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Protein structure prediction and analysis using the Robetta server

D. E. Kim, D. Chivian, D. Baker
<span title="2004-07-01">2004</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
The Robetta server (http://robetta.bakerlab.org) provides automated tools for protein structure prediction and analysis.  ...  For structure prediction, sequences submitted to the server are parsed into putative domains and structural models are generated using either comparative modeling or de novo structure prediction methods  ...  We additionally appreciate the useful feedback we have received from Adam Godzik and Leszek Rychlewski, who have also generously allowed Robetta to utilize information from their servers, as well as  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkh468">doi:10.1093/nar/gkh468</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15215442">pmid:15215442</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC441606/">pmcid:PMC441606</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/25v3b6x2lzdw7nthjwshhy2ffi">fatcat:25v3b6x2lzdw7nthjwshhy2ffi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20040914041823/http://www.robetta.org:80/articles/nar.32-2_W526-31.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/69/22/69222ea9ce3eb71515ad1ffef944b4e0f07d9b31.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkh468"> <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/PMC441606" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Ranking predicted protein structures with support vector regression

Jian Qiu, Will Sheffler, David Baker, William Stafford Noble
<span title="2007-11-14">2007</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fkowqlvuffe5lnyfwblj3fcp7i" style="color: black;">Proteins: Structure, Function, and Bioinformatics</a> </i> &nbsp;
Most protein structure prediction approaches generate multiple candidate models first, and then use a scoring function to select Proteins 2008; 71:1175-1182. V V C 2007 Wiley-Liss, Inc.  ...  The availability of high quality predicted protein structures would greatly enhance our ability to understand the functions of the proteins, redesign proteins of interest, and develop drugs interacting  ...  ACKNOWLEDGMENTS The authors thank Bin Qian for valuable discussions and Dylan Chivian for help with the Robetta data set.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/prot.21809">doi:10.1002/prot.21809</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18004754">pmid:18004754</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pm3drhmfm5bvpez26znqj3onrq">fatcat:pm3drhmfm5bvpez26znqj3onrq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20090115211232/http://depts.washington.edu/bakerpg/papers/18004754.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/52/01/5201522ac8911c532863a1e0e6c6155a54041ee6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/prot.21809"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a>

KFC Server: interactive forecasting of protein interaction hot spots

S. J. Darnell, L. LeGault, J. C. Mitchell
<span title="2008-05-19">2008</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;
After the computational analysis, the user can visualize the results using an interactive job viewer able to quickly highlight predicted hot spots and surrounding structural features within the protein  ...  The server facilitates the automated analysis of a user submitted protein-protein or protein-DNA interface and the visualization of its hot spot predictions.  ...  ACKNOWLEDGEMENTS This work was supported by the NIH-NLM (5T15LM 007359 to SJD) and U.S. Department of Energy (DE-FG02-04ER25627 to JCM).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkn346">doi:10.1093/nar/gkn346</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18539611">pmid:18539611</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2447760/">pmcid:PMC2447760</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/afig4ceatzgtnpe7i3mszi5hxy">fatcat:afig4ceatzgtnpe7i3mszi5hxy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190302125642/http://pdfs.semanticscholar.org/a3b2/d6a8a60fb28548c9ff9fcc457dce32e0be0e.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/a3/b2/a3b2d6a8a60fb28548c9ff9fcc457dce32e0be0e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkn346"> <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/PMC2447760" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Is unphosphorylated Rex, as multifunctional protein of HTLV-1, a fully intrinsically disordered protein? An in silico study

