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iDPF-PseRAAAC: A Web-Server for Identifying the Defensin Peptide Family and Subfamily Using Pseudo Reduced Amino Acid Alphabet Composition

Yongchun Zuo, Yang Lv, Zhuying Wei, Lei Yang, Guangpeng Li, Guoliang Fan, Junwen Wang
<span title="2015-12-29">2015</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
Defensins as one of the most abundant classes of antimicrobial peptides are an essential part of the innate immunity that has evolved in most living organisms from lower organisms to humans.  ...  A friendly guide is provided to describe how to use the web server. We anticipate that iDPF-PseRAAAC may become a useful highthroughput tool for both basic research and drug design.  ...  Acknowledgments We wish to express our gratitude to the editor and three anonymous reviewers whose constructive comments were very helpful in strengthening the presentation of this paper.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0145541">doi:10.1371/journal.pone.0145541</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26713618">pmid:26713618</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4694767/">pmcid:PMC4694767</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vvxovo3uajavzf67nlablauqsu">fatcat:vvxovo3uajavzf67nlablauqsu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171011114339/http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0145541&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/e0/bf/e0bfa4586ac35abdc94bdcb2eb86d8f82820d5fb.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0145541"> <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/PMC4694767" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

BACTIBASE: a new web-accessible database for bacteriocin characterization

Riadh Hammami, Abdelmajid Zouhir, Jeannette Ben Hamida, Ismail Fliss
<span title="">2007</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/jlhrb3d6ujhjtijkq4fva6oeha" style="color: black;">BMC Microbiology</a> </i> &nbsp;
Conclusion BACTIBASE allows all bacteriocins sequence and information data to be accessed via a userfriendly, web-based interface.  ...  Conclusion The BACTIBASE database is freely available at http://bactibase.pfba-lab.org, web-based platform enabling easy retrieval, via various filters, of sets of bacteriocins that will enable detailed  ...  AZ participated in the design of the study, interacted with RH to carry out the microbiological and physicochemical data and provided specialist knowledge on bacteriocin sequences.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2180-7-89">doi:10.1186/1471-2180-7-89</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17941971">pmid:17941971</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2211298/">pmcid:PMC2211298</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7nntck5qq5fobindso4y7fwtke">fatcat:7nntck5qq5fobindso4y7fwtke</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20071018020554/http://www.biomedcentral.com/content/pdf/1471-2180-7-89.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/da/5a/da5a05a42418808f74001e8da8e4857c08521b04.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2180-7-89"> <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/PMC2211298" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

BACTIBASE second release: a database and tool platform for bacteriocin characterization

Riadh Hammami, Abdelmajid Zouhir, Christophe Le Lay, Jeannette Ben Hamida, Ismail Fliss
<span title="">2010</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/jlhrb3d6ujhjtijkq4fva6oeha" style="color: black;">BMC Microbiology</a> </i> &nbsp;
BACTIBASE is an integrated open-access database designed for the characterization of bacterial antimicrobial peptides, commonly known as bacteriocins.  ...  Conclusion: The provided features should make BACTIBASE a useful tool in food preservation or food safety applications and could have implications for the development of new drugs for medical use.  ...  Not only does BACTIBASE (version 2, July 2009) contain significantly more antimicrobial peptides of bacterial origin, than the APD2 and CAMP databases (177 in BACTI-BASE versus~120 in APD2 and~68 in CAMP  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2180-10-22">doi:10.1186/1471-2180-10-22</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20105292">pmid:20105292</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2824694/">pmcid:PMC2824694</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jijlvxuucrbgnc7a7c2q67fxj4">fatcat:jijlvxuucrbgnc7a7c2q67fxj4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170829192327/https://bmcmicrobiol.biomedcentral.com/track/pdf/10.1186/1471-2180-10-22?site=http://bmcmicrobiol.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/9d/95/9d9518295d5ed42688c693032fc91f6d123de503.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2180-10-22"> <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/PMC2824694" 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 Approaches for the Design and Optimization of Interfering Peptides Against Protein-Protein Interactions

