Filters








1,676 Hits in 3.2 sec

CDD: conserved domains and protein three-dimensional structure

Aron Marchler-Bauer, Chanjuan Zheng, Farideh Chitsaz, Myra K. Derbyshire, Lewis Y. Geer, Renata C. Geer, Noreen R. Gonzales, Marc Gwadz, David I. Hurwitz, Christopher J. Lanczycki, Fu Lu, Shennan Lu (+6 others)
<span title="2012-11-28">2012</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;
protein domain families, as supported by available protein three-dimensional (3D) structure and the published literature.  ...  CDD, the Conserved Domain Database, is part of NCBI's Entrez query and retrieval system and is also accessible via http://www.ncbi.nlm.nih.gov/ Structure/cdd/cdd.shtml.  ...  We are grateful to the authors of Pfam, SMART, COGs, TIGRFAMs and NCBI's Protein Clusters database for providing such vital resources.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gks1243">doi:10.1093/nar/gks1243</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23197659">pmid:23197659</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3531192/">pmcid:PMC3531192</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kyfhbmseffcrjpuj7ie33t7trq">fatcat:kyfhbmseffcrjpuj7ie33t7trq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190224062853/http://pdfs.semanticscholar.org/5dc7/237f225f72fcbca8cef7bcb83591a14608a1.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/5d/c7/5dc7237f225f72fcbca8cef7bcb83591a14608a1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gks1243"> <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/PMC3531192" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

CDD: a curated Entrez database of conserved domain alignments

A. Marchler-Bauer
<span title="2003-01-01">2003</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
Users may also employ the CD-Search service to identify conserved domains in new sequences, at http://www.ncbi.nlm.nih.gov/ Structure/cdd/wrpsb.cgi.  ...  The Conserved Domain Database (CDD) is now indexed as a separate database within the Entrez system and linked to other Entrez databases such as MEDLINE 1 .  ...  We thank the authors of Pfam, SMART and LOAD, for creating invaluable resources and for helping with access to data.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkg087">doi:10.1093/nar/gkg087</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/12520028">pmid:12520028</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC165534/">pmcid:PMC165534</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qexucece6reudeilu2swyzjg3i">fatcat:qexucece6reudeilu2swyzjg3i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180728135950/https://watermark.silverchair.com/gkg087.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAZ0wggGZBgkqhkiG9w0BBwagggGKMIIBhgIBADCCAX8GCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQM2EOdxCGRXTv7vOfwAgEQgIIBUNkM98nmmv27M6i_l8mN31N6OilaYtmnHJUFW2zMFoiMwPvfWKMHamgTCQLaAKgdrTwh5Jk4V7gbPDGBFPuqdZyTeUPe3UkpvsysqeEdpSYrJnCGiWAd-iQ_XX8KVLWV6e8oxHxc_qhBn1d_V_0zgLJ0CMsw8XWh8yFp9vjOv1rZYuMXiltZb2dalj6NNly29ccvCG1ZRo05Ci9SFjE1wRCE2xKzBa5Tyc3Vy2ymVx7F0bK8gJmwiuIl4XdExQvH0CunYHfCAYSqKtaTywdk24bgvUXYFyZcQN2I6ytc5PCVZGaqqXiI0z5RDxY6BV2yv6r4NZ9NFkmJjFbIEfeL-Ze4nOBAFq61cgmfRLDvzDN_o9tF_uNVhR4rJJR0rUSXtTxOxu0E6_EcTWIKwQVkgPiI8h_E2yqytm1a5gfu6BQcb-aOKbZtyF5hE_oyd3zfuw" 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/d8/07/d807376e20634360ac3eae139d5203e00f9c688c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkg087"> <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/PMC165534" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

CDD: a database of conserved domain alignments with links to domain three-dimensional structure

