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SALIGN: a web server for alignment of multiple protein sequences and structures

H. Braberg, B. M. Webb, E. Tjioe, U. Pieper, A. Sali, M. S. Madhusudhan
<span title="2012-05-21">2012</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
Described here is a web interface to SALIGN, the versatile protein multiple sequence/structure alignment module of MODELLER.  ...  Accurate alignment of protein sequences and/or structures is crucial for many biological analyses, including functional annotation of proteins, classifying protein sequences into families, and comparative  ...  ACKNOWLEDGEMENTS We thank Eric Pettersen for helpful discussions. Funding: National Institutes of Health (NIH), U.S.A [U54 GM094662 and R01 GM54762 to A.S.]  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bts302">doi:10.1093/bioinformatics/bts302</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22618536">pmid:22618536</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3400954/">pmcid:PMC3400954</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ixs3i5sp35a6bjcw3uc2lwubse">fatcat:ixs3i5sp35a6bjcw3uc2lwubse</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200502094654/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC3400954&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/00/a4/00a4b1b0863411db5a8c4dc1ff6b8114a47235cd.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bts302"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3400954" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

DBAli tools: mining the protein structure space

M. A. Marti-Renom, U. Pieper, M. S. Madhusudhan, A. Rossi, N. Eswar, F. P. Davis, F. Al-Shahrour, J. Dopazo, A. Sali
<span title="2007-05-08">2007</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;
that identifies domains as recurrent structural fragments and (v) an implementation of the COMPARER method in the SALIGN command in MODELLER that creates a multiple structure alignment for a set of related  ...  The DBAli tools use a comprehensive set of structural alignments in the DBAli database to leverage the structural information deposited in the Protein Data Bank (PDB).  ...  ACKNOWLEDGEMENTS We are grateful to Dr Angel Ortiz for the MAMMOTH program. We would also like to thank the JMol team, Erik Bosrup and Stijn van Dongen for JMol, overLib and MCL, respectively.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkm236">doi:10.1093/nar/gkm236</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17478513">pmid:17478513</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1933139/">pmcid:PMC1933139</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/uimvsv7rgrajlczypwgi6jfnyy">fatcat:uimvsv7rgrajlczypwgi6jfnyy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190305123906/http://pdfs.semanticscholar.org/d315/934df57ad2cc522c386a4c6d550ce2d5b122.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/d3/15/d315934df57ad2cc522c386a4c6d550ce2d5b122.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkm236"> <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/PMC1933139" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Alignment of protein sequences by their profiles

M. A. Marti-Renom
<span title="2004-04-01">2004</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6bubxfqklvdwthsc43yvjbtjae" style="color: black;">Protein Science</a> </i> &nbsp;
Thirteen different protocols for creating and comparing profiles corresponding to the multiple sequence alignments are implemented in the SALIGN command of MODELLER.  ...  We optimize and benchmark such an approach that relies on aligning two multiple sequence alignments, each one including one of the two protein sequences.  ...  Acknowledgments We thank our group members for many discussions about the alignment problem. M.A.M.-R. was the Presidential Postdoctoral Fellow from the Rockefeller University, and M.S.M. was a C.H.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1110/ps.03379804">doi:10.1110/ps.03379804</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15044736">pmid:15044736</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2280052/">pmcid:PMC2280052</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/imx2fjtcrjbrjgfaat3675mt7i">fatcat:imx2fjtcrjbrjgfaat3675mt7i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180722015503/https://salilab.org/pdf/Marti-Renom_ProteinSci_2004.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/43/7b/437bf9c01c319f5952f65ce414bea40591a1e022.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1110/ps.03379804"> <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/PMC2280052" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Low-homology protein threading

J. Peng, J. Xu
<span title="2010-06-06">2010</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
This is significant considering that Zhang-Server and other top CASP8 servers use a combination of multiple structure-prediction techniques including consensus method, multiple-template modeling, template-free  ...  A protein is low-homology if we cannot obtain sufficient amount of homologous information for it from existing protein sequence databases.  ...  We use TM-align (Zhang and Skolnick, 2005b) to build a reference alignment for a protein pair in SALIGN.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btq192">doi:10.1093/bioinformatics/btq192</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20529920">pmid:20529920</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2881377/">pmcid:PMC2881377</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zimwub4iezgzjizfkapyjru42e">fatcat:zimwub4iezgzjizfkapyjru42e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200209030813/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC2881377&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/73/e0/73e07f426be121be3dff052df299f43455136bdb.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btq192"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2881377" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Alignment of multiple protein structures based on sequence and structure features