Zahra Sadat Hashemi, Mahboubeh Zarei, Mohsen Karami Fath, Mahmoud Ganji, Mahboube Shahrabi Farahani, Fatemeh Afsharnouri, Navid Pourzardosht, Bahman Khalesi, Abolfazl Jahangiri, Mohammad Reza Rahbar, Saeed Khalili
<span title="2021-04-28">2021</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/zqzewb742bdglfxhkef3ke6cla" style="color: black;">Frontiers in Molecular Biosciences</a> </i> &nbsp;
Moreover, different databases and software tools have been created to predict the peptide structures and their interactions with target protein complexes.  ...  High-throughput screening of large peptide libraries against PPIs; "hotspot" identification; structure-based and off-structure approaches of peptide design; 3D peptide modeling; peptide optimization strategies  ...  ACKNOWLEDGMENTS The authors wish to thank Shahid Rajaee Teacher Training University for supporting the conduct of this research.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fmolb.2021.669431">doi:10.3389/fmolb.2021.669431</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33996914">pmid:33996914</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8113820/">pmcid:PMC8113820</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/j2ie7erd3rcfbfrnlh3yvzzm3q">fatcat:j2ie7erd3rcfbfrnlh3yvzzm3q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210518104352/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC8113820&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/d2/ec/d2ec10b59d0be69f6a4a7126b3772adffa9071dc.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fmolb.2021.669431"> <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/PMC8113820" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline

<span title="2019-07-02">2019</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;
Secondary metabolites produced by bacteria and fungi are an important source of antimicrobials and other bioactive compounds.  ...  Since 2011, the 'antibiotics and secondary metabolite analysis shell-antiSMASH' (https://antismash.secondarymetabolites.org) has assisted researchers in this, both as a web server and a standalone tool  ...  ACKNOWLEDGEMENTS We thank Justin J.J. van der Hooft for critical comments on the manuscript and providing documentation and Emilia Palazzotto and Tetiana Gren for helpful discussions and user testing of  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkz310">doi:10.1093/nar/gkz310</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31032519">pmid:31032519</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6602434/">pmcid:PMC6602434</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mwhhpowtdjh5rctcumwhzoigzm">fatcat:mwhhpowtdjh5rctcumwhzoigzm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200323034239/https://backend.orbit.dtu.dk/ws/portalfiles/portal/186186018/gkz310.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/a2/10/a2100b5a6cd2747c3a04802b6698db4ec229e54d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkz310"> <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/PMC6602434" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Phylogenetic classification of transporters and other membrane proteins from Saccharomyces cerevisiae

Benoît De Hertogh, Elvira Carvajal, Emmanuel Talla, Bernard Dujon, Philippe Baret, André Goffeau
<span title="">2002</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ooijrfx355hftca5wjh26oojqa" style="color: black;">Functional &amp; Integrative Genomics</a> </i> &nbsp;
On the basis of functional and phylogenetic criteria, we have identified a total of 229 subfamilies and 111 singletons predicted to carry out transport or other membrane functions in Saccharomyces cerevisiae  ...  Compared with a previous TC of the yeast genome, we classified an additional set of 538 membrane proteins (transporters and non-transporters) and identified 111 novel phylogenetic subfamilies.  ...  Bart Nelissen and Professor Milton Saier (San Diego) for comments, advice, and critical reading.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s10142-002-0060-8">doi:10.1007/s10142-002-0060-8</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/12192589">pmid:12192589</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rkxuxsgqwjaspmaztkwxu4ovie">fatcat:rkxuxsgqwjaspmaztkwxu4ovie</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170812072015/http://www.philagri.net/wp-content/uploads/2013/03/Phylogenetic-classification-of-transporters-and-other-membrane-proteins-from-Saccharomyces-cerevisiae_2002_Functional-and-Integrative-Genomics.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/23/53/2353164f541bc9780ea1167db09626d22d0131f1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s10142-002-0060-8"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

A survey on Big Data and Machine Learning for Chemistry [article]

