Matt: Local Flexibility Aids Protein Multiple Structure Alignment
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{"title"=>"Matt: Local flexibility aids protein multiple structure alignment", "type"=>"journal", "authors"=>[{"first_name"=>"Matthew", "last_name"=>"Menke", "scopus_author_id"=>"7004046757"}, {"first_name"=>"Bonnie", "last_name"=>"Berger", "scopus_author_id"=>"7201838430"}, {"first_name"=>"Lenore", "last_name"=>"Cowen", "scopus_author_id"=>"7003498528"}], "year"=>2008, "source"=>"PLoS Computational Biology", "identifiers"=>{"sgr"=>"38949150854", "doi"=>"10.1371/journal.pcbi.0040010", "pui"=>"351230858", "pmid"=>"18193941", "scopus"=>"2-s2.0-38949150854", "issn"=>"1553734X", "isbn"=>"1553-7358 (Electronic)\\r1553-734X (Linking)"}, "id"=>"645b71a5-c4e5-3284-b768-88e2ed28104e", "abstract"=>"Even when there is agreement on what measure a protein multiple structure alignment should be optimizing, finding the optimal alignment is computationally prohibitive. One approach used by many previous methods is aligned fragment pair chaining, where short structural fragments from all the proteins are aligned against each other optimally, and the final alignment chains these together in geometrically consistent ways. Ye and Godzik have recently suggested that adding geometric flexibility may help better model protein structures in a variety of contexts. We introduce the program Matt (Multiple Alignment with Translations and Twists), an aligned fragment pair chaining algorithm that, in intermediate steps, allows local flexibility between fragments: small translations and rotations are temporarily allowed to bring sets of aligned fragments closer, even if they are physically impossible under rigid body transformations. After a dynamic programming assembly guided by these \"bent\" alignments, geometric consistency is restored in the final step before the alignment is output. Matt is tested against other recent multiple protein structure alignment programs on the popular Homstrad and SABmark benchmark datasets. Matt's global performance is competitive with the other programs on Homstrad, but outperforms the other programs on SABmark, a benchmark of multiple structure alignments of proteins with more distant homology. On both datasets, Matt demonstrates an ability to better align the ends of alpha-helices and beta-strands, an important characteristic of any structure alignment program intended to help construct a structural template library for threading approaches to the inverse protein-folding problem. The related question of whether Matt alignments can be used to distinguish distantly homologous structure pairs from pairs of proteins that are not homologous is also considered. For this purpose, a p-value score based on the length of the common core and average root mean squared deviation (RMSD) of Matt alignments is shown to largely separate decoys from homologous protein structures in the SABmark benchmark dataset. We postulate that Matt's strong performance comes from its ability to model proteins in different conformational states and, perhaps even more important, its ability to model backbone distortions in more distantly related proteins.", "link"=>"http://www.mendeley.com/research/matt-local-flexibility-aids-protein-multiple-structure-alignment", "reader_count"=>99, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>4, "Researcher"=>29, "Student > Ph. D. Student"=>29, "Student > Postgraduate"=>2, "Student > Master"=>11, "Other"=>3, "Student > Bachelor"=>13, "Lecturer"=>1, "Professor"=>7}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>4, "Researcher"=>29, "Student > Ph. D. Student"=>29, "Student > Postgraduate"=>2, "Student > Master"=>11, "Other"=>3, "Student > Bachelor"=>13, "Lecturer"=>1, "Professor"=>7}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>11, "Mathematics"=>1, "Agricultural and Biological Sciences"=>59, "Medicine and Dentistry"=>2, "Business, Management and Accounting"=>1, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Physics and Astronomy"=>3, "Chemistry"=>5, "Computer Science"=>16}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Chemistry"=>{"Chemistry"=>5}, "Physics and Astronomy"=>{"Physics and Astronomy"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>59}, "Computer Science"=>{"Computer Science"=>16}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>11}, "Mathematics"=>{"Mathematics"=>1}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}}, "reader_count_by_country"=>{"Argentina"=>1, "Korea (South)"=>1, "United States"=>10, "China"=>1, "Brazil"=>1, "Denmark"=>1, "United Kingdom"=>1, "Italy"=>2, "France"=>3, "Germany"=>1, "Spain"=>2}, "group_count"=>6}

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Figshare

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  • {"files"=>["https://ndownloader.figshare.com/files/939536"], "description"=>"<p>Average pairwise RMSD versus average number of residue positions placed in the common core for the Homstrad multiple alignment benchmark.</p>", "links"=>[], "tags"=>["homstrad"], "article_id"=>609987, "categories"=>["Biological Sciences"], "users"=>["Matthew Menke", "Bonnie Berger", "Lenore Cowen"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.0040010.g002", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Matt_Homstrad_Performance_Tradeoffs_/609987", "title"=>"Matt Homstrad Performance Tradeoffs", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 11:17:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/939395"], "description"=>"<p>Overview of the Matt Algorithm</p>", "links"=>[], "tags"=>["matt"], "article_id"=>609846, "categories"=>["Biological Sciences"], "users"=>["Matthew Menke", "Bonnie Berger", "Lenore Cowen"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.0040010.g001", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Overview_of_the_Matt_Algorithm_/609846", "title"=>"Overview of the Matt Algorithm", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 11:16:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/939632"], "description"=>"<p>Average pairwise RMSD versus average number of residue positions placed in the common core for the SABmark superfamily benchmark.</p>", "links"=>[], "tags"=>["sabmark"], "article_id"=>610083, "categories"=>["Biological Sciences"], "users"=>["Matthew Menke", "Bonnie Berger", "Lenore Cowen"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.0040010.g003", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Matt_SABmark_Performance_Tradeoffs_/610083", "title"=>"Matt SABmark Performance Tradeoffs", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 11:17:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/940112"], "description"=>"<p>Block pair <i>BC</i> precedes block pair <i>DE</i> because <i>B</i> precedes <i>D</i> and <i>C</i> precedes <i>E</i> in their respective protein sequences.</p>", "links"=>[], "tags"=>["sequential", "pairs"], "article_id"=>610556, "categories"=>["Biological Sciences"], "users"=>["Matthew Menke", "Bonnie Berger", "Lenore Cowen"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.0040010.g007", "stats"=>{"downloads"=>5, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Two_Sequential_Block_Pairs_that_Could_Form_Part_of_an_Assembly_/610556", "title"=>"Two Sequential Block Pairs that Could Form Part of an Assembly", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 11:20:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/939861"], "description"=>"<p>Aligned portions of the eight SABmark domains in the set Group 144, consisting of the left-handed β-helix fold as aligned by Posa, Mustang, MultiProt, and Matt. Backbone atoms that participate in the common core of the alignment show up colored as red (PDB ID d1hm9a1), green (PDB ID d1kk6a), blue (PDB ID d1krra), magenta (PDB ID d1lxa), yellow (PDB Is that are not placed into the alignment by the tested algorithm are shown in gray. These pictureD d1ocxa), orange (PDB ID d1qrea), cyan (PDB ID d1xat), and pink (PDB ID d3tdt); residues in all three chains were generated by the Swiss PDB Viewer (DeepView) [<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0040010#pcbi-0040010-b043\" target=\"_blank\">43</a>].</p>", "links"=>[], "tags"=>["Computational biology"], "article_id"=>610306, "categories"=>["Biological Sciences"], "users"=>["Matthew Menke", "Bonnie Berger", "Lenore Cowen"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.0040010.g005", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparative_946_Helix_Alignments_/610306", "title"=>"Comparative β-Helix Alignments", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 11:19:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/939966"], "description"=>"<p>Positive (blue) and SABmark decoy (red) pairwise alignments plotted by RMSD versus number of residues for Matt, FlexProt, MultiProt, and Mustang on the SABmark superfamily set.</p>", "links"=>[], "tags"=>["alignable", "structures"], "article_id"=>610414, "categories"=>["Biological Sciences"], "users"=>["Matthew Menke", "Bonnie Berger", "Lenore Cowen"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.0040010.g006", "stats"=>{"downloads"=>1, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distinguishing_Alignable_Structures_from_Decoys_/610414", "title"=>"Distinguishing Alignable Structures from Decoys", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 11:19:38"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"3", "full-text"=>"3", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"3", "full-text"=>"3", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}
  • {"unique-ip"=>"5", "full-text"=>"3", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"8"}
  • {"unique-ip"=>"14", "full-text"=>"15", "pdf"=>"6", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"9"}
  • {"unique-ip"=>"13", "full-text"=>"12", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"10"}
  • {"unique-ip"=>"11", "full-text"=>"7", "pdf"=>"8", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"5", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"12"}
  • {"unique-ip"=>"16", "full-text"=>"15", "pdf"=>"7", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"6", "year"=>"2020", "month"=>"2"}
  • {"unique-ip"=>"6", "full-text"=>"4", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"3"}
  • {"unique-ip"=>"14", "full-text"=>"15", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"4"}

Relative Metric

{"start_date"=>"2008-01-01T00:00:00Z", "end_date"=>"2008-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences", "average_usage"=>[324, 674, 863, 1015, 1146, 1259, 1360, 1452, 1540, 1621, 1704, 1776, 1843, 1905, 1968, 2029, 2097, 2162, 2233, 2289, 2352, 2412, 2476, 2538, 2601, 2655, 2714, 2777, 2841, 2894, 2946, 2998, 3047, 3103, 3151, 3201, 3258, 3317, