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Efficient and automated large-scale detection of structural relationships in proteins with a flexible aligner

Fernando I. Gutiérrez, Felipe Rodriguez-Valenzuela, Ignacio L. Ibarra, Damien P. Devos, Francisco Melo
<span title="2016-01-05">2016</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
We validate the performance of the method for fold and superfamily assignment in a large benchmark set of protein structures.  ...  However, comparable accurate flexible structural aligners to perform efficient whole database searches of multi-domain proteins are not yet available.  ...  The method, as implemented in MOMA computer tool, is able to detect distant structural relationships in proteins in an automated fashion and efficiently, which makes it suitable to search the complete  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-015-0866-8">doi:10.1186/s12859-015-0866-8</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26732380">pmid:26732380</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4702403/">pmcid:PMC4702403</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/e2xinqyxvnautfrh2dkhoihc3y">fatcat:e2xinqyxvnautfrh2dkhoihc3y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170830115204/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-015-0866-8?site=http://bmcbioinformatics.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/64/33/6433d006af61cd561e57578e022af8f993f6e10c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-015-0866-8"> <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/PMC4702403" 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 functional epitopes: hot spots, dynamics and combinatorial libraries

Buyong Ma, Haim J Wolfson, Ruth Nussinov
<span title="">2001</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/uzv6ve6frfevrcjkqzfvw36bfu" style="color: black;">Current Opinion in Structural Biology</a> </i> &nbsp;
Recent studies increasingly point to the importance of structural flexibility and plasticity in proteins, highlighting the evolutionary advantage.  ...  There are an increasing number of cases in which given, presumably specific, binding sites have been shown to bind a range of ligands with different compositions and shapes.  ...  The research of R Nussinov and HJ Wolfson in Israel has been supported in part by the Magnet grant, by the Ministry of Science grant, and by the 'Center of Excellence in Geometric Computing and its Applications  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s0959-440x(00)00216-5">doi:10.1016/s0959-440x(00)00216-5</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/11406388">pmid:11406388</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4m2lrhvd4rebna76vd3yhh56yu">fatcat:4m2lrhvd4rebna76vd3yhh56yu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190302113407/http://pdfs.semanticscholar.org/a2a7/da7dfd24466a9fca27643ec9f196b09c38a2.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/a2/a7/a2a7da7dfd24466a9fca27643ec9f196b09c38a2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s0959-440x(00)00216-5"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Automated Protein Structure Classification: A Survey [article]

Oktie Hassanzadeh
<span title="2009-07-13">2009</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Classification of proteins based on their structure provides a valuable resource for studying protein structure, function and evolutionary relationships.  ...  With the rapidly increasing number of known protein structures, manual and semi-automatic classification is becoming ever more difficult and prohibitively slow.  ...  Automated classification of protein structures is still an attractive research topic with a lot of interesting possibilities for further improvements in the accuracy and efficiency.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/0907.1990v1">arXiv:0907.1990v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/v4o77i5yvbgkfe45nr4y637edu">fatcat:v4o77i5yvbgkfe45nr4y637edu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200912122831/https://arxiv.org/pdf/0907.1990v1.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/fa/d0/fad0283ab5f6d49fbbb93253c4535b19a83622ed.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/0907.1990v1" 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>

From Structure to Function: Methods and Applications

Haim Wolfson, Maxim Shatsky, Dina Schneidman-Duhovny, Oranit Dror, Alexandra Shulman-Peleg, Buyong Ma, Ruth Nussinov
<span title="2005-04-01">2005</span> <i title="Bentham Science Publishers Ltd."> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/5hjswyhgundllot6mrv73p3j5y" style="color: black;">Current protein and peptide science</a> </i> &nbsp;
We provide examples, synergistically merging structural modeling, rigid and flexible structural alignment and detection of conserved structural patterns and docking (rigid and flexible with hinge-bending  ...  The rapid increase in experimental data along with recent progress in computational methods has brought modern biology a step closer toward solving one of the most challenging problems: prediction of protein  ...  ACKNOWLEDGEMENTS We thank our Structural Bioinformatics Group in Tel Aviv and in Frederick. The research of R. Nussinov and H. J.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2174/1389203053545435">doi:10.2174/1389203053545435</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15853653">pmid:15853653</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/t6se7n6msnhsfe54rss2xrvnhe">fatcat:t6se7n6msnhsfe54rss2xrvnhe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20060223002955/http://www.cs.tau.ac.il:80/~shulmana/papers/CurrProtPeptSci-05-Rev.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/09/16/0916069586fe4698b48c1e521a0885760c5a04fe.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2174/1389203053545435"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Protein Structure Prediction and Structural Genomics

