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Simulated Epidemics in 3D Protein Structures to Detect Functional Properties [article]

Mattia Miotto, Lorenzo Di Rienzo, Pietro Corsi, Giancarlo Ruocco, Domenico Raimondo, Edoardo Milanetti
<span title="2019-12-12">2019</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Our approach allowed to probe the overall stability and the capability to propagate information in the complex 3D-structures and proved to be very efficient in addressing different problems, from the assessment  ...  Likewise, protein functions depend on the 3D arrangement of their residues and on the underlying energetic interaction network.  ...  network due to their biological functional role in the 3D structure.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1906.05390v2">arXiv:1906.05390v2</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xcvcv27bs5gh7jwjjtbp5eqfdm">fatcat:xcvcv27bs5gh7jwjjtbp5eqfdm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200916141046/https://arxiv.org/pdf/1906.05390v2.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/a9/27a90938d4c8989f51d7a2da2c922246adb6819c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1906.05390v2" 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>

Discovery of potential drug-like compounds against Viral protein (VP40) of Marburg Virus using pharmacophoric based virtual screening from ZINC database [article]

Sameer Quazi, Javid Ahmad Malik, Komal Singh Suman, Arnaud Martino Capuzzo, Zeshan Haider
<span title="2021-05-14">2021</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Marburg virus (MARV) has been confirmed to cause extreme hemorrhagic fever (HFM) in human and animals.  ...  The effective and suitable vaccine to treat the MARV virus is not commercialized in public and demands rigorously tested on several scales.  ...  The highest DOPE score [Discrete Optimized Protein Power] was used to select the premium structure.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.05.13.444037">doi:10.1101/2021.05.13.444037</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bwps7pefqfgdjnmkgitsitmjhm">fatcat:bwps7pefqfgdjnmkgitsitmjhm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210715011500/https://www.biorxiv.org/content/biorxiv/early/2021/05/14/2021.05.13.444037.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/6c/56/6c567cea5f18d981a6781b2f71322dfc4ea67813.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.05.13.444037"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Computational Approach for Screening the Whole Proteome of Hantavirus and Designing a Multi-Epitope Subunit Vaccine [article]

Faruq Abdulla, Zulkar Nain, Md. Moyazzem Hossain, Sifat Bin Sayed, Md. Shakil Ahmed Khan, Utpal Kumar Adhikari
<span title="2019-11-06">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
In immune simulation, significantly high levels of IgM and IgG1 immunoglobulins, TC and TH-cell populations, and various cytokines (i.e.  ...  Finally, disulfide engineering enhanced vaccine stability and in silico cloning confirmed the better expression in E. coli K12.  ...  The quality score outside the characteristic range of native proteins indicates possible errors in the predicted 3D structure.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/832980">doi:10.1101/832980</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fxc3qapxabcsdaktbro74vhzlq">fatcat:fxc3qapxabcsdaktbro74vhzlq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200325000913/https://www.biorxiv.org/content/biorxiv/early/2019/11/06/832980.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/b8/18/b8187f299feec407e8b9c9913400feaf7ae99abf.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/832980"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Computational drug discovery for the Zika virus

Melina Mottin, Joyce Villa Verde Bastos Borba, Cleber Camilo Melo-Filho, Bruno Junior Neves, Eugene Muratov, Pedro Henrique Monteiro Torres, Rodolpho Campos Braga, Alexander Perryman, Sean Ekins, Carolina Horta Andrade
<span title="2018-11-08">2018</span> <i title="FapUNIFESP (SciELO)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6ddeoh2wwffi3m5p3fi6vb67lu" style="color: black;">Brazilian Journal of Pharmaceutical Sciences</a> </i> &nbsp;
Few Zika virus (ZIKV) outbreaks had been reported since its first detection in 1947, until the recent epidemics occurred in South America (2014/2015) and expeditiously became a global public health emergency  ...  Advances in ZIKV drug discovery have been made recently and constitute promising approaches to ZIKV treatment.  ...  CHA is Research Fellow in productivity of CNPq.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1590/s2175-97902018000001002">doi:10.1590/s2175-97902018000001002</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/my5jploksre23evm3bnofgmtne">fatcat:my5jploksre23evm3bnofgmtne</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190502075732/http://www.scielo.br/pdf/bjps/v54nspe/2175-9790-bjps-54-spe-e01002.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/4d/90/4d900d07d639f08e99a394ac32358e88ce23efab.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1590/s2175-97902018000001002"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> scielo.br </button> </a>