Mitra Kheirabadi, Majid Taghdir
<span title="">2016</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/crnyolissrboxmovz6o63ldobq" style="color: black;">Biochemistry and Biophysics Reports</a> </i> &nbsp;
In silico analysis of Rex physicochemical properties and also predicted SLiMs and binding regions sites confirms that unphosphorylated Rex protein in HTLV-1 as Rev protin in HIV is wholly disordered protein  ...  The3D models of Rex protein were obtained by various In Silico methods, such as homology modeling, threading and ab initio, including; I-TASSER, LOMETS, SPARSKS, ROBBETA and QUARK servers.  ...  The best models of Rex protein were predicted with the LOMET and Robetta server.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bbrep.2016.07.018">doi:10.1016/j.bbrep.2016.07.018</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28955936">pmid:28955936</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5613702/">pmcid:PMC5613702</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3yil3ylsifahjca67dajlvdcb4">fatcat:3yil3ylsifahjca67dajlvdcb4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171004001203/http://publisher-connector.core.ac.uk/resourcesync/data/elsevier/pdf/d52/aHR0cDovL2FwaS5lbHNldmllci5jb20vY29udGVudC9hcnRpY2xlL3BpaS9zMjQwNTU4MDgxNjMwMTI2MQ%3D%3D.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/05/9e/059ef49da6603dc63470393e3a5b8baec3e9660f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bbrep.2016.07.018"> <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/PMC5613702" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Prediction of CASP6 structures using automated robetta protocols

Dylan Chivian, David E. Kim, Lars Malmström, Jack Schonbrun, Carol A. Rohl, David Baker
<span title="">2005</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fkowqlvuffe5lnyfwblj3fcp7i" style="color: black;">Proteins: Structure, Function, and Bioinformatics</a> </i> &nbsp;
The Robetta server and revised automatic protocols were used to predict structures for CASP-6 targets.  ...  Robetta is a publicly available protein structure prediction server (http://robetta.bakerlab.org/) that uses the Rosetta de novo structure prediction method.  ...  protein structure prediction.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/prot.20733">doi:10.1002/prot.20733</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16187358">pmid:16187358</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/e2zaiwkyl5azddsuisbdq2dyrq">fatcat:e2zaiwkyl5azddsuisbdq2dyrq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20070418155943/http://depts.washington.edu/bakerpg/papers/MonOct3110:00:442005.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/29/c7/29c729b44e339e06fa5f61d88a903d16023f32ea.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/prot.20733"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a>

Structural predictions for curli amyloid fibril subunits CsgA and CsgB

E. P. DeBenedictis, D. Ma, S. Keten
<span title="">2017</span> <i title="Royal Society of Chemistry (RSC)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/x6heqyfrkfhzlnbbt24hnmjoda" style="color: black;">RSC Advances</a> </i> &nbsp;
CsgA are the building blocks of curli fibrils.  ...  structure predictions can misguide overall topology predictions, and that decoy segments may be biased toward the fragment library used. 68 The RaptorX server uses template-based structure prediction  ...  Although this highlights the difficulty in predicting amyloid structures using current protein structure prediction servers, the performance of these methods in general is welldocumented in several reviews  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1039/c7ra08030a">doi:10.1039/c7ra08030a</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fclvybmgojbhdpxwn3nmosnq3q">fatcat:fclvybmgojbhdpxwn3nmosnq3q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190503065559/https://pubs.rsc.org/en/content/articlepdf/2017/ra/c7ra08030a" 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/c8/b9/c8b9be15be36545d429f71429b5652383b62dfc0.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1039/c7ra08030a"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a>

Improved de novo structure prediction in CASP11 by incorporating coevolution information into Rosetta

Sergey Ovchinnikov, David E. Kim, Ray Yu-Ruei Wang, Yuan Liu, Frank DiMaio, David Baker
<span title="2016-02-24">2016</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fkowqlvuffe5lnyfwblj3fcp7i" style="color: black;">Proteins: Structure, Function, and Bioinformatics</a> </i> &nbsp;
We describe CASP11 de novo blind structure predictions made using the Rosetta structure prediction methodology with both automatic and human assisted protocols.  ...  sequences in the family was more than three times the length of the protein.  ...  They also thank the CASP11 organizers, the structural biologists who generously provided targets, and Jinbo Xu (RaptorX), Johannes Söding (HHSearch), and Yaoqi Zhou (Sparks-X) for making their excellent  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/prot.24974">doi:10.1002/prot.24974</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26677056">pmid:26677056</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5490371/">pmcid:PMC5490371</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kbecdlptafdrdbat3qeld5h3mu">fatcat:kbecdlptafdrdbat3qeld5h3mu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170808221238/https://www.bakerlab.org/wp-content/uploads/2015/12/Ovchinnikov_Proteins_2015.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/6a/c7/6ac77852b198e5ee0823846901971db409f9f463.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/prot.24974"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5490371" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Comments on "Applications of simulated annealing for the design of special digital filters"

T. Ciloglu, Z. Unver
<span title="">1996</span> <i title="Institute of Electrical and Electronics Engineers (IEEE)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/gkn2pu46ozb4tmkxczacnmtvkq" style="color: black;">IEEE Transactions on Signal Processing</a> </i> &nbsp;
This web server can be used for analysis of any protein-protein interface which can be utilized by researchers working on binding sites characterization and rational design of small molecules for protein  ...  Here, we present a web server, HotPoint, which predicts hot spots in protein interfaces using an empirical model.  ...  Turan for his help in developing the web service. Conflict of interest statement. None declared.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/78.492550">doi:10.1109/78.492550</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/74qoedd7hnd3rpxt4k54kvctfi">fatcat:74qoedd7hnd3rpxt4k54kvctfi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210427094902/https://open.metu.edu.tr/bitstream/handle/11511/43314/index.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/7c/55/7c55daedc17a1b3f8ee1e5d0510c1e0de1050bf0.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/78.492550"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

HotPoint: hot spot prediction server for protein interfaces

N. Tuncbag, O. Keskin, A. Gursoy
<span title="2010-05-05">2010</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
This web server can be used for analysis of any protein-protein interface which can be utilized by researchers working on binding sites characterization and rational design of small molecules for protein  ...  Here, we present a web server, HotPoint, which predicts hot spots in protein interfaces using an empirical model.  ...  Turan for his help in developing the web service. Conflict of interest statement. None declared.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkq323">doi:10.1093/nar/gkq323</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20444871">pmid:20444871</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2896123/">pmcid:PMC2896123</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7iqcpxiw6rh3nfvmf7o2t52wqy">fatcat:7iqcpxiw6rh3nfvmf7o2t52wqy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190304132900/http://pdfs.semanticscholar.org/dced/106948015287d111a22d3a715e2cae0255ba.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/ed/dced106948015287d111a22d3a715e2cae0255ba.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkq323"> <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/PMC2896123" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Targeting the EGFR in cancer cells by fusion protein consisting of arazyme and third loop of TGF-alpha: an in silico study

Abdolamir Ghadaksaz, Abbas Ali Imani Fooladi, Hamideh Mahmoodzadeh Hosseini, Taher Nejad Satari, Mohsen Amin
<span title="2021-08-11">2021</span> <i title="Taylor &amp; Francis"> figshare.com </i> &nbsp;
The I-TASSER and Robetta web servers were employed to predict the territory structures of the Arazyme-linker-TGFαL3, and TGFαL3-linker-Arazyme.  ...  Finally, linear and conformational epitopes of B cells, as well as MHC class I and MHC class II were predicted by using different web servers.  ...  The templates used by I-Tasser and Robetta servers for homology modeling of fusion proteins. Table S2 .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.6084/m9.figshare.15149390.v1">doi:10.6084/m9.figshare.15149390.v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ggxho3tvejdl7b5y6zx6h5cpsu">fatcat:ggxho3tvejdl7b5y6zx6h5cpsu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210813071143/https://s3-eu-west-1.amazonaws.com/pstorage-tf-iopjsd8797887/29102156/tbsd_a_1963318_sm5730.pdf?X-Amz-Algorithm=AWS4-HMAC-SHA256&amp;X-Amz-Expires=10&amp;X-Amz-SignedHeaders=host&amp;X-Amz-Signature=020f09c3d2a9060fe1564279e6eb2981dfa1c85e924bcdc8b92da0001066212a&amp;X-Amz-Date=20210813T071142Z&amp;X-Amz-Credential=AKIAJ45OKHUICFE2DW6Q/20210813/eu-west-1/s3/aws4_request" 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/eb/d4eb6f22bf41bd70d29a744d8ccf5dc25da4d829.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.6084/m9.figshare.15149390.v1"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> figshare.com </button> </a>