M.S. Madhusudhan, B. M. Webb, M. A. Marti-Renom, N. Eswar, A. Sali
<span title="2009-07-08">2009</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ri37vaeu3jhgpjsg5cqia2yrmq" style="color: black;">Protein Engineering Design &amp; Selection</a> </i> &nbsp;
Here, we align the sequences of multiple protein structures by a dynamic programming optimization of a scoring function that is a sum of an affine gap penalty and terms dependent on various sequence and  ...  Using multiple structure alignments in the HOMSTRAD database, SALIGN was benchmarked against MUSTANG for multiple alignments as well as against TM-align and CE for pairwise alignments.  ...  Acknowledgements We are grateful to Hannes Braberg, Fred Davis and other members of the Sali lab who helped test SALIGN and gave insightful criticisms.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/protein/gzp040">doi:10.1093/protein/gzp040</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19587024">pmid:19587024</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2909824/">pmcid:PMC2909824</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ztc3rqxlvnfurbviufhbbj57iy">fatcat:ztc3rqxlvnfurbviufhbbj57iy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180729132849/https://watermark.silverchair.com/gzp040.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAaMwggGfBgkqhkiG9w0BBwagggGQMIIBjAIBADCCAYUGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMYJh6lJreWspwCRisAgEQgIIBVmrBSEkKDd1-kjToNFdj4cWYpN2HsorqyHa9vJvjukIOMUdFIffwoPBlstsMB8_PlMVKL797n8bwIr6oH_qgQtpZgaz1CNFZCXEtNRL39H3HIltXoArQLWFLWTJACLTR9gWNDN__C-CmE8DwxobyH-a9NL_7_1lVGMxk1dUfktY8W-d9I39rf4uLrSiKsrCHmuGF3vdt4Invw-Qt6NVkspF1DyNhdDQxFb4MqdTvOcEMjC9qF7rW5mhfza2mS8v8nrM_liQaB3Vr7X9fwWLdzXXQG9aSQ7UzAPihFwwc6d-CP4yCAxJgSZW8Qz_iKUoFMu_K89yNovzu5Nb4QgbokG-FXjFUAlHIdw9H_m7O_ouzGW8sGHpLsN_boxb12htOD-7AQnu5AmLhFw0Tj07J72Z1cDzvf0L3wmtOSy3UoSyKjvF5BGE5_VYxFpCb2QqBEQ4fiuUIZA" 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/5c/2f/5c2f23b5d8f3d12dc1514b84f79b4b3ed130baf3.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/protein/gzp040"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2909824" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

ModBase, a database of annotated comparative protein structure models, and associated resources

U. Pieper, B. M. Webb, D. T. Barkan, D. Schneidman-Duhovny, A. Schlessinger, H. Braberg, Z. Yang, E. C. Meng, E. F. Pettersen, C. C. Huang, R. S. Datta, P. Sampathkumar (+5 others)
<span title="2010-11-19">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;
ModBase (http://salilab.org/modbase) is a database of annotated comparative protein structure models.  ...  The models are calculated by ModPipe, an automated modeling pipeline that relies primarily on Modeller for fold assignment, sequence-structure alignment, model building and model assessment (http://salilab.org  ...  The SALIGN web-server (http://salilab.org/ salign) performs sequence-sequence, sequence-structure and structure-structure alignments of two or more proteins (H.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkq1091">doi:10.1093/nar/gkq1091</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21097780">pmid:21097780</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3013688/">pmcid:PMC3013688</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kmqbpcx7sfek7jxgh4mmv2vley">fatcat:kmqbpcx7sfek7jxgh4mmv2vley</a> </span>
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PSSweb: protein structural statistics web server

Thomas Gaillard, Roland H. Stote, Annick Dejaegere
<span title="2016-05-12">2016</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;
It takes as input an ensemble of PDB files of protein structures, performs a multiple sequence alignment and computes structural statistics for each position of the alignment.  ...  PSSweb is a web server for protein structural statistics.  ...  It performs a multiple sequence alignment, and computes structural statistics for each position of the alignment.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkw332">doi:10.1093/nar/gkw332</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27174930">pmid:27174930</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4987900/">pmcid:PMC4987900</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/htfk65lyirbxjhrwfvkd4dahxu">fatcat:htfk65lyirbxjhrwfvkd4dahxu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190228031957/http://pdfs.semanticscholar.org/8b4f/3ae54327c8bebd712ecfb42f13c3c2ea3378.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/8b/4f/8b4f3ae54327c8bebd712ecfb42f13c3c2ea3378.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkw332"> <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/PMC4987900" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