Nanorobot Hardware Architecture for Medical Defense

Adriano Cavalcanti, Bijan Shirinzadeh, Mingjun Zhang, Luiz Kretly
<span title="2008-05-06">2008</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/taedaf6aozg7vitz5dpgkojane" style="color: black;">Sensors</a> </i> &nbsp;
To demonstrate the practical application of medical nanorobotics, a 3D simulation based on clinical data addresses how to integrate communication with nanorobots using RFID, mobile phones, and satellites  ...  This work presents a new approach with details on the integrated platform and hardware architecture for nanorobots application in epidemic control, which should enable real time in vivo prognosis of biohazard  ...  In the 3D simulation, the nanorobots were able to efficiently detect alpha-NAGA signals in the bloodstream, with the integrated system retrieving information about a person infected with influenza.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/s8052932">doi:10.3390/s8052932</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27879858">pmid:27879858</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3675524/">pmcid:PMC3675524</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/k3ytyn2whjdeth3ldtjquz5dmq">fatcat:k3ytyn2whjdeth3ldtjquz5dmq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170808205502/http://www.123seminarsonly.com/Seminar-Reports/039/76339815-Nanorobot-Hardware-Architecture-for-Medical-Defense.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/45/72/4572a8588d9d97cf1aa46241f2cf9e4a4d52dab8.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/s8052932"> <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/PMC3675524" 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 Survey on Applications of Artificial Intelligence in Fighting Against COVID-19 [article]

Jianguo Chen, Kenli Li, Zhaolei Zhang, Keqin Li, Philip S. Yu
<span title="2021-03-11">2021</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
and epidemic and transmission prediction.  ...  In this survey, we investigate the main scope and contributions of AI in combating COVID-19 from the aspects of disease detection and diagnosis, virology and pathogenesis, drug and vaccine development,  ...  The MT-DTI model uses SMILES strings and amino-acid sequences to predict target proteins with 3D crystal structures.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2007.02202v2">arXiv:2007.02202v2</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ss6r2ijaq5d7hi6qlrpwcnltvi">fatcat:ss6r2ijaq5d7hi6qlrpwcnltvi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200720134148/https://arxiv.org/pdf/2007.02202v1.pdf" title="fulltext PDF download [not primary version]" 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] <span style="color: #f43e3e;">&#10033;</span> <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/10/94/109484663c706d9441c39d57313268345997cb96.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2007.02202v2" 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>

The Natural Oligoribonucleotides Functionalized by D-Mannitol Affected Interactions of Hemagglutinin with Glycan Receptor Indicating Anti-Influenza Activity

Zenoviy Tkachuk, Nataliia Melnichuk, Roman Nikolaiev, Kosma Szutkowski, Igor Zhukov
<span title="2021-09-30">2021</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/psjbgfbhdvezfh25cavrxzuivy" style="color: black;">Membranes</a> </i> &nbsp;
The natural oligoribonucleotides (ORNs) as well as their derivatives functionalized with D-mannitol (ORNs-D-M) possess anti-influenza properties in vitro and in vivo due to interaction with HA receptor  ...  Quenching fluorescence intensity of the HA suggests that titration by ORNs and ORNs-D-M probably leads to changes in the HA structure.  ...  Figure S4: The docking simulations performed with AutoDock Vina program includer in Yasara software bundle. (A) 3D structure of complex HA3 with A3-ORNs-D-M.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/membranes11100757">doi:10.3390/membranes11100757</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/34677523">pmid:34677523</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5kz742abobc3zpr7tv4zlpeeke">fatcat:5kz742abobc3zpr7tv4zlpeeke</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20211013185738/https://mdpi-res.com/d_attachment/membranes/membranes-11-00757/article_deploy/membranes-11-00757-v4.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/42/af42f74aa2321e6ee0d1f648e66cd5e2f793a4bb.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/membranes11100757"> <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>

Natural Compound ZINC12899676 Reduces Porcine Epidemic Diarrhea Virus Replication by Inhibiting the Viral NTPase Activity