D. Baker
<span title="2001-10-05">2001</span> <i title="American Association for the Advancement of Science (AAAS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/qirzh7firjdsjhg4tutxtir6ey" style="color: black;">Science</a> </i> &nbsp;
De novo methods start from the assumption that the native state of a protein is at the global free energy minimum and carry out a large-scale search of conformational space for protein tertiary structures  ...  proteins and on the scale of whole genomes.  ...  Automation and large-scale modeling with de novo methods have lagged behind those of comparative modeling methods, because of the relatively poor quality of the models produced and the relatively large  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1126/science.1065659">doi:10.1126/science.1065659</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/11588250">pmid:11588250</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rqo3clxiwvfvndsksddmgiabpe">fatcat:rqo3clxiwvfvndsksddmgiabpe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20041130093640/http://www.biocheminfo.org:80/cs401/spring03/papers/g4_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/2a/37/2a37e40d53eb79e0543c2b031b44a4f0cf2e4234.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1126/science.1065659"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> sciencemag.org </button> </a>

GeneQuiz: a workbench for sequence analysis

M Scharf, R Schneider, G Casari, P Bork, A Valencia, C Ouzounis, C Sander
<span title="">1994</span> <i > <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/q33b3suvffclbkvfvrsg3ljwjm" style="color: black;">Proceedings. International Conference on Intelligent Systems for Molecular Biology</a> </i> &nbsp;
We present the prototype of a software system, called GeneQuiz, for large-scale biological sequence analysis.  ...  The principal design requirement for the first part was the complete automation of all repetitive actions: database updates, efficient sequence similarity searches and sampling of results in a uniform  ...  However, the basis has been laid oul, with the design and construction of simple automated systems that link database and software for large-scale sequence analysis in genome projects.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/7584411">pmid:7584411</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/o47hzvoquncd5kfppeulygidnu">fatcat:o47hzvoquncd5kfppeulygidnu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190216132629/http://orbilu.uni.lu/bitstream/10993/19519/1/GeneQuiz_ISMB_1994.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/05/4d/054d7d95ca61622a851df89298b737399a4b79a3.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a>

Smolign: A Spatial Motifs-Based Protein Multiple Structural Alignment Method

Hong Sun, Ahmet Sacan, Hakan Ferhatosmanoglu, Yusu Wang
<span title="">2012</span> <i title="Institute of Electrical and Electronics Engineers (IEEE)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/q75ftrlivrhrnno5ijjuyufx5a" style="color: black;">IEEE/ACM Transactions on Computational Biology &amp; Bioinformatics</a> </i> &nbsp;
The ability of our strategy to detect multiple correspondences simultaneously, to catch alignments globally, and to support flexible alignments, endorse a sensitive and robust automated algorithm that  ...  We introduce a novel strategy based on: building a contact-window based motif library from the protein structural data, discovery and extension of common alignment seeds from this library, and optimal  ...  In Section 3.2, we describe a flexible alignment case in detail. Finally, in Section 3.3, we provide a large scale comparison with other MSTA methods using the Homstrad benchmark [28] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/tcbb.2011.67">doi:10.1109/tcbb.2011.67</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21464513">pmid:21464513</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mwfhmds5mnhfrkpbclwh37npze">fatcat:mwfhmds5mnhfrkpbclwh37npze</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20120106131016/http://www.cse.ohio-state.edu/~yusu/papers/Smolign_TCBB.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/e3/43e3f17bca4b9c3400193dcc34dfe92883011e38.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/tcbb.2011.67"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