In Silico Prediction of Cross-Reactive Epitopes of Tropomyosin from Shrimp and Other Arthropods Involved in Allergy

Jirakrit Saetang, Varomyalin Tipmanee, Soottawat Benjakul
<span title="2022-04-21">2022</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dstyyzbt45gknhqqjsh45p55h4" style="color: black;">Molecules</a> </i> &nbsp;
The 3D structures were derived from the AlphaFold or modeled using the Robetta.  ...  The protein sequences of tropomyosin, including Der f 10, Mac r 1, Pen a 1, Pen m 1, Per a 7, and Bla g 7, were retrieved from the UniProt database.  ...  The structures of Bla g 7, Mac r 1, and Pen a 1 were modeled using the Robetta protein structure prediction server with the RoseTTAFold algorithm, a deep learning-based method that showed the topranked  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/molecules27092667">doi:10.3390/molecules27092667</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/35566021">pmid:35566021</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC9104922/">pmcid:PMC9104922</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ggiics4cgnewfplb76rhniws6m">fatcat:ggiics4cgnewfplb76rhniws6m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220425032823/https://mdpi-res.com/d_attachment/molecules/molecules-27-02667/article_deploy/molecules-27-02667.pdf?version=1650536288" 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/b5/a2b5f3383e75450ef699c947e5e2279ff990acb5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/molecules27092667"> <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/PMC9104922" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Structural and functional characterization of a hypothetical protein in the RD7 region in clinical isolates of Mycobacterium tuberculosis — an in silico approach to candidate vaccines

Kaviya Parambath Kootery, Suma Sarojini
<span title="2022-04-08">2022</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/buxmpajbijamphndj5gvow4pea" style="color: black;">Journal of Genetic Engineering and Biotechnology</a> </i> &nbsp;
Tertiary structure of the protein was predicted using the Robetta server using the Mycobacterium smegmatis protein as the putative protein with homology.  ...  Secondary structure of the protein predicted 30% alpha helices, 20% beta strands, and 48% random coils.  ...  Both authors acknowledge the Department of Life Sciences, CHRIST (Deemed to be University), Bangalore, Karnataka, India, for the research fellowship and infrastructure facilities.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s43141-022-00340-5">doi:10.1186/s43141-022-00340-5</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/35394551">pmid:35394551</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8993957/">pmcid:PMC8993957</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cu7l7d3lbbahhmwdb24ojubloe">fatcat:cu7l7d3lbbahhmwdb24ojubloe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220519232657/https://jgeb.springeropen.com/track/pdf/10.1186/s43141-022-00340-5.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/c0/25/c0253a0b2a4f792f7a85c2ca17bfb9e7b1a22af3.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s43141-022-00340-5"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8993957" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Automatic consensus-based fold recognition using Pcons, ProQ, and Pmodeller