Jose F Rodrigues Jr, Larisa Florea, Maria C F de Oliveira, Dermot Diamond, Osvaldo N Oliveira Jr
<span title="2019-04-23">2019</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
In the survey, we propose a roadmap for future developments, with emphasis on materials discovery and chemical sensing, and within the context of the Internet of Things (IoT), both prominent research fields  ...  But the potential benefits of ML come at the cost of big data production; that is, the algorithms, in order to learn, demand large volumes of data of various natures and from different sources, from materials  ...  In another example of antimicrobial activity prediction, ML was employed to determine the activity of 78 sequences of antimicrobial peptides generated through a linguistic model.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1904.10370v1">arXiv:1904.10370v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wsdoqori7jbrdg3sf6pizcynhu">fatcat:wsdoqori7jbrdg3sf6pizcynhu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200830230028/https://arxiv.org/ftp/arxiv/papers/1904/1904.10370.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/d4/8b/d48b4ee84acb53b3c28d9d9dc3a841ca3c117333.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1904.10370v1" 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>

D3.18 Fourth periodic report on JRP

WP3
<span title="2022-04-26">2022</span> <i title="Zenodo"> Zenodo </i> &nbsp;
D3.18 Fourth periodic report on JRP  ...  This web tool can be run on an assembly and puts out the amount of hits to both sets (Table 2 ).  ...  We have developed a method, focused on the detection of CPE, which is based on 6 peptides generated by its tryptic digestion, achieving a sequence coverage of 19.7%.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.6488954">doi:10.5281/zenodo.6488954</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4ft7tb3wenbineukevwf3fdhia">fatcat:4ft7tb3wenbineukevwf3fdhia</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220430225529/https://zenodo.org/record/6488955/files/D3.18%204th%20Periodic%20Report%20on%20JRP-Final%20version.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] </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.6488954"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> zenodo.org </button> </a>

D3.15- 3rd periodic report on JRPs [article]

Sciensano
<span title="2021-06-03">2021</span> <i title="Zenodo"> Zenodo </i> &nbsp;
Duration 60 Months DOCUMENT MANAGEMENT Title OHEJP deliverable D3.15 Third periodic report on JRP WP and task WP3 Leader Sciensano Other contributors ANSES Due month of the deliverable M39 Actual submission  ...  It is based on the detection of 6 peptides generated by the tryptic digestion of CPE, achieving a sequence coverage of 19.7%.  ...  However, empirical data on the impact of bacterial transformation in the environment are lacking.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.4897319">doi:10.5281/zenodo.4897319</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dtppotwzlrhzzbzrmm2lvpvqbi">fatcat:dtppotwzlrhzzbzrmm2lvpvqbi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210608023535/https://zenodo.org/record/4897319/files/D3.15-3rd-Periodic-Report-on-JRP-Final.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] </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.4897319"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> zenodo.org </button> </a>

Imaging Enterobacteriaceae infection in vivo with 18F-fluorodeoxysorbitol positron emission tomography

E. A. Weinstein, A. A. Ordonez, V. P. DeMarco, A. M. Murawski, S. Pokkali, E. M. MacDonald, M. Klunk, R. C. Mease, M. G. Pomper, S. K. Jain
<span title="2014-10-22">2014</span> <i title="American Association for the Advancement of Science (AAAS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/yfp7fpewebcjxcnf3x5jsya7hi" style="color: black;">Science Translational Medicine</a> </i> &nbsp;
As a consequence, new tools are urgently needed to specifically identify and localize infections due to Enterobacteriaceae and to monitor antimicrobial efficacy.  ...  The Enterobacteriaceae are a family of rod-shaped Gram-negative bacteria that normally inhabit the gastrointestinal tract and are the most common cause of Gram-negative bacterial infections in humans.  ...  Muller (NIH/National Institute on Drug Abuse) for performance of mass spectrometric analysis; P. Mister and K.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1126/scitranslmed.3009815">doi:10.1126/scitranslmed.3009815</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25338757">pmid:25338757</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4327834/">pmcid:PMC4327834</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/v4jzm7oqujajfjjxwdi2wnieva">fatcat:v4jzm7oqujajfjjxwdi2wnieva</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200206205209/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC4327834&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/93/e0/93e00c5e9805cc8b85fd47de450ab391ed8ed7ad.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1126/scitranslmed.3009815"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> sciencemag.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4327834" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

