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A Template-Matching Approach for Protein Surface Clustering

L. Baldacci, M. Golfarelli, A. Lumini, S. Rizzi
<span title="">2006</span> <i title="IEEE"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/jsl2pgelqja2piczru3a6nqkg4" style="color: black;">18th International Conference on Pattern Recognition (ICPR&#39;06)</a> </i> &nbsp;
In this paper we propose an original template-matching algorithm for multi-feature surface clustering in the biochemical context.  ...  The effectiveness of our clustering algorithm in capturing surface similarities is then discussed within a larger framework for protein classification based on surface comparison, with the support of tests  ...  To this end, after briefly discussing the specific requirements raised by protein comparison, we propose a multi-feature clustering technique, based on a template-matching algorithm, that starting from  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/icpr.2006.183">doi:10.1109/icpr.2006.183</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/icpr/BaldacciGLR06.html">dblp:conf/icpr/BaldacciGLR06</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bvj5rgjahjbm5nuluadugcnbna">fatcat:bvj5rgjahjbm5nuluadugcnbna</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20120316150826/http://bias.csr.unibo.it:80/golfarelli/Papers/ICPR06.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/e6/6d/e66d4abd102d9747ee0cf17ab666202531ef7372.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/icpr.2006.183"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

Clustering techniques for protein surfaces

L. Baldacci, M. Golfarelli, A. Lumini, S. Rizzi
<span title="">2006</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/jm6w2xclfzguxnhmnmq5omebpi" style="color: black;">Pattern Recognition</a> </i> &nbsp;
and on an original template matching algorithm.  ...  Surface-based techniques for protein comparison typically require applying clustering algorithms to the punctual 3D description of the surface in order to produce a compact surface representation, capable  ...  requirements for surface clustering in the biochemical domain, in preparing the mutation chains, and in validating the clustering and classification results.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.patcog.2006.02.024">doi:10.1016/j.patcog.2006.02.024</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cnhidete7ndphgxcf3ve3hrata">fatcat:cnhidete7ndphgxcf3ve3hrata</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809095110/http://bias.csr.unibo.it/golfarelli/papers/patrec06.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/de/31/de31aabb633b311f6833fe219cceeff7753af7c8.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.patcog.2006.02.024"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Evolutionary approach to predicting the binding site residues of a protein from its primary sequence

Y. Y. Tseng, W.-H. Li
<span title="2011-03-14">2011</span> <i title="Proceedings of the National Academy of Sciences"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nvtuoas5pbdsllkntnhizy4f4q" style="color: black;">Proceedings of the National Academy of Sciences of the United States of America</a> </i> &nbsp;
To use this database, we designed a template-matching technique, termed residuematching profiling, and established a criterion for selecting templates for a query sequence.  ...  Then, for an uncharacterized protein, one can search for putative templates in the library in the hope of matching attributes of the query with those of characterized templates.  ...  Herbert Edelsbrunner for helpful discussions and Dr. Jie Liang for the Volbl package. This study was supported by National Institutes of Health Grant GM30998.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1073/pnas.1102210108">doi:10.1073/pnas.1102210108</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21402946">pmid:21402946</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3069214/">pmcid:PMC3069214</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tdn7ij7lzfgthchuqtafo5ygte">fatcat:tdn7ij7lzfgthchuqtafo5ygte</a> </span>
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Improved Methods for Template-Matching in Electron-Density Maps Using Spherical Harmonics

Frank DiMaio, Ameet Soni, George N. Phillips, Jude W. Shavlik
<span title="">2007</span> <i title="IEEE"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/p543puajlnhttk4gqgacas2q7y" style="color: black;">2007 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2007)</a> </i> &nbsp;
An important step in the previous method requires searching the density map for many small template protein-fragments.  ...  This previous approach uses Fourier convolution to quickly match some rotation of the template to the entire density map.  ...  Acknowledgements This work is supported by NLM grant 1R01 LM008796, NLM Grant 1T15 LM007359, and NIH U54 GM074901 to the Center for Eukaryotic Structural Genomics.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/bibm.2007.58">doi:10.1109/bibm.2007.58</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/bibm/HeathP07.html">dblp:conf/bibm/HeathP07</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ca5ulsmllndspelcrmncmjtimm">fatcat:ca5ulsmllndspelcrmncmjtimm</a> </span>
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Prediction of enzyme function based on 3D templates of evolutionarily important amino acids