A. Marchler-Bauer
<span title="2002-01-01">2002</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 molecular structure viewer Cn3D serves as a tool to interactively visualize alignments and three-dimensional structure, and to link three-dimensional residue coordinates to descriptions of evolutionary  ...  The Conserved Domain Database (CDD) is a compilation of multiple sequence alignments representing protein domains conserved in molecular evolution.  ...  We thank Chris Ponting, Alex Bateman, Eugene Koonin and David Lipman for discussions and helpful suggestions, L.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/30.1.281">doi:10.1093/nar/30.1.281</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/11752315">pmid:11752315</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC99109/">pmcid:PMC99109</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bbra2ceqbrhannorscvbnga4ra">fatcat:bbra2ceqbrhannorscvbnga4ra</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190221034054/http://pdfs.semanticscholar.org/32e9/ad5353ea18904447116bf613e896adb9af25.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/32/e9/32e9ad5353ea18904447116bf613e896adb9af25.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/30.1.281"> <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/PMC99109" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

CDD: a Conserved Domain Database for protein classification

A. Marchler-Bauer
<span title="2004-12-17">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 Conserved Domain Database (CDD) is the protein classification component of NCBI's Entrez query and retrieval system.  ...  CD-Search, which is available at http://www.ncbi.nlm.nih.gov/Structure/ cdd/wrpsb.cgi, is a fast, interactive tool to identify conserved domains in new protein sequences.  ...  We are grateful to the NCBI BLAST group for developing RPS-BLAST and for continuous support. Comments, suggestions and questions are welcome and should be directed to info@ncbi.nlm.nih.gov.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gki069">doi:10.1093/nar/gki069</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15608175">pmid:15608175</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC540023/">pmcid:PMC540023</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/yk7toda26vee7jutivsxy5mete">fatcat:yk7toda26vee7jutivsxy5mete</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190305014221/http://pdfs.semanticscholar.org/cd4e/f5b8da1a543871357f4bca7483e89ff9e3b5.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/cd/4e/cd4ef5b8da1a543871357f4bca7483e89ff9e3b5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gki069"> <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/PMC540023" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Comparative Genomic Studies of Hypothetical Proteins in Cyanophages

S. G.Sanmukh, M. Rahman, W. N. Paunikar
<span title="2012-05-31">2012</span> <i title="Foundation of Computer Science"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/b637noqf3vhmhjevdfk3h5pdsu" style="color: black;">International Journal of Computer Applications</a> </i> &nbsp;
conserved domains.  ...  While tertiary structures were constructed using PS 2 Server-Protein Structure Prediction server. This study revealed presences of functional domain in 258 uncharacterized proteins.  ...  The (PS) 2 Server built the three dimensional structures for 28 hypothetical proteins satisfactorily using best scored orthologous template.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5120/6855-9405">doi:10.5120/6855-9405</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wm2gmustrrhpncavzwktt254cm">fatcat:wm2gmustrrhpncavzwktt254cm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180604071411/https://research.ijcaonline.org/volume45/number15/pxc3879405.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/36/4b/364b7205b0fa109a7cda6ba55a78502011030352.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5120/6855-9405"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Comparative Functional Genomics Studies for Understanding the Hypothetical Proteins in Mycobacterium tuberculosis KZN 1435

Swapnil Sanmukh, Sumita Goswami, Sandhya Swaminathan, Waman Paunikar
<span title="2012-12-18">2012</span> <i title="Foundation of Computer Science"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/b637noqf3vhmhjevdfk3h5pdsu" style="color: black;">International Journal of Computer Applications</a> </i> &nbsp;
The Bioinformatics web tools like CDD-BLAST, INTERPROSCAN, PFAM and COGs were used for the prediction of functions in the proteins by searching protein databases for the presence of conserved domains;  ...  whereas, tertiary structures were constructed using PS 2 Server-Protein Structure Prediction server.  ...  This predicted functions and three dimensional structures may assist in establishing their role in life cycle of Mycobacterium tuberculosis KZN 1435 which are still unclear and can be used in future for  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5120/9653-3943">doi:10.5120/9653-3943</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rsufjcmi3fg3pf2tikr5fb6ega">fatcat:rsufjcmi3fg3pf2tikr5fb6ega</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180603003257/https://research.ijcaonline.org/volume60/number1/pxc3883943.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/99/2b/992bda93c5afbdf14bf8f1e4624c0722bec556f2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5120/9653-3943"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