Bj�rn Wallner, Huisheng Fang, Arne Elofsson
<span title="">2003</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fkowqlvuffe5lnyfwblj3fcp7i" style="color: black;">Proteins: Structure, Function, and Bioinformatics</a> </i> &nbsp;
., Protein Sci 2001; 10(11):2354 -2365) the first "consensus" predictor that uses predictions from many other servers.  ...  Therefore, the success of Pmodeller and other consensus servers should be seen as a tribute to the collective of all developers of fold recognition servers.  ...  We are also grateful for the support from Leszek Rychlewski for the development of the Meta-Server.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/prot.10536">doi:10.1002/prot.10536</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/14579343">pmid:14579343</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/boyhoa3b4ne3fnjv77ugnxri2i">fatcat:boyhoa3b4ne3fnjv77ugnxri2i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170811030154/http://www.sbc.su.se/~bjornw/papers/pmodeller.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/39/ad/39adf29ae7284b9221a28a3f84b391655f4134d9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/prot.10536"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a>

SPARKS 2 and SP3 servers in CASP6

Hongyi Zhou, Yaoqi Zhou
<span title="">2005</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fkowqlvuffe5lnyfwblj3fcp7i" style="color: black;">Proteins: Structure, Function, and Bioinformatics</a> </i> &nbsp;
Two single-method servers, SPARKS 2 and SP 3 , participated in automatic-server predictions in CASP6.  ...  SPARKS 2 and SP 3 fold recognition servers, as well as their executables, are freely available for all academic users on http://theory.med. buffalo.edu. Proteins 2005;Suppl 7:152-156.  ...  ACKNOWLEDGMENTS Our thanks to Professor Jeff Skolnick and Dr. Yang Zhang for providing us the TM-Score results, and to Dr. Chi Zhang for preparing Figure 1 for us.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/prot.20732">doi:10.1002/prot.20732</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16187357">pmid:16187357</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5rc5bv4vqzdc5ccxqzi6y2gmju">fatcat:5rc5bv4vqzdc5ccxqzi6y2gmju</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20070824163725/http://sparks.informatics.iupui.edu/Publications_files/zhou74.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/83/cb/83cb7ef57ac851408457fdd5692032190b6b6c94.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/prot.20732"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a>

Classification and Computational Analysis of Arabidopsis thaliana Sperm Cell-Specific F-Box Protein Gene 3p.AtFBP113

Afsheen Malik, Alvina Gul, Rabia Amir, Faiza Munir, Mustafeez Mujtaba Babar, Syeda Marriam Bakhtiar, Muhammad Qasim Hayat, Rehan Zafar Paracha, Zoya Khalid, Hadi Alipour
<span title="2020-12-14">2020</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/r7trx2kj6je5jhtaoy3rztibgy" style="color: black;">Frontiers in Genetics</a> </i> &nbsp;
Moreover, various potential post/co-translational modifications were anticipated and the predicted tertiary structure also showed the presence of characteristic domains and fold.  ...  Gene ontology based functional annotation and tissue-specific gene co-expression analysis further strengthened its role in protein binding and ubiquitination.  ...  Since the search did not yield any suitable template, so I-TASSER 32 and Robetta 33 servers were used for the prediction of 3p.AtFBP113 structure and function.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fgene.2020.609668">doi:10.3389/fgene.2020.609668</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33381153">pmid:33381153</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7767997/">pmcid:PMC7767997</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/b723zpa645a3zaw2n6aebmkk5u">fatcat:b723zpa645a3zaw2n6aebmkk5u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201218121100/https://fjfsdata01prod.blob.core.windows.net/articles/files/609668/pubmed-zip/.versions/1/.package-entries/fgene-11-609668/fgene-11-609668.pdf?sv=2018-03-28&amp;sr=b&amp;sig=KYe4qbB2Bi8Ly9mw57Lc3M%2F8EnQy6bvW4jCaUX138l8%3D&amp;se=2020-12-18T12%3A11%3A30Z&amp;sp=r&amp;rscd=attachment%3B%20filename%2A%3DUTF-8%27%27fgene-11-609668.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/0e/cf/0ecfd08a99fc3291763a48b01300e64b9700a897.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fgene.2020.609668"> <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/PMC7767997" 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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