CLICK—topology-independent comparison of biomolecular 3D structures

M. N. Nguyen, K. P. Tan, M. S. Madhusudhan
<span title="2011-05-20">2011</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;
CLICK has been extensively benchmarked and compared with other popular methods for protein and RNA structural alignments.  ...  For this purpose, the server produces complementary alignments to maximize the extent of detectable similarity. Various examples showcase the utility of our web server.  ...  We also offer special thanks to Yong Taipang for his help in setting up, maintaining and improving the server.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkr393">doi:10.1093/nar/gkr393</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21602266">pmid:21602266</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3125785/">pmcid:PMC3125785</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/yaqulndc4bb6dcg7uv6nahpapi">fatcat:yaqulndc4bb6dcg7uv6nahpapi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190308002137/http://pdfs.semanticscholar.org/df3f/5276f63d4f205a73bd085cfd4dd40d687557.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/df/3f/df3f5276f63d4f205a73bd085cfd4dd40d687557.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkr393"> <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/PMC3125785" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

POSA: a user-driven, interactive multiple protein structure alignment server

Zhanwen Li, Padmaja Natarajan, Yuzhen Ye, Thomas Hrabe, Adam Godzik
<span title="2014-05-16">2014</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;
POSA (Partial Order Structure Alignment), available at http://posa.godziklab.org, is a server for multiple protein structure alignment introduced in 2005 (Ye,Y. and Godzik,A. (2005) Multiple flexible structure  ...  The second improvement is an interactive visualization with options that allow the user to view all superposed structures in one window (a typical solution for visualizing results of multiple structure  ...  ACKNOWLEDGMENT We thank Drs Alexey Eroshkin and Lukasz Jaroszewski of Sanford-Burnham Medical Research Institute, La Jolla, CA, for their suggestions for the POSA upgrade.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gku394">doi:10.1093/nar/gku394</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24838569">pmid:24838569</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4086100/">pmcid:PMC4086100</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/quojw6yewncvzksa5t6rkyre6m">fatcat:quojw6yewncvzksa5t6rkyre6m</a> </span>
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An evaluation of automated homology modelling methods at low target template sequence similarity

J. A. R. Dalton, R. M. Jackson
<span title="2007-05-17">2007</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
These include three new sequence-structure alignment programs: 3D-Coffee, Staccato and SAlign, plus five homology modelling programs and their respective loop building methods: Builder, Nest, Modeller,  ...  Motivation: There are two main areas of difficulty in homology modelling that are particularly important when sequence identity between target and template falls below 50%: sequence alignment and loop  ...  ACKNOWLEDGEMENTS We thank all the authors of the programs used in this study for their help with implementation. We also thank the BBSRC for funding in the form of a studentship for J.A.R.D.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btm262">doi:10.1093/bioinformatics/btm262</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17510171">pmid:17510171</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ogwxuwety5c6dcmam6k4bnnt3y">fatcat:ogwxuwety5c6dcmam6k4bnnt3y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170716201553/https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/bioinformatics/23/15/10.1093/bioinformatics/btm262/2/btm262.pdf?Expires=1500329754&amp;Signature=WS9Zeb2QbhhoWISTVJw1qcDeb3ip8~JWWS7bwHxaoLpODbXwWBn4sHP8Luma0H1cM6ihUNXg53t3Ph5rwRko0K0JdYunUosuLYgohPZS2nw~Pk6CGxwbf2waJrBEAXsM746D-5lhtPuQFdcGefrBaXdNI~E9khxjVcPyTS3GxrbbigolGLx7nK7Btb8d8LTEXvnS3c7ClHbv8ZVA37MOH8yVenIBEYc8xN80KAqoBdoO~~Z7T5dBaXNyuKzVnaNijhaqI~nR6CunZNp2a1lRcDEMT4GpBHz1D7x7qjCuSS~clx8bby~2QpbdlKHMG-pQWxGVxU3q9IFhkVvjCcGOKg__&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/a3/af/a3af39235b55214bf26f35b3b763a923dfaa77e9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btm262"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

Statistical inference for template-based protein structure prediction [article]

Jian Peng
<span title="2013-06-19">2013</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
By minimizing the discordance between the pairwise alignments of the protein and templates, we are able to construct a multiple sequence/structure alignment, which leads to better structure predictions  ...  In this thesis, I will introduce a number of statistical machine learning methods to build accurate alignments between a protein sequence and its template structures, especially for proteins having only  ...  We use TM-align to build a reference alignment for a protein pair in SALIGN.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1306.4420v1">arXiv:1306.4420v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/nqllgpxl2nbkndm2blh6tmcggq">fatcat:nqllgpxl2nbkndm2blh6tmcggq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191025124449/https://arxiv.org/pdf/1306.4420v1.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/54/dd/54dd3f06e5adad64178c6aafea7a78decc2b7ca0.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1306.4420v1" 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>