MMDB: Entrez's 3D-structure database

J. Chen
<span title="2003-01-01">2003</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;
Three-dimensional structures are now known within most protein families and it is likely, when searching a sequence database, that one will identify a homolog of known structure.  ...  ; and (iii) structure and sequence/structure alignment visualization.  ...  Correspondence between 3D domains and conserved domains is not exact.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkg086">doi:10.1093/nar/gkg086</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/12520055">pmid:12520055</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC165533/">pmcid:PMC165533</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6olyiaitk5bi3cgjqufknjd234">fatcat:6olyiaitk5bi3cgjqufknjd234</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191128232818/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC165533&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/c9/8c/c98c138a8ebf98d65a71b6886f69c93983750f3e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkg086"> <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/PMC165533" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

MMDB: Entrez's 3D-structure database

Y. Wang
<span title="2002-01-01">2002</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;
Three-dimensional structures are now known within most protein families and it is likely, when searching a sequence database, that one will identify a homolog of known structure.  ...  ; and (iii) structure and sequence/structure alignment visualization.  ...  Correspondence between 3D domains and conserved domains is not exact.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/30.1.249">doi:10.1093/nar/30.1.249</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/11752307">pmid:11752307</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC99072/">pmcid:PMC99072</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7h543blngjf6dcned5wqb6uou4">fatcat:7h543blngjf6dcned5wqb6uou4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191128232818/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC165533&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/c9/8c/c98c138a8ebf98d65a71b6886f69c93983750f3e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/30.1.249"> <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/PMC99072" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Protein homologous cores and loops: important clues to evolutionary relationships between structurally similar proteins

Thomas Madej, Anna R Panchenko, Jie Chen, Stephen H Bryant
<span title="">2007</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/m36qvjwuvnegpgzopqbhvg7k3e" style="color: black;">BMC Structural Biology</a> </i> &nbsp;
To discover remote evolutionary relationships and functional similarities between proteins, biologists rely on comparative sequence analysis, and when structures are available, on structural alignments  ...  Conclusion: The HCS, LHM, and GSAS scores are easily computable quantities that allow users of structure-neighbor databases to more easily identify interesting structural similarities between proteins.  ...  Acknowledgements The authors want to thank Aron Marchler-Bauer for helpful discussions and suggestions. We would also like to thank Siqian He for assistance with the database work for the new scores.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1472-6807-7-23">doi:10.1186/1472-6807-7-23</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17425794">pmid:17425794</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1852803/">pmcid:PMC1852803</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/inr2xhveineidpyujgpmolqnpe">fatcat:inr2xhveineidpyujgpmolqnpe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170819033313/https://bmcstructbiol.biomedcentral.com/track/pdf/10.1186/1472-6807-7-23?site=bmcstructbiol.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/5a/25/5a2585393ca57db9145fabc791ac66751fb2105e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1472-6807-7-23"> <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/PMC1852803" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Analysis and prediction of functionally important sites in proteins

Saikat Chakrabarti, Christopher J. Lanczycki
<span title="">2007</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6bubxfqklvdwthsc43yvjbtjae" style="color: black;">Protein Science</a> </i> &nbsp;
The rapidly increasing volume of sequence and structure information available for proteins poses the daunting task of determining their functional importance.  ...  a wide range of protein families.  ...  Anna Panchenko for critically reading the manuscript and for providing useful suggestions, and Dr. Stephen H. Bryant for useful discussions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1110/ps.062506407">doi:10.1110/ps.062506407</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17192586">pmid:17192586</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2222836/">pmcid:PMC2222836</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/z6cx2gj6zvaqtohbrd25d5tkoy">fatcat:z6cx2gj6zvaqtohbrd25d5tkoy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191123052749/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC2222836&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/56/42/5642640f46d563b165f231da767051540c0996aa.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1110/ps.062506407"> <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/PMC2222836" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