Comparative Protein Structure Modeling of Genes and Genomes

Marc A. Martí-Renom, Ashley C. Stuart, András Fiser, Roberto Sánchez, Francisco Melo, Andrej Šali
<span title="">2000</span> <i title="Annual Reviews"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ue4iu7lvx5gqfjtwlcqo4gisya" style="color: black;">Annual Review of Biophysics and Biomolecular Structure</a> </i> &nbsp;
Further advances are necessary in recognizing weak sequence-structure similarities, aligning sequences with structures, modeling of rigid body shifts, distortions, loops and side chains, as well as detecting  ...  s Abstract Comparative modeling predicts the three-dimensional structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates).  ...  This aim will be achieved by a focused, large-scale determination of protein structures by X-ray crystallography and NMR spectroscopy, combined efficiently with accurate protein structure modeling techniques  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1146/annurev.biophys.29.1.291">doi:10.1146/annurev.biophys.29.1.291</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/10940251">pmid:10940251</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/uptwquo3pfhotkog3e5qlnsuha">fatcat:uptwquo3pfhotkog3e5qlnsuha</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809040119/http://www.csb.pitt.edu/BBSI/2005/jc_paper/sexton.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/f1/68/f168ac242ae9762b612d8dc3c5b1ddfebae73aa1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1146/annurev.biophys.29.1.291"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Recapitulation of Protein Family Divergence using Flexible Backbone Protein Design

Christopher T. Saunders, David Baker
<span title="">2005</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nk6zopmzsjfizb6z5kztdu477y" style="color: black;">Journal of Molecular Biology</a> </i> &nbsp;
We use flexible backbone protein design to explore the sequence and structure neighborhoods of naturally occurring proteins.  ...  The method samples sequence and structure space in the vicinity of a known sequence and structure by alternately optimizing the sequence for a fixed protein backbone using rotamer based sequence search  ...  Figure 1 was prepared using VMD; 35 all other molecular graphics were created with PyMOL. 36 This work was supported by NIH training grant T32 HG00035 and the HHMI.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jmb.2004.11.062">doi:10.1016/j.jmb.2004.11.062</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15670610">pmid:15670610</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/r74rsggk7zhthjckzcalqn6aje">fatcat:r74rsggk7zhthjckzcalqn6aje</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20060914154220/http://depts.washington.edu/bakerpg/papers/Saunders-JMB-v346-p631.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/c1/dfc12f64f82d17b57c573c6455e03744eb8e4e69.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jmb.2004.11.062"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Solving Complex Puzzles: Automated Protein Complex Assembly From Cryo-Electron Microscopy Data Via Multi-Resolution Modeling

Jochen Heyd, Stefan Birmanns
<span title="">2009</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dez2wau7t5aqvklzwrcsreuwq4" style="color: black;">Biophysical Journal</a> </i> &nbsp;
Currently, one of the central problems in structural biology is the better understanding of large protein complexes.  ...  The recent development of neural maps with kernel-based activation rules facilitates a reliable detection of features in arbitrary signals.  ...  The recent development of neural maps with kernel-based activation rules facilitates a reliable detection of features in arbitrary signals.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2008.12.2101">doi:10.1016/j.bpj.2008.12.2101</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/w74mqfhb5zhzxnhq6x5ygfi5rq">fatcat:w74mqfhb5zhzxnhq6x5ygfi5rq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170929001701/http://publisher-connector.core.ac.uk/resourcesync/data/elsevier/pdf/6fc/aHR0cDovL2FwaS5lbHNldmllci5jb20vY29udGVudC9hcnRpY2xlL3BpaS9zMDAwNjM0OTUwODAyMzIxNw%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/2c/c7/2cc7e7feb31f74250627c9e1f8cc6d1167dfebaf.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2008.12.2101"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Comparative Modeling of Drug Target Proteins☆ [chapter]

