
Our whole-genome approach provides a comprehensive and unbiased description of nonsynonymous SNPs (nsSNPs) in tumoral versus normal tissues.  ...  Single-nucleotide polymorphisms (SNPs), the most common form of DNA variation in humans, emerge as an invaluable tool for cancer association studies.  ...  Research in MZ's laboratory was supported by grants from the Research Grants Council of Hong Kong. MZ is a Croucher Foundation Senior Research Fellow.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/sj.onc.1208745">doi:10.1038/sj.onc.1208745</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15897869">pmid:15897869</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cpjvbh6jevf3zdvhbifrgauarm">fatcat:cpjvbh6jevf3zdvhbifrgauarm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170811121714/http://bcz102.ust.hk/publications/2005/1208745a.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/52/0f/520fbe130c059fc7e2e8d4c446d9aa34a07610d0.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/sj.onc.1208745"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Correlated Mutations: A Hallmark of Phenotypic Amino Acid Substitutions

Andreas Kowarsch, Angelika Fuchs, Dmitrij Frishman, Philipp Pagel, Thomas Lengauer
<span title="2010-09-16">2010</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ch57atmlprauhhbqdf7x4ytejm" style="color: black;">PLoS Computational Biology</a> </i> &nbsp;
In this work, we put forward the hypothesis that in addition to conservation, co-evolution of residues in a protein influences the likelihood of a residue to be functionally important and thus associated  ...  While the basic idea of a relation between co-evolution and functional sites has been explored before, we have conducted the first systematic and comprehensive analysis of point mutations causing disease  ...  Thanks to Eva Hoffmann for her initial analysis of multiple correlations on which we built and to Jeremias Weihmann for excellent technical help.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1000923">doi:10.1371/journal.pcbi.1000923</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20862353">pmid:20862353</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2940720/">pmcid:PMC2940720</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3zcl5rz3d5fz3hqsiwmkk3hynq">fatcat:3zcl5rz3d5fz3hqsiwmkk3hynq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171015132134/http://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000923&amp;type=printable" 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/10/a5/10a5a4d477b5b463fb3edde0152f29d5192a59b3.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1000923"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2940720" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Macromolecular Modeling with Rosetta

Rhiju Das, David Baker
<span title="">2008</span> <i title="Annual Reviews"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/k4xilfaaarb7ngi345nlojrsmq" style="color: black;">Annual Review of Biochemistry</a> </i> &nbsp;
A unified energetic and kinematic framework in the Rosetta program allows a wide range of molecular modeling problems, from fibril structure prediction to RNA folding to the design of new protein interfaces  ...  Advances over the past few years have begun to enable prediction and design of macromolecular structures at near-atomic accuracy.  ...  ACKNOWLEDGMENT It it impossible for us to adequately thank the many dozens of wonderful scientists who have contributed to the development of the Rosetta macromolecular modeling program.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1146/annurev.biochem.77.062906.171838">doi:10.1146/annurev.biochem.77.062906.171838</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18410248">pmid:18410248</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fohys2g6rngzjpigbhlpgkmyiq">fatcat:fohys2g6rngzjpigbhlpgkmyiq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20090115211432/http://depts.washington.edu/bakerpg/papers/18410248.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/af/ee/afee69afea0fcc8a8efbaf83a42d2272c526bd84.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1146/annurev.biochem.77.062906.171838"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Alterations of the pro-survival Bcl-2 protein interactome in breast cancer at the transcriptional, mutational and structural level [article]

Simon Mathis Konig, Vendela Rissler, Thilde Terkelsen, Matteo Lambrughi, Elena Papaleo
<span title="2019-07-08">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Pro-survival Bcl-2 family members carry out their function by binding the BH3 short linear motif of pro-apoptotic proteins in a modular way, creating a complex network of protein-protein interactions.  ...  We analyzed the changes in expression of the Bcl-2 proteins and their BH3-containing interactors, in breast cancer samples.  ...  These results suggest the importance of: i) hydrophobic residues in binding the amphipathic helix comprising the BH3 motif; ii) propensity to small side chains adjacent to the h2 and h3 hydrophobic residues  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/695379">doi:10.1101/695379</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gfymamkirzfkhkk6bcsuxkzeii">fatcat:gfymamkirzfkhkk6bcsuxkzeii</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200711140822/https://www.biorxiv.org/content/biorxiv/early/2019/07/08/695379.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/27/88/278861fd1c51743435ee6bcc4f33ac993bac6f20.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/695379"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Use of Bioinformatics Tools in Different Spheres of Life Sciences