Tools for comparative protein structure modeling and analysis

N. Eswar
<span title="2003-07-01">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;
; MODVIEW, a Netscape plugin for Linux that integrates viewing of multiple sequences and structures; and SNPWEB, a web server for structurebased prediction of the functional impact of a single amino acid  ...  , a web server for automated comparative modeling that relies on PSI-BLAST, IMPALA and MODELLER; MODLOOP, a web server for automated loop modeling that relies on MODELLER; MOULDER, a CPU intensive protocol  ...  web server for automated and continuous assessment of comparative protein structure modeling web servers (15, 16) .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkg543">doi:10.1093/nar/gkg543</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/12824331">pmid:12824331</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC168950/">pmcid:PMC168950</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7h4x7vmc7rbh7nzath35dod2x4">fatcat:7h4x7vmc7rbh7nzath35dod2x4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190224141402/http://pdfs.semanticscholar.org/567a/19aa04862b1b96cfe3573703d2918546a9ad.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/56/7a/567a19aa04862b1b96cfe3573703d2918546a9ad.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkg543"> <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/PMC168950" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Progressive structure-based alignment of homologous proteins: Adopting sequence comparison strategies

Agnel Praveen Joseph, Narayanaswamy Srinivasan, Alexandre G. de Brevern
<span title="">2012</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/lghpknjtojbgplyc2rshxw5ofm" style="color: black;">Biochimie</a> </i> &nbsp;
Comparison of multiple protein structures has a broad range of applications in the analysis of protein structure, function and evolution.  ...  In this study, we have developed a method for multiple structure comparison largely based on sequence alignment techniques.  ...  Both SALIGN and MASS had the top scores for the alignment of two families.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.biochi.2012.05.028">doi:10.1016/j.biochi.2012.05.028</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22676903">pmid:22676903</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5hk3t7wwgrdxxacxakd26mxxam">fatcat:5hk3t7wwgrdxxacxakd26mxxam</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20140831184229/http://hal.inria.fr/docs/00/75/03/25/PDF/Joseph_Srinivasan_de_Brevern_Biochimie_2012_preprint.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/ca/0e/ca0effd37c8596fa2a7e1a01d711c4577297337e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.biochi.2012.05.028"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

mulPBA: an efficient multiple protein structure alignment method based on a structural alphabet

Sylvain Léonard, Agnel Praveen Joseph, Narayanaswamy Srinivasan, Jean-Christophe Gelly, Alexandre G. de Brevern
<span title="2013-05-10">2013</span> <i title="Informa UK Limited"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/kfwansfrvzehjdbhmp2vk4gr3e" style="color: black;">Journal of Biomolecular Structure and Dynamics</a> </i> &nbsp;
For this purpose, we propose a new web server called mulPBA (multiple Protein Block Alignment).  ...  Indeed, multiple structural alignments are essential for analysis of function, evolution and architecture of protein structures.  ...  The web-server provides a good platform for multiple structure comparisons. Different measures for determining the quality of alignments are incorporated.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1080/07391102.2013.787026">doi:10.1080/07391102.2013.787026</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23659291">pmid:23659291</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ig63cguykbhfhjdryojjbbgf5m">fatcat:ig63cguykbhfhjdryojjbbgf5m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190305020219/http://pdfs.semanticscholar.org/c490/7aeec653a5c7b980a9059eef62a881944a08.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/c4/90/c4907aeec653a5c7b980a9059eef62a881944a08.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1080/07391102.2013.787026"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> tandfonline.com </button> </a>

MODBASE, a database of annotated comparative protein structure models, and associated resources

U. Pieper
<span title="2004-01-01">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;
ModBase (http://salilab.org/modbase) is a database of annotated comparative protein structure models.  ...  The models are calculated by ModPipe, an automated modeling pipeline that relies primarily on Modeller for fold assignment, sequence-structure alignment, model building and model assessment  ...  Conflict of interest statement. None declared.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkh095">doi:10.1093/nar/gkh095</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/14681398">pmid:14681398</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC308829/">pmcid:PMC308829</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/blq5hwxzh5gobc32e6c5y3gu6a">fatcat:blq5hwxzh5gobc32e6c5y3gu6a</a> </span>
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