Pengcheng Wang, Xianwei Wang, Xing Liu, Meng Sun, Xiao Liang, Juan Bai, Ping Jiang
<span title="2022-05-04">2022</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/qigargnicncadmdn56ei23yjnu" style="color: black;">Frontiers in Pharmacology</a> </i> &nbsp;
had high binding potential to NTPase and showed drug-like property.  ...  Porcine epidemic diarrhea virus (PEDV) is an alphacoronavirus (α-CoV) that causes high mortality in suckling piglets, leading to severe economic losses worldwide.  ...  using three methods: I-TASSER, designed for protein structure modeling by iterative threading assembly simulations Roy et al., 2010; Zhang, 2008) ; SWISS-MODEL, dedicated to protein structure homology  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fphar.2022.879733">doi:10.3389/fphar.2022.879733</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/35600889">pmid:35600889</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC9114645/">pmcid:PMC9114645</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/md7gdyldyrb37c7yv74fhlzmty">fatcat:md7gdyldyrb37c7yv74fhlzmty</a> </span>
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Screening of potent drug inhibitors against SARS-CoV-2 RNA polymerase: an in silico approach

Sanjay Kumar Singh, Atul Kumar Upadhyay, M. Sudhakara Reddy
<span title="2021-01-24">2021</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/by5shwibsvfk3acyvniuab5bra" style="color: black;">3 Biotech</a> </i> &nbsp;
Further, 3l (Ribavirin) was docked with 6M71 and molecular dynamic simulation of the complex was also performed to check the stability of the conformation.  ...  Present situation invigorated researchers to look for potent targets, development as well as repurposing of conventional therapeutic drugs.  ...  Pocket detection and selection For determining the specific functional part of protein, active site prediction is necessary.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s13205-020-02610-w">doi:10.1007/s13205-020-02610-w</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33520579">pmid:33520579</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7826501/">pmcid:PMC7826501</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fc4o5cmwrncnpganjde64u2hyy">fatcat:fc4o5cmwrncnpganjde64u2hyy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210428191546/https://link.springer.com/content/pdf/10.1007/s13205-020-02610-w.pdf?error=cookies_not_supported&amp;code=5c6ca89b-485e-4aeb-9c4c-e8e9ebc4b179" 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/d3/3e/d33e26f1db126d89eae20b8a3de8d87022c0fffb.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s13205-020-02610-w"> <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/PMC7826501" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Phylodynamic Reconstruction Reveals Norovirus GII.4 Epidemic Expansions and their Molecular Determinants

J. Joukje Siebenga, Philippe Lemey, Sergei L. Kosakovsky Pond, Andrew Rambaut, Harry Vennema, Marion Koopmans, Colin Parrish
<span title="2010-05-06">2010</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/bcchuruegramvpr4vupdzp5jfm" style="color: black;">PLoS Pathogens</a> </i> &nbsp;
or compensatory evolution due to secondary RNA structures, relevant in virus-replication.  ...  Therefore, we set out to study the population structure and changes thereof of GII.4 strains detected through systematic outbreak surveillance since the early 1990s.  ...  Acknowledgments We thank the participants of Noronet and the FBVE network, for sharing their NoV sequences, (some of) which were used in these analyses. We especially thank Dr. R.M.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.ppat.1000884">doi:10.1371/journal.ppat.1000884</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20463813">pmid:20463813</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2865530/">pmcid:PMC2865530</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vebyrnkvhrcsxndx6m45fwrmxu">fatcat:vebyrnkvhrcsxndx6m45fwrmxu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170811041748/http://origem.info/FIC/pdf/Siebenga_etal_Phylo_recon_norovirus_epi_exp_PLoSPath_May10.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/1c/00/1c0070f2cea560c814d58cefdfffc7550b599d86.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.ppat.1000884"> <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/PMC2865530" 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 Analysis of Plant Flavonoids as Potential Inhibitors of Newcastle Disease Virus V Protein