Muhammad Aamer Mehmood
<span title="">2014</span> <i title="OMICS Publishing Group"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hmrskfm5pbadvccahnbzdxp6gm" style="color: black;">Journal of Data Mining in Genomics &amp; Proteomics</a> </i> &nbsp;
Acknowledgment Authors thank Higher Education Commission (HEC), Pakistan, for funding their research work and apologise to all those colleagues whose work could not be discussed here due to space constraints  ...  For example, signal transduction pathways databases may include protein-protein, protein-DNA, Protein-RNA, DNA-RNA, DNAsubstrate interactions [88] .  ...  [146] HADDOCK Describes the modelling and interaction of bio-molecular complexes such as protein-protein, protein-DNA [83] BIND A database that provides access to molecular interaction and bio-complexes  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4172/2153-0602.1000158">doi:10.4172/2153-0602.1000158</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/m5ziueg3ifaobfnovyguaqlixa">fatcat:m5ziueg3ifaobfnovyguaqlixa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170816105024/https://www.omicsonline.org/open-access/use-of-bioinformatics-tools-in-different-spheres-of-life-sciences-2153-0602-5-158.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/08/6c/086cb4e75ec71d4eb8cc4b114087ae068fb82069.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4172/2153-0602.1000158"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Molecular Structure, Binding Affinity, and Biological Activity in the Epigenome

Balázs Zoltán Zsidó, Csaba Hetényi
<span title="2020-06-10">2020</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;
An emphasis is placed on emerging trends and permanent challenges of new discoveries of SARs in the context of proteins as epigenetic drug targets.  ...  The present review is based on selected methodologies and applications supplying molecular structure, binding affinity and biological activity data for the development of new SARs.  ...  The work was supported by the ÚNKP-19-4 New National Excellence Program of the Ministry for Innovation and Technology.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/ijms21114134">doi:10.3390/ijms21114134</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32531926">pmid:32531926</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7311975/">pmcid:PMC7311975</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ynebldceh5enzkulclyhuakcge">fatcat:ynebldceh5enzkulclyhuakcge</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200611093044/https://res.mdpi.com/d_attachment/ijms/ijms-21-04134/article_deploy/ijms-21-04134.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/dc/f9/dcf9313f75b6eb472f074fb031217a2d81fce8ec.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/ijms21114134"> <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/PMC7311975" 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 Glycosylation and Tumor Microenvironment Alterations Driving Cancer Hallmarks

Andreia Peixoto, Marta Relvas-Santos, Rita Azevedo, Lúcio Lara Santos, José Alexandre Ferreira
<span title="2019-05-14">2019</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/mefn5t5kjndavkrqau5bzfpaoe" style="color: black;">Frontiers in Oncology</a> </i> &nbsp;
Decades of research have disclosed a plethora of alterations in protein glycosylation that decisively impact in all stages of disease and ultimately contribute to more aggressive cell phenotypes.  ...  Focus is also set on the pressing need to include glycans and glycoconjugates in comprehensive panomics models envisaging molecular-based precision medicine capable of improving patient care.  ...  Epigenetic modifications through DNA methylation, posttranslational modification of histone proteins, and interactions of non-coding RNAs with proteins or other nucleic acids also largely drive cancer  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fonc.2019.00380">doi:10.3389/fonc.2019.00380</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31157165">pmid:31157165</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6530332/">pmcid:PMC6530332</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3sfzcxpgbzaqzj2nvikokpipzq">fatcat:3sfzcxpgbzaqzj2nvikokpipzq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200215034758/https://fjfsdata01prod.blob.core.windows.net/articles/files/460344/pubmed-zip/.versions/1/.package-entries/fonc-09-00380/fonc-09-00380.pdf?sv=2015-12-11&amp;sr=b&amp;sig=sm%2BLrztKWjdBVHUdgmFf6TN8UKMZ8xJP3F59%2F4Zrz8s%3D&amp;se=2020-02-15T03%3A48%3A27Z&amp;sp=r&amp;rscd=attachment%3B%20filename%2A%3DUTF-8%27%27fonc-09-00380.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/e0/82/e082c81716f60f8f725ae28d8e897c0a0216d807.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fonc.2019.00380"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> frontiersin.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6530332" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Functional evolution of the OAS1 viral sensor: Insights from old world primates