David M Kristensen, R Matthew Ward, Andreas Lisewski, Serkan Erdin, Brian Y Chen, Viacheslav Y Fofanov, Marek Kimmel, Lydia E Kavraki, Olivier Lichtarge
<span title="">2008</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Since, unlike other 3D template approaches, the ETA method bypasses the need for experimental knowledge of the catalytic mechanism, it should prove a useful, large scale, and general adjunct to combine  ...  Since experimentally determined functional sites are not common enough to define 3D templates on a large scale, this work tests a computational strategy to select relevant residues for 3D templates.  ...  This work was also supported by training fellowships from the Keck Center for Interdisciplinary Bioscience Training from the W.M.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-9-17">doi:10.1186/1471-2105-9-17</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18190718">pmid:18190718</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2219985/">pmcid:PMC2219985</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mnd2blcczzc33ainjaglz4tulm">fatcat:mnd2blcczzc33ainjaglz4tulm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170830123730/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-9-17?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/44/b1/44b1bf82e0b6969abb9bb25b425b3d57c41fd65a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-9-17"> <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/PMC2219985" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Prediction of protein–protein interactions: unifying evolution and structure at protein interfaces

Nurcan Tuncbag, Attila Gursoy, Ozlem Keskin
<span title="2011-05-13">2011</span> <i title="IOP Publishing"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ibqja2gehvestmbozn57swysy4" style="color: black;">Physical Biology</a> </i> &nbsp;
As a sample approach for modeling protein interactions, PRISM is detailed which combines structural similarity and evolutionary conservation in protein interfaces to infer structures of complexes in the  ...  In this work, we focus on the question 'how do proteins interact?' rather than 'which proteins interact?' and we review structure-based protein-protein interaction prediction approaches.  ...  NT is supported by a TUBITAK fellowship. We thank Vicki Taylor for editing the manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1088/1478-3975/8/3/035006">doi:10.1088/1478-3975/8/3/035006</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21572173">pmid:21572173</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pvaijwej3jgcxfjnc4v6ow44hq">fatcat:pvaijwej3jgcxfjnc4v6ow44hq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170810102736/http://home.ku.edu.tr/~okeskin/tuncbag_PhysBiol.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/b0/d3b0215c1a9a157fd130f2ae1d55d9aa3b93979a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1088/1478-3975/8/3/035006"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> iop.org </button> </a>

Prediction and experimental validation of enzyme substrate specificity in protein structures

S. R. Amin, S. Erdin, R. M. Ward, R. C. Lua, O. Lichtarge
<span title="2013-10-21">2013</span> <i title="Proceedings of the National Academy of Sciences"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nvtuoas5pbdsllkntnhizy4f4q" style="color: black;">Proceedings of the National Academy of Sciences of the United States of America</a> </i> &nbsp;
Accordingly, given a query protein of unknown function, the ET Annotation pipeline (ETA) builds a 3D template from five or six top-ranked ET residues that also cluster together on surface regions of protein  ...  ETA then searches already annotated protein structures, the targets, for those that match the query 3D template ( Fig. 1 and Movie S1).  ...  We thank the following University of Saint Thomas students for bioinformatic support: Anthony Pham, Anthony Tran, Brian Bui, and Medina Baitemirova.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1073/pnas.1305162110">doi:10.1073/pnas.1305162110</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24145433">pmid:24145433</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3831482/">pmcid:PMC3831482</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/welgjhgjijdo5jzrnvhcgqe6pe">fatcat:welgjhgjijdo5jzrnvhcgqe6pe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190304174342/http://pdfs.semanticscholar.org/e029/0e0dbabc62a0c247e4d24810579106672478.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/e0/29/e0290e0dbabc62a0c247e4d24810579106672478.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1073/pnas.1305162110"> <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/PMC3831482" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Function prediction from networks of local evolutionary similarity in protein structure