Waseem Sarwar, Iram Liaqat, Tahira Yasmeen, Nazia Nahid, Saad Alkahtani, Ahmed A. Al-Qahtani, Muhammad Shah Nawaz-ul-Rehman, Muhammad Mubin
<span title="2022-05-09">2022</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/vt2hc3xcijfofb7cwnxv4hhszi" style="color: black;">Processes</a> </i> &nbsp;
Sequence analysis and physicochemical properties showed that V protein is negatively charged, acidic in nature, and relatively unstable.  ...  To build the three-dimensional structure of V protein, a homology-modeling method was used.  ...  Acknowledgments: We are thankful to the members of the virology lab for their contributions and help. We are thankful to Waqar for his help in simulation experiments.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/pr10050935">doi:10.3390/pr10050935</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/yyc3filnlvedxodmzs4dib5gw4">fatcat:yyc3filnlvedxodmzs4dib5gw4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220511200910/https://mdpi-res.com/d_attachment/processes/processes-10-00935/article_deploy/processes-10-00935.pdf?version=1652081106" 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/6f/77/6f77953589add1473095b95c800cb62af1b5f765.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/pr10050935"> <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 systematic strategy for the investigation of vaccines and drugs targeting bacteria

Fangfang Yan, Feng Gao
<span title="2020-06-12">2020</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/cmflnsn2l5gylcviv447te3mku" style="color: black;">Computational and Structural Biotechnology Journal</a> </i> &nbsp;
The 3D structures of the desired target proteins, drugs and epitopes can be predicted and modeled through target analysis.  ...  Infectious and epidemic diseases induced by bacteria have historically caused great distress to people, and have even resulted in a large number of deaths worldwide.  ...  In addition to the tools described above, PEPFOLD [146] can also be utilized to design the 3D structures of the epitopes according to amino acid sequence.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.csbj.2020.06.008">doi:10.1016/j.csbj.2020.06.008</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32637049">pmid:32637049</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7327267/">pmcid:PMC7327267</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lznperlwgjav7amumkbjqryudu">fatcat:lznperlwgjav7amumkbjqryudu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200613020423/https://pdf.sciencedirectassets.com/311228/AIP/1-s2.0-S200103702030297X/main.pdf?X-Amz-Security-Token=IQoJb3JpZ2luX2VjEPH%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FwEaCXVzLWVhc3QtMSJIMEYCIQC%2FcpmEm5YWswashd%2FO%2BmxXa%2Bcz7Dq4CcscHJkyRxFZuwIhAMW92J7ijyjsS7LuyA%2BJFAXnhev03TKguAI3A8CURYg1KrQDCGoQAxoMMDU5MDAzNTQ2ODY1IgwvCnvM4EaX8JPQpvUqkQOQkAJ013UHSJ5BO%2FhO7WuKE89ieucwdDYgNkAJ94ND%2FVugLULKybrI956PZ4PZZZinnFDk5L8Opp1epEOsUeaT9tKgGx%2Bp59SgZrEzVa279PBayyH1gUt0z%2BCJy2w5k%2FmHvzWcqrW870R5LcGmmcI5%2Fu5xt7ahur%2FfExVtdU0a2mNg9Cn9sSglQcihc1vGUD%2FbWOrf6rzmBAOQxfGBP%2Fc18SAyAjnoKYxzgX2akrhSCleFM2VqIdA8KvezLzkqSEs8D4CcT0E3zKiFYdguo5e%2BzI%2BYCadSeEsEkFNdmrHvpgCbnQAN5oq%2F4S4eeyxYr1kFSBGV8AvrHeZLDFw7TYxxpii1egcV7Y2lPo8GLr0%2BFIxUp%2BcqwEwRYDSxPchGW3i%2Bjw%2Fbe95Xy7vcpWUsoDxs2nLqxVrOWpHo2G69Quyoh4wZ4hYAfE%2BgCruwyeX42JUYBkska452BhTWjN%2FR8MJmyflMph8tjOhl14vo5RUncojy04iIemNIykgCagF538Kn0JFWtfY3%2Bh9jw9%2BFqYMRuzDlyZD3BTrqAQsHsI2FkbWu4ItH%2FIP7ttqJFSw45yFAO2ZUCW18FSvcmGhRItsrPpeQybXJwg%2BOkq%2Bn%2FQnVYyA9IlzAazaBDazc6Kdbpu6V9G0RVtSY8aepr%2F7fzcr2%2BRWhHnzrT2%2BL%2Bmy0R6P8BZI%2FGB69QTq2sE6qWwOUBph2DA4QCZ88P1rZ3u2g2BzmfFMHp1%2FRRDYDIenCrp%2FVz75NRo8zW9cYwstFDc7s0Fdq9cBp0V%2F2wz7RWD8WMSgD8pnDXv7JMcKcXYuYsigwvwkG6VVads52A60J11xAONMhdw4jpHjf%2FVnoQGvq0rHYc3TuKQ%3D%3D&amp;X-Amz-Algorithm=AWS4-HMAC-SHA256&amp;X-Amz-Date=20200613T020348Z&amp;X-Amz-SignedHeaders=host&amp;X-Amz-Expires=300&amp;X-Amz-Credential=ASIAQ3PHCVTYV6Y3F6N4%2F20200613%2Fus-east-1%2Fs3%2Faws4_request&amp;X-Amz-Signature=4e602fb99468bb787bb67594e1d45518c248ea68a2cc020dbbe63cc3625cb0d0&amp;hash=7cc93ca2cfde2fa9cb245505de5605cc66015207aabc7e1632ef515addf43d6a&amp;host=68042c943591013ac2b2430a89b270f6af2c76d8dfd086a07176afe7c76c2c61&amp;pii=S200103702030297X&amp;tid=spdf-771483d2-4d51-4507-a2df-03175bc8508a&amp;sid=b8d02f3f83c0e34efb18b1949ad25bcf6548gxrqa&amp;type=client" 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/77/4f/774fe914051a9b51f2228a6ff65c41ace6852013.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.csbj.2020.06.008"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7327267" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Polarized Resolved Single-Molecule Localization-Based Super-Resolution Fluorescence Microscopy Reveals Orientation Order in Bio-Molecular Assemblies