Ian Fish, Stéphane Boissinot
<span title="">2016</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3sxjova6ja6zhrsmgugwam33a" style="color: black;">Infection, Genetics and Evolution</a> </i> &nbsp;
We identified a total of 35 codons with the earmarks of positive selection and we performed a comprehensive analysis of their functional significance using in silico modeling of the OAS1 protein.  ...  Following their up-regulation by the interferon pathway, OASs bind viral dsRNA and then signal ribonuclease L (RNase L) to degrade RNA, shutting down viral and host protein synthesis.  ...  Schrödinger, LLC; Fish and Boissinot Page 12 Infect Genet Evol. Author manuscript; available in PMC 2017 October 01.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.meegid.2016.07.005">doi:10.1016/j.meegid.2016.07.005</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27393659">pmid:27393659</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5371728/">pmcid:PMC5371728</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/yqoienpbvrexrnn3jv3jdeaqay">fatcat:yqoienpbvrexrnn3jv3jdeaqay</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200208222051/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5371728&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/6c/12/6c12ef4888817c1769b6b0977ca621aa5fce5293.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.meegid.2016.07.005"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5371728" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Single-Domain Antibodies As Versatile Affinity Reagents for Analytical and Diagnostic Applications

Gualberto Gonzalez-Sapienza, Martín A. Rossotti, Sofía Tabares-da Rosa
<span title="2017-08-21">2017</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/t7exsmmojvgjnhq3pflf7pk6zq" style="color: black;">Frontiers in Immunology</a> </i> &nbsp;
With just three CDRs in their variable domains, the antigen-binding site of camelid heavy-chain-only antibodies (HcAbs) has a more limited structural diversity than that of conventional antibodies.  ...  Here, we critically reviewed each of these properties and highlight their relevance with regard to recent developments in different fields of immunosensing applications.  ...  In framework (FR) 2 (dark gray), the amino acids shown in cyan [in this case Phe42, Glu49, Arg50, and Phe52 (IMGT numbering)] represent the hallmark residues that substitute the critical amino acids of  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fimmu.2017.00977">doi:10.3389/fimmu.2017.00977</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28871254">pmid:28871254</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5566570/">pmcid:PMC5566570</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jcav6ral2nczzc4msd27lakb24">fatcat:jcav6ral2nczzc4msd27lakb24</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190226121222/http://pdfs.semanticscholar.org/7e25/55ab186c286afc2860803c496bc5f53116f8.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/7e/25/7e2555ab186c286afc2860803c496bc5f53116f8.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fimmu.2017.00977"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> frontiersin.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5566570" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Identification of protein-protected mRNA fragments and structured excised intron RNAs in human plasma by TGIRT-seq peak calling [article]

Jun Yao, Douglas C. Wu, Ryan M. Nottingham, Alan M. Lambowitz
<span title="2020-06-27">2020</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Many of the mRNA fragments identified by peak calling correspond to annotated protein-binding sites and/or have stable predicted secondary structures that could afford protection from plasma nucleases.  ...  Peak calling also identified novel repeat RNAs, miRNA-sized RNAs, and putatively structured intron RNAs of potential biological, evolutionary, and biomarker significance, including a family of full-length  ...  Empirical Bayes analysis of strand specificity of repeat regions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.06.25.171439">doi:10.1101/2020.06.25.171439</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/j2srhtl3zzchpi36hhagw7lxh4">fatcat:j2srhtl3zzchpi36hhagw7lxh4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201108051657/https://www.biorxiv.org/content/biorxiv/early/2020/06/27/2020.06.25.171439.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/6b/3f/6b3fe34516332c9b911b24b528f99e30fe97c1a5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.06.25.171439"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Genome organization: Balancing stability and plasticity

Malte Wachsmuth, Maïwen Caudron-Herger, Karsten Rippe
<span title="">2008</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/mq63wvvyczbbzc4rio3dzrv5gu" style="color: black;">BBA - Molecular Cell Research</a> </i> &nbsp;
Here, we review different contributions to the dynamic features of the genome, describe how they are determined experimentally, and discuss the results of these measurements in terms of how the requirements  ...  These dynamics occur on the nanometer to micrometer length scale, i.e. ranging from the level of single proteins up to that of whole chromosomes, and on a microsecond to hour time scale.  ...  Acknowledgements This work was supported by DFG grant Ri 828/5-3 to KR and a grant of the Christiane Nüsslein-Volhard Foundation to MCH.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bbamcr.2008.07.022">doi:10.1016/j.bbamcr.2008.07.022</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18722483">pmid:18722483</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lsivf6ilc5gj3oach4dsirkb64">fatcat:lsivf6ilc5gj3oach4dsirkb64</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190313212032/https://core.ac.uk/download/pdf/82737258.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/50/ef/50ef17b6f19b7c4b4a07273631efb21e20be6035.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bbamcr.2008.07.022"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>
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