Serkan Erdin, Eric Venner, Andreas Lisewski, Olivier Lichtarge
<span title="">2013</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Therefore, the number of templates for a given protein was dictated by the number of identified distinct clusters of evolutionary important surface residues for that protein.  ...  In order to generate multiple templates, ETA first identifies a cluster containing at least 11 important surface residues as the first cluster.  ...  If there are n nodes, W is n by n and W ij is set to the weight calculated above if a match is detected between protein i and j, or set to 0 if there is no such match.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-14-s3-s6">doi:10.1186/1471-2105-14-s3-s6</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23514548">pmid:23514548</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3584919/">pmcid:PMC3584919</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mgyjllmz4vghro6cmhi5t6etcy">fatcat:mgyjllmz4vghro6cmhi5t6etcy</a> </span>
<a target="_blank" rel="noopener" href="https://archive.org/download/pubmed-PMC3584919/PMC3584919-1471-2105-14-S3-S6.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> File Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/74/63/74636ae54b5df8987bad27fc0ab95f6a5f323c8e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-14-s3-s6"> <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/PMC3584919" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

PRISM: protein interactions by structural matching

U. Ogmen, O. Keskin, A. S. Aytuna, R. Nussinov, A. Gursoy
<span title="2005-07-01">2005</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;
Prism (http://gordion.hpc.eng.ku.edu.tr/prism) is a website for protein interface analysis and prediction of putative protein-protein interactions.  ...  a particular protein.  ...  The Open Access publication charges for this article were waived by Oxford University Press. Conflict of interest statement. None declared.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gki585">doi:10.1093/nar/gki585</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15991339">pmid:15991339</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1160261/">pmcid:PMC1160261</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ujruzkkeh5dctkdaeglqtq34t4">fatcat:ujruzkkeh5dctkdaeglqtq34t4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170808201010/http://home.ku.edu.tr/~okeskin/papers/nar.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/9f/38/9f38320eeb4c2833a7e56071622bfcecb2fc6f32.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gki585"> <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/PMC1160261" 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 templates for comparative protein docking

Ivan Anishchenko, Petras J. Kundrotas, Alexander V. Tuzikov, Ilya A. Vakser
<span title="2015-06-13">2015</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;
Along with the traditional protein-protein docking (free search for a match between two proteins), comparative (template-based) modeling of protein-protein complexes has been gaining popularity.  ...  The value of the clustering threshold was determined from the analysis of the clusters and the docking performance on a benchmark set.  ...  Calculations were conducted in part on ITTC computer cluster at The University of Kansas.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/prot.24736">doi:10.1002/prot.24736</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25488330">pmid:25488330</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4461561/">pmcid:PMC4461561</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vxmu2qumwbbmvd2s2y2uthmf64">fatcat:vxmu2qumwbbmvd2s2y2uthmf64</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200306021654/https://kuscholarworks.ku.edu/bitstream/handle/1808/23997/Kundrotas_2015.pdf;jsessionid=6E0D5E3E17476DF316D4F7CE016EF950?sequence=1" 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/28/6e/286ef6c25ce0f03203eaae106db4e96cbfe11994.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/prot.24736"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4461561" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Predicting protein function from sequence and structural data

James D Watson, Roman A Laskowski, Janet M Thornton
<span title="">2005</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;
Many structurebased approaches exist (e.g. fold similarity, three-dimensional templates), but as no single method can be expected to be successful in all cases, a more prudent approach involves combining  ...  Should this process fail, analysis of the protein structure can provide functional clues or confirm tentative functional assignments inferred from the sequence.  ...  match.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.sbi.2005.04.003">doi:10.1016/j.sbi.2005.04.003</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15963890">pmid:15963890</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/q6pnujf7djfhzpmon4w6her7e4">fatcat:q6pnujf7djfhzpmon4w6her7e4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170829212422/http://www.cs.hiram.edu/~walkerel/intd388/ProtStructFunction.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/01/42/014217bfc43d857167a326f457d9781a1db77ea6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.sbi.2005.04.003"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

The use of evolutionary patterns in protein annotation

Angela D. Wilkins, Benjamin J. Bachman, Serkan Erdin, Olivier Lichtarge
<span title="">2012</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;
With genomic data skyrocketing, their biological interpretation remains a serious challenge.  ...  Acknowledgments We wish to thank Rhonald Lua and Eric Venner for helpful discussions, and gratefully acknowledge grant support from the National Institute of Health through R01GM079656 and R01GM066099,  ...  The approach ties all-against-all ETA matches among all known protein structures into a network, in which nodes represent protein structures and links indicate ETA 3D structural template matches between  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.sbi.2012.05.001">doi:10.1016/j.sbi.2012.05.001</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22633559">pmid:22633559</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3439137/">pmcid:PMC3439137</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qxuy52wc4nhodpdx5jdc3vsoii">fatcat:qxuy52wc4nhodpdx5jdc3vsoii</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191128160407/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC3439137&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/ee/44/ee44489593d15190b2abddeb7604de91e34c6125.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.sbi.2012.05.001"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439137" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Evolutionary Trace for Prediction and Redesign of Protein Functional Sites [chapter]