Haitham Ahmed Shaban, Cesar A. Valades-Cruz, Julien Savatier, Serge Monneret, Herve Rigneault, Nicolas Bertaux, Sophie Brasselet
<span title="">2014</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dez2wau7t5aqvklzwrcsreuwq4" style="color: black;">Biophysical Journal</a> </i> &nbsp;
Furthermore, understanding organization and functionality of molecular machines often requires the determination of the orientation of molecules within cellular structures and the relation between one  ...  To image nucleoid distribution within mt network, we employed 3D superresolution fluorescent photoactivable localization microscopy (FPALM)(2), in conjunction with photoconvertible fluorescent protein  ...  the diameter and the functional and structural organization of the collagen fibers variability in various tissues.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2013.11.1196">doi:10.1016/j.bpj.2013.11.1196</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jmhqmqqlanen7bekiwayf5ku24">fatcat:jmhqmqqlanen7bekiwayf5ku24</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190416201417/https://core.ac.uk/download/pdf/82018780.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/f2/9c/f29c1fb8c20e194718a8cda1fa9394b503e3815d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2013.11.1196"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Femtomolar-level detection of SARS-CoV-2 spike proteins using toroidal plasmonic metasensors [article]

Arash Ahmadivand, Burak Gerislioglu, Zeinab Ramezani, Ajeet Kaushik, Pandiaraj Manickam, S. Amir Ghoreishi
<span title="2020-06-15">2020</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Possessing molecular weight around ~76 kDa allowed us to detect the presence of spike protein with significantly low LoD ~4.2 fmol.  ...  In this direction, one of appropriate alternative approach to detect SARS-CoV-2 at low level (fmol) is exploring plasmonic metasensor technology for COVID-19 diagnostics, which offers exquisite opportunities  ...  of position along x-axis, simulated for a unit cell at the toroidal dipole frequency, showing significant intensity of the confined fields at the capacitive openings in each resonator. b, 3D E-field enhancement  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2006.08536v1">arXiv:2006.08536v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fdfvuabflbeatfy3zv6b7k3jja">fatcat:fdfvuabflbeatfy3zv6b7k3jja</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200905150718/https://arxiv.org/ftp/arxiv/papers/2006/2006.08536.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/b6/d4b620d322062b8277d47fbce4828d597758c21e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2006.08536v1" 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>