CyanoMetDB, a comprehensive public database of secondary metabolites from cyanobacteria

Martin R. Jones, Ernani Pinto, Mariana A. Torres, Fabiane Dörr, Hanna Mazur-Marzec, Karolina Szubert, Luciana Tartaglione, Carmela Dell'Aversano, Christopher O. Miles, Daniel G. Beach, Pearse McCarron, Kaarina Sivonen (+3 others)
<span title="2021-03-08">2021</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ge6v5555gze5zbpoiatmjdlhli" style="color: black;">Water Research</a> </i> &nbsp;
of novel natural products from cyanobacteria; (3) research on biosynthesis of cyanobacterial secondary metabolites, including substructure searches; and (4) the investigation of their abundance, persistence  ...  This has nearly doubled the number of entries with complete literature metadata and structural composition information compared to previously available open access databases.  ...  communication, comparison and interpretation of results.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.watres.2021.117017">doi:10.1016/j.watres.2021.117017</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33765498">pmid:33765498</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wwzvakdzujffdd6zpck3fttt7e">fatcat:wwzvakdzujffdd6zpck3fttt7e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210715075357/https://www.dora.lib4ri.ch/eawag/islandora/object/eawag%3A22310/datastream/PDF/Jones-2021-CyanoMetDB%2C_a_comprehensive_public_database-%28published_version%29.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/a5/13/a51376ac686e147300b8552cd39aa287b5f70b1e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.watres.2021.117017"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Comparative Genomics and Evolution of the Alpha-Defensin Multigene Family in Primates

S. Das, N. Nikolaidis, H. Goto, C. McCallister, J. Li, M. Hirano, M. D. Cooper
<span title="2010-05-09">2010</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4bimmtjdczetrfmnc3ijbmwpoy" style="color: black;">Molecular biology and evolution</a> </i> &nbsp;
Defensin genes encode small cationic antimicrobial peptides that form an important part of the innate immune system.  ...  Analysis of the encoded peptides of the a-defensin genes indicates that despite the overall high level of sequence divergence, certain amino acid residues or motifs are conserved within and between the  ...  Acknowledgments We thank Jan Klein, Masatoshi Nei, and Masafumi Nozawa for valuable comments and suggestions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/molbev/msq118">doi:10.1093/molbev/msq118</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20457584">pmid:20457584</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2981490/">pmcid:PMC2981490</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5oewl3eltngr7hf5r2tzrewhva">fatcat:5oewl3eltngr7hf5r2tzrewhva</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20160220205630/http://biology.fullerton.edu:80/nnikolaidis/PDFs/Das2010b.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/40/4f/404ff6ef335ca5eae97b3044dd4fe1e49ae461b1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/molbev/msq118"> <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/PMC2981490" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Loss and Gain of Function in SERPINB11: An Example of a Gene under Selection on Standing Variation, with Implications for Host-Pathogen Interactions

Susana Seixas, Nevyana Ivanova, Zelia Ferreira, Jorge Rocha, Bruno L. Victor, Robert B. Sim
<span title="2012-02-29">2012</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
The present study sought a better understanding of the evolutionary history of SERPINB11, with special focus on evaluating its selective signature.  ...  This work represents the first description of a resurrected gene in humans, and may well exemplify selection on standing variation triggered by drastic ecological shifts.  ...  Beals for editing the manuscript and anonymous reviewers for comments on the manuscript and helpful suggestions. Author Contributions Conceived and designed the experiments: SS JR.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0032518">doi:10.1371/journal.pone.0032518</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22393410">pmid:22393410</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3290568/">pmcid:PMC3290568</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zmr3cmguk5at3jgx4so54irh2q">fatcat:zmr3cmguk5at3jgx4so54irh2q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171003064314/http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0032518&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/f7/dc/f7dccdff4923682d68c3708a54530dbb9bf698b1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0032518"> <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/PMC3290568" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Computational and experimental approaches to chart theEscherichia colicell-envelope-associated proteome and interactome