Angela Wilkins, Serkan Erdin, Rhonald Lua, Olivier Lichtarge
<span title="2011-11-24">2011</span> <i title="Springer New York"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6v4flwr6afbfrmhdyu6xe3dyvm" style="color: black;">Msphere</a> </i> &nbsp;
sites of a protein.  ...  The evolutionary trace (ET) is the single most validated approach to identify protein functional determinants and to target mutational analysis, protein engineering and drug design to the most relevant  ...  Next, the server predicts a functional site template by identifying a cluster of evolutionarily important residues on the surface of the protein, picking the six most important ones.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-1-61779-465-0_3">doi:10.1007/978-1-61779-465-0_3</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22183528">pmid:22183528</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4892863/">pmcid:PMC4892863</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/h5sqfghcfzcr3hfrpcbqvkr4yq">fatcat:h5sqfghcfzcr3hfrpcbqvkr4yq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200210225711/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC4892863&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/96/72/9672716cd87dd43a969595be1242b50030c28d64.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-1-61779-465-0_3"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4892863" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

NSiteMatch: Prediction of Binding Sites of Nucleotides by Identifying the Structure Similarity of Local Surface Patches

Jie Sun, Ke Chen
<span title="">2017</span> <i title="Hindawi Limited"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/xytabl7eh5a5lle2ofnetovd7u" style="color: black;">Computational and Mathematical Methods in Medicine</a> </i> &nbsp;
Unlike a traditional template-based predictor, which identifies global similarity between target structure and template, NSiteMatch concerns the local similarity between a surface patch of the target protein  ...  Nucleotides play a central role in life-form metabolism, by interacting with proteins and mediating the function of proteins.  ...  For every pair of the matched atoms, we create a corresponding vertex ( , ) on a new graph , where is the atom from the binding site and is the atom from the selected surface patch and matches .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2017/5471607">doi:10.1155/2017/5471607</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28811833">pmid:28811833</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5547728/">pmcid:PMC5547728</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/in6xason6nfkfo7aqfan7et6na">fatcat:in6xason6nfkfo7aqfan7et6na</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190219082151/http://pdfs.semanticscholar.org/177f/ba733c2fe075f2624dd0ad2d089a53b593fa.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/17/7f/177fba733c2fe075f2624dd0ad2d089a53b593fa.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2017/5471607"> <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/PMC5547728" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Spherical-harmonic decomposition for molecular recognition in electron-density maps

Frank P. DiMaio, Ameet B. Soni, George N. Phillips, Jude W. Shavlik
<span title="">2009</span> <i title="Inderscience Publishers"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tgezmywupbfp5fgtit4wz7f3ym" style="color: black;">International Journal of Data Mining and Bioinformatics</a> </i> &nbsp;
DiMaio et al. (2006) describe an automated approach to this otherwise time-consuming process. One important step involves searching the density map for many small protein fragments, or templates.  ...  We show our new template-matching method improves accuracy and reduces running time, compared to our previous approach.  ...  Acknowledgements This work is supported by NLM grant 1R01 LM008796, NLM Grant 1T15 LM007359, and NIH U54 GM074901 to the Center for Eukaryotic Structural Genomics.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1504/ijdmb.2009.024852">doi:10.1504/ijdmb.2009.024852</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19517990">pmid:19517990</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2696052/">pmcid:PMC2696052</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tsoom2ozfzgojmhukwfypsxchq">fatcat:tsoom2ozfzgojmhukwfypsxchq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809095201/https://www.cs.swarthmore.edu/~soni/pubs/dimaio.ijdmb09.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/4c/4d/4c4d91dc1fcc870981ec1d4186bdf30df0a4977e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1504/ijdmb.2009.024852"> <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/PMC2696052" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
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