B. Webb, N. Eswar, H. Fan, N. Khuri, U. Pieper, G.Q. Dong, A. Sali
<span title="">2014</span> <i title="Elsevier"> Reference Module in Chemistry, Molecular Sciences and Chemical Engineering </i> &nbsp;
, NIH R01 GM54762, P01 GM71790, P01 A135707, and U54 GM62529, as well as Sun, IBM, and Intel for hardware gifts.  ...  Acknowledgments This article is partially based on papers by Jacobson and Sali, 201 Fiser and Sali, 339 and Madhusudhan et al. 340 We also acknowledge the funds from Sandler Family Supporting Foundation  ...  Automation encourages development of better methods, improves their testing, allows application on a large scale, and makes the technology more accessible to both experts and non-specialists alike.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/b978-0-12-409547-2.11133-3">doi:10.1016/b978-0-12-409547-2.11133-3</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mf5ms2yylbburgrdihq5xpjhye">fatcat:mf5ms2yylbburgrdihq5xpjhye</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200329211228/https://pdf.sciencedirectassets.com/287291/3-s2.0-B9780124095472111333/3-s2.0-B9780124095472111333/main.pdf?X-Amz-Security-Token=IQoJb3JpZ2luX2VjEOX%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FwEaCXVzLWVhc3QtMSJIMEYCIQD95Snbpeh%2B7GSeygz5ODgM0s5p%2B9HlXaSf14B3mXhmLAIhAIss09KSSBNLDJVYey8TrLYDuf4jbj6M7Ds1Pn0Tbfz1Kr0DCN7%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FwEQAhoMMDU5MDAzNTQ2ODY1Igx%2BiYsdalJPpYSrLEYqkQOsBL6SwCEx3eplxakIiLRIL7yMEBUkVxUco0uI9HFByutylAWRfYY%2BHBI0gs2GaSPCQ7NEhSxTlTeFHi%2BDWZshHbwBoNFRWpeyxtyhgoeMkysslNf2UIT2kgIo2LBYSUGno1JJWnk91qARSO1gBKjLmpJ6DX5g%2FQgoOwDxSDQ5Evox2VurJmmzoFfnoBkFODnkbuoIXrj7NloKAF9waSvrzwOwy%2FzpqT1qo6urObtnNQaRCOYvVjl6KGksHLjsyU70bYD3FCCVbBZ6r8vrms%2FStMnBkLmpFJnCVQD9Mw9BzILtKehR8ywsfCIjrvbnZvPoLf%2FnHDPmUiiEzDrekigch%2Fev1I6rRX9%2BxwuzGTso0qHM1L2mH4fszmIarA%2BCIf0s5GvX0dVs4Glrj4L9oEJ9I848r4wUa4ZKRLobSrQov2usxCW2eoFCXwA7K2vpdv0KhaknBw3IXGMz1eVMCJ91GI29a5%2BX6xUYQvks9IA64KfJzb5nuNF6g%2FDyY1txrqeaAYmDv90E5PWKUpvJX0dpIDDrkIT0BTrqAYHOSaXGKadnm8KvhaLq3cQOjJUSzrMAHAQGED8FtQ8rmaeWw6C0uhcQqAN%2BV4d1vjTdZ1GN4rOLlNjPoNI%2FReUeWE%2BcM2cnFdaW9jFYdtrUslwOyPcrabHDN4Gkfj8ALYJVZJELtmwZjwrrKhzK%2Fs%2FkDOS%2BRKB%2BSxoJInuNiUJCC8x0LwGkmfcPrheQJ9BnTAFHFSotTS2MrO4qxcJjFORQJHcBISU3Xbn2X%2FO10NDrGo3EvbxkIk4vRHoA3WIOeKJj4yKWunmsxN5PTHjE%2B5iwfA5rWzg%2Fx%2B3KFdJgTiCm0FQ0cOSqBQ2BFA%3D%3D&amp;X-Amz-Algorithm=AWS4-HMAC-SHA256&amp;X-Amz-Date=20200329T211201Z&amp;X-Amz-SignedHeaders=host&amp;X-Amz-Expires=300&amp;X-Amz-Credential=ASIAQ3PHCVTY3NW5NPNX%2F20200329%2Fus-east-1%2Fs3%2Faws4_request&amp;X-Amz-Signature=4baadb0dabcacdb42659281d374afa91b330141cc057eb606a25146adcef105d&amp;hash=8963c61076e47de3ea8c95b135b5c487fcd6d00ebefd57666442ba483f01d0a5&amp;host=68042c943591013ac2b2430a89b270f6af2c76d8dfd086a07176afe7c76c2c61&amp;pii=B9780124095472111333&amp;tid=spdf-eebea936-10cc-4bf0-9b66-7f0863674f06&amp;sid=e72e8d1c77a2f249bd29f7888570d242e6degxrqa&amp;type=client" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/2b/d5/2bd52c295a15a88514a25608a27147fcd43526a6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/b978-0-12-409547-2.11133-3"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