CD-Search: protein domain annotations on the fly

A. Marchler-Bauer, S. H. Bryant
<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;
We describe the Conserved Domain Search service (CD-Search), a web-based tool for the detection of structural and functional domains in protein sequences.  ...  Search results may be visualized in further detail by embedding the query sequence into multiple alignment displays and by mapping onto three-dimensional molecular graphic displays of known structures  ...  We thank the architects of the Pfam, SMART and COGs collections and the curators of the CDD for their invaluable contributions. We also thank the NIH Intramural Research Program for support.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkh454">doi:10.1093/nar/gkh454</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15215404">pmid:15215404</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC441592/">pmcid:PMC441592</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kqqxv7qtwbfx7cwdz2ktmbkvhe">fatcat:kqqxv7qtwbfx7cwdz2ktmbkvhe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170716185557/https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/nar/32/suppl_2/10.1093/nar/gkh454/3/gkh454.pdf?Expires=1500324957&amp;Signature=EHoJYa802Yr2iOxxL1qBirQuhieCvc2cE6lwUiNKNbOMfju8fi2~R5cpmam7JfU1ifSbn7dVWyKvEj7RjxefNC5il64IWxK4TrUmu7hynMdEIY~Ew~DNdXMr35baXl0sdKbwip9TDMp5h5FWCxFEwKi9MgOKw8V1x6u7R1f84KAKD0ThOdw13lF3Jz8CghfHsd~EmNywZz0n4u~q5U-mprz3r~pMXy6-bpUtnTSmYpkZ~VqGBupaJhvx4~0n9dmauJGeQ~PfZ5OKE1v4Es31RYZA3raH5JzNxOeSCelluqf08CXUEbstwB~6CiajWd~Bon4-AQvJQ9kQMLIcTqN1Wg__&amp;Key-Pair-Id=APKAIUCZBIA4LVPAVW3Q" 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/db/28/db286b309dabb63a0f28591346e4263d5803d8b4.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkh454"> <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/PMC441592" 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 Elucidation of IF-3 Protein of Chloroflexus aurantiacus Involved in Protein Biosynthesis: An In Silico Approach

Abu Saim Mohammad Saikat, Md. Ekhlas Uddin, Tasnim Ahmad, Shahriar Mahmud, Md. Abu Sayeed Imran, Sohel Ahmed, Salem A. Alyami, Mohammad Ali Moni, Rita Casadio
<span title="2021-07-01">2021</span> <i title="Hindawi Limited"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/icbhosh775h7bgzgot6avm3cua" style="color: black;">BioMed Research International</a> </i> &nbsp;
This in silico viewpoint provides copious properties, including the physicochemical properties, subcellular location, three-dimensional structure, protein-protein interactions, and functional elucidation  ...  This study is aimed at allocating the structure and function through an in silico approach required for bacterial protein biosynthesis.  ...  Thanks are due to the coauthors who supported proper assistance, financial support, revision, and writing to conduct a successful study. The submission of the manuscript is in ChemRxiv.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2021/9050026">doi:10.1155/2021/9050026</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/34307671">pmid:34307671</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8270711/">pmcid:PMC8270711</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2pjouyw2zfchzfmd3x2fvq47ee">fatcat:2pjouyw2zfchzfmd3x2fvq47ee</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210707073516/https://downloads.hindawi.com/journals/bmri/2021/9050026.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/1a/be/1abe1e16d17fbac71b11a646ac322be1c4f037ef.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2021/9050026"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> hindawi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8270711" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Homology Modelling,Bioinformatics Analysis and Insilico Functional Annotation of an Antitoxin Protein from Streptomyces coelicolor A3 (2)