Understanding infectious agents from an in silico perspective

Joo Chuan Tong, Lisa F.P. Ng
<span title="2010-10-23">2011</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/q2rzh4rosrd2rhrlmpfocas4qa" style="color: black;">Drug Discovery Today</a> </i> &nbsp;
Here, we describe how considerable advances in computational methods of data mining, mathematical modeling in epidemiology and simulation have been used to enhance our understanding of infectious agents  ...  Knowledge of infectious diseases now emerging from genomic, proteomic, epidemiological and clinical data can provide insights into the mechanisms of immune function, disease pathogenesis and epidemiology  ...  Analyzing genetic variability Similarity between related sequences can give clues to the structure, function or homology to the common ancestor [19] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.drudis.2010.10.007">doi:10.1016/j.drudis.2010.10.007</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20974283">pmid:20974283</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7185741/">pmcid:PMC7185741</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vf7f3ruebrc43ca6pyy2dz3co4">fatcat:vf7f3ruebrc43ca6pyy2dz3co4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200407095345/https://pdf.sciencedirectassets.com/271275/1-s2.0-S1359644610X00137/1-s2.0-S1359644610007774/main.pdf?X-Amz-Security-Token=IQoJb3JpZ2luX2VjELH%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FwEaCXVzLWVhc3QtMSJHMEUCIQD%2FgXVj7OXbQhkuUkNxGKok5lWStem77uDziE3YgrrvdwIgaLdUVvTICASH0Q480vQhpEpJ5IIcGWJjJx6d8cWY7P0qvQMIuv%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FARADGgwwNTkwMDM1NDY4NjUiDOnvEBx8Lo68ogw%2BLSqRAweCa0tVyHxrIq3TAoA5srmXfl114lvXAnwW598eId6HzVPNnBxeK%2FveAyCDajuUWgpJq%2Bo6iDjgRUHkcBKV9tNVK3vENXZ2NQ2JBeZAQlOBHcffbz0F6X5TPx12st%2FZnhueDIa6ee48PLOZnZBXUJcGqXH%2Bb6ukPSefzdjMGSJj6cT5oJExFuJiT655Ea3C9xqcCT2z4WM8O5n%2FZArQY6Z%2B9EWW0BuF%2Fo1EpxyEfrcgCZ37tq8apCRwXV%2FkVSWKfbGvMCKtpJ0wZk733meNsZO9EayIHkg8NChzBgsa1F%2BXKmBMc7bs9LR5iZGNSacvQpilBUfrtkr%2FdSaeLidCcq2dEpFS%2FwZhoDPWcBaZYMKuK%2B6%2FkRIm68yuacf1s%2FLRoq3S%2FxsMeZ%2BEHRHQN2WdgbqHaWh4R8gx9GweBdQMGhaW4I00DsXXc3E6fHtEtE8X8A%2BC35fuATqsvli%2Bo7I5cWSpp%2FUAhRn56zMH8rCFt0LWHc%2FZ96wluDkUN2r2xiFaamzTv2YA0kpS2d4sbJxod%2BJPMJ3%2BsPQFOusBzoFIz9QFAF5%2BdA%2FCHsygsBTvpMzqHSpBLC7PwRiUp8BJZSI4CZSwUUwT8UaPIhKFfP6SJOTyNp87jg4hY1wG6GK1eKCwK8LqYYYlW2ZpNSTOk6O%2B3A9u39yhnlsqp0L7TYnmlFIvq2L9GKUK7IaIOVPcBAutspNvHWYx7Zlg1pe%2BRzk%2BpjuZrRAxfiZprDwFqBRlHeSBLA7xMd6jui7sZTtSqobImQmmQ1ZTFYE04E2IVDhXgxXk96Xzjt6WZ5BLDqml0y12rEN6cZAnkmKHK3W6ZLDsgshorluFh8L7goHEPNn%2FP%2FLxxrLslw%3D%3D&amp;X-Amz-Algorithm=AWS4-HMAC-SHA256&amp;X-Amz-Date=20200407T095340Z&amp;X-Amz-SignedHeaders=host&amp;X-Amz-Expires=300&amp;X-Amz-Credential=ASIAQ3PHCVTYVOVO7RPV%2F20200407%2Fus-east-1%2Fs3%2Faws4_request&amp;X-Amz-Signature=b406d725b3758942ad4768fa9b6f1fc6bd57b8c2d8f9e0ba31e17069e8898800&amp;hash=4d6780922180663bfd77390de9f0d82f4e2699da4fb362d1f229485057cd9499&amp;host=68042c943591013ac2b2430a89b270f6af2c76d8dfd086a07176afe7c76c2c61&amp;pii=S1359644610007774&amp;tid=spdf-8cfdce0f-b2ed-441b-ac29-2d34eda4b643&amp;sid=1aef5cf87f933348353bc0242f7d097d88f0gxrqa&amp;type=client" 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/c9/c8/c9c88208f2ed154aed0de66930665470b167e36d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.drudis.2010.10.007"> <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/PMC7185741" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
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