FAST: A novel protein structure alignment algorithm

Jianhua Zhu, Zhiping Weng
<span title="2004-12-17">2004</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 present a novel algorithm named FAST for aligning protein three-dimensional structures.  ...  Typical pairwise alignments take FAST less than a second with a Pentium III 1.2GHz CPU. FAST software and a web server are available at http:// biowulf.bu.edu/FAST/. Proteins 2005;58:618 -627.  ...  Calculations were performed on a Linux computer cluster supported by NSF MRI DBI-0116574. We thank Joseph Szustakowski for insightful discussions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/prot.20331">doi:10.1002/prot.20331</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15609341">pmid:15609341</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lod7v3rlsjbo7aalpcxkd6mh4e">fatcat:lod7v3rlsjbo7aalpcxkd6mh4e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20100629125813/http://zlab.umassmed.edu/zlab/publications/FAST.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b8/ac/b8ac2e8ffbd2265d85c959d6083babe82e5d2ba7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/prot.20331"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a>

Integrating protein structural dynamics and evolutionary analysis with Bio3D

Lars Skjærven, Xin-Qiu Yao, Guido Scarabelli, Barry J Grant
<span title="">2014</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
large protein families, remains a considerable challenge.  ...  We demonstrate these integrated capabilities with example applications to dihydrofolate reductase and heterotrimeric G-protein families along with a discussion of the mechanistic insight provided in each  ...  We acknowledge the University of Bergen (LS) and University of Michigan (XY, GS and BJG) for funding.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-014-0399-6">doi:10.1186/s12859-014-0399-6</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25491031">pmid:25491031</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4279791/">pmcid:PMC4279791</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/q2qsknwvbzhx7kymw57jx76s34">fatcat:q2qsknwvbzhx7kymw57jx76s34</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180719050152/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-014-0399-6?site=bmcbioinformatics.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/2d/67/2d67d47362efac05f64d9b10ef8a78d56b6df8e3.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-014-0399-6"> <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/PMC4279791" 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 structural similarity search by Ramachandran codes

Wei-Cheng Lo, Po-Jung Huang, Chih-Hung Chang, Ping-Chiang Lyu
<span title="">2007</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
These search tools are supposed applicable to automated and highthroughput functional annotations or predictions for the ever increasing number of published protein structures in this post-genomic era.  ...  Its accuracy is similar to Combinatorial Extension (CE) and works over 243,000 times faster, searching 34,000 proteins in 0.34 sec with a 3.2-GHz CPU.  ...  Because of its high efficiency and portability, we hypothesize that SARST will be useful in automated and highthroughput functional annotations or predictions of the rapidly increasing protein structures  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-8-307">doi:10.1186/1471-2105-8-307</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17716377">pmid:17716377</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2194796/">pmcid:PMC2194796</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kh7un76udbb4jpmnogn4nczze4">fatcat:kh7un76udbb4jpmnogn4nczze4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170830114016/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-8-307?site=http://bmcbioinformatics.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/62/de/62deb0d94e059522cd4d0b141398be63b0957ca7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-8-307"> <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/PMC2194796" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

New York-Structural GenomiX Research Consortium (NYSGXRC): A Large Scale Center for the Protein Structure Initiative

Jeffrey B. Bonanno, Steven C. Almo, Anne Bresnick, Mark R. Chance, Andras Fiser, S. Swaminathan, J. Jiang, F. William Studier, Lawrence Shapiro, Christopher D. Lima, Theresa M. Gaasterland, Andrej Sali (+10 others)
<span title="">2005</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/pwcu5srt7nafvasezofrdon6ai" style="color: black;">Journal of Structural and Functional Genomics</a> </i> &nbsp;
Structural GenomiX, Inc.  ...  This feature facilitates detection of remote relationships and functional annotation of proteins previously annotated as hypothetical.  ...  Large scale subcloning of NYSGXRC targets exhibiting minimal proteolysis with new N-and/or C-termini and expression of the resulting truncations in E. coli are nearly complete.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s10969-005-6827-0">doi:10.1007/s10969-005-6827-0</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16211523">pmid:16211523</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kbu3tj36ebasbaskyhe2tbynmm">fatcat:kbu3tj36ebasbaskyhe2tbynmm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20120507221721/http://salilab.org/pdf/Bonanno_JStructFunctGenom_2005.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/c2/39c2b1d4ca8d886347c61889aca3b0e81c3bcffb.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s10969-005-6827-0"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>
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