<span title="2015-12-30">2015</span> <i title="Avens Publishing Group"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/clqons3wpbcnjcwus3nkoo322i" style="color: black;">Journal of Proteomics &amp; Computational Biology</a> </i> &nbsp;
Validation of the three-dimensional structure was obtained through PROCHECK and QMEAN6 programs.  ...  Homology model was obtained and PDB ID: 3D55: A served as a template having 71% homology with the protein SCO2235. The three-dimensional structure was predicted through Modeller.  ...  For this purpose three different bioinformatics tools and databases including Proteins Families Database (Pfam), NCBI Conserved Domains Database (NCBI-CDD) and SUPERFAMILY were used [24] [25] [26] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.13188/2572-8679.1000006">doi:10.13188/2572-8679.1000006</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qqsfhs5rz5anpojzzwzgkz4nlm">fatcat:qqsfhs5rz5anpojzzwzgkz4nlm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190428145511/http://www.avensonline.org/wp-content/uploads/JPCB-2572-8679-02-0006.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/50/23/5023a312838b65d50555ef9e2ab977cbac07a49b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.13188/2572-8679.1000006"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Unique features of Plasmids among different Citrobacter species

Swapnil Sanmukh, Waman Paunikar
<span title="2012-01-25">2012</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/gfizkffjyzhple2sfhgk46dk2e" style="color: black;">Nature Precedings</a> </i> &nbsp;
Online automated servers can predict the three dimensional structures for protein sequences by using the strategy of aligning target sequences with orthologous sequences by virtue of sequence homology  ...  AND FUNCTIONS IN CITROBACTER RODENTIUM ICC168 PLASMID PCROD1 NCBI Gene ID CDD-Blast Interproscan pfam COGs Structure 8703859 NO NO Ring hydroxylating alpha subunit (catalytic domain) NO  ...  Where the selection of template was based on the same conserved domain detected in the functional annotations and which must be available in the structure alignment for modeling purpose [11, 14] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/npre.2012.6836.1">doi:10.1038/npre.2012.6836.1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qhly6xbn4zc7farniygdmhmmg4">fatcat:qhly6xbn4zc7farniygdmhmmg4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170813235756/http://precedings.nature.com/documents/6836/version/1/files/npre20126836-1.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/c4/4a/c44a79f1fc9d1411de08ecb019b8cddbe7ada684.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/npre.2012.6836.1"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> nature.com </button> </a>

Homology Modeling and Functional Characterization of PR-1a Protein of Hordeum vulgare subsp. Vulgare

Vahid Aslanzadeh, Mostafa Ghaderia
<span title="2012-09-11">2012</span> <i title="Biomedical Informatics"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/iztfdaqh6bclfpgb2mitxtn5sm" style="color: black;">Bioinformation</a> </i> &nbsp;
Families Database (Pfam), and NCBI Conserved Domains Database (NCBI-CDD).  ...  However, three dimensional structure of HvPR-1a is still unknown. 3D structure can be used for determining protein function, and identifying novel protein folds and potential targets for regulation.  ...  For identifying conserved domains and functional annotation of the HvPR-1a protein we used three different web tools including InterProScan, Pfam, and NCBI-CDD.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.6026/97320630008807">doi:10.6026/97320630008807</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23139589">pmid:23139589</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3488842/">pmcid:PMC3488842</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gpkclxtbovehzckfsuhjp55wzq">fatcat:gpkclxtbovehzckfsuhjp55wzq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170808213408/http://www.bioinformation.net/008/97320630008807.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/fe/1e/fe1e5eb378ff6b732a462a8f0232c4285dc414f4.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.6026/97320630008807"> <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> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3488842" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
&laquo; Previous Showing results 1 &mdash; 15 out of 1,676 results