Juan Javier Díaz-Mejía, Mohan Babu, Andrew Emili
<span title="">2009</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/7mlyljxtzvarvmr4qilllwug2q" style="color: black;">FEMS Microbiology Reviews</a> </i> &nbsp;
We also provide a comprehensive comparative benchmarking analysis on the performance of different bioinformatic and proteomic methods commonly used to determine the subcellular localization of bacterial  ...  This includes extensive descriptions of the molecular identities, biochemical activities and evolutionary trajectories of integral transmembrane proteins, many of which play critical roles in infectious  ...  Acknowledgements The authors wish to thank Sadhna Phanse, and the anonymous reviewers for their motivating comments during the preparation of this manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1111/j.1574-6976.2008.00141.x">doi:10.1111/j.1574-6976.2008.00141.x</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19054114">pmid:19054114</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2704936/">pmcid:PMC2704936</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mohn3yvjangdzest5i7z3f2dgm">fatcat:mohn3yvjangdzest5i7z3f2dgm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20160628101759/http://femsre.oxfordjournals.org/content/femsre/33/1/66.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/d1/4a/d14a2fe8b838562cf62c7f35d216257e8cf2af30.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1111/j.1574-6976.2008.00141.x"> <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/PMC2704936" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Health Care–Associated Infection (HAI): A Critical Appraisal of the Emerging Threat—Proceedings of the HAI Summit

Marin H. Kollef
<span title="">2008</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fqtbedntkradrazql46dneyyry" style="color: black;">Clinical Infectious Diseases</a> </i> &nbsp;
https://academic.oup.com/cid/article-abstract/47/Supplement_2/S55/280345 by guest on 28 July 2018 d Amikacin, gentamicin, netilmicin, or tobramycin. e Clindamycin or metronidazole.  ...  Complicated intra-abdominal infections (cIAIs) are defined as infections that extend beyond the hollow viscus of origin into the peritoneal space and are associated with either abcess for-Downloaded from  ...  Researchers developed a complex point-scoring tool based on logistic regression, which employed good screening characteristics for candidemia.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1086/590938">doi:10.1086/590938</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ayattm3f65eqvjfghojazhitpu">fatcat:ayattm3f65eqvjfghojazhitpu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180728064147/https://watermark.silverchair.com/47-Supplement_2-S55.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAbkwggG1BgkqhkiG9w0BBwagggGmMIIBogIBADCCAZsGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMHqRh8Bfh_VcMSJf9AgEQgIIBbChwtqpsyYRNU4Ve5v1ZAZaLB_0E-Pu2CyL5IISVCBM_qHPVx4CmPfFpyFMEnogPwjHzvwNKpKS5heOSbtX0fxq0NU6Z7oQO2TQyraLWsIhTR0-CKAXpOZqM-yr3NbZn6YQVKqCUmMKAKR-APzg0Vu3gRXN0XmHJAqwaEEQUmxIzc-UXMb8g97KbqMaiJwC-OQxWBjzKRTlu4jRq3D8qvepjBVxmuU3Bjom4u9hDHev2xUestzXtF5M_7MgDh7ZPJflLAhFBTIuS8-Mrfhg8KbgH049LzC2XF7p65-Qfo0QmZQMPBRXVkdHOw6wvbavApRCmOgzvDQa5XzIFt2lHeV4oe7LgsBf_1OljnP5edZu6PLHPUf7fq2EKFfquUPQGpQH4K6NAGxm_w4WR66NORSyMQMEi6mMWSPF4bpUIXofYWaW36dpIoGdaW9U-_VPbSYpTcd-12o_FF5UoX4gaP1MNEPIeFpMmzQ42PgY" 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/b5/66/b5667510e86e63fccc78d68c4e6b2b198e71eecb.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1086/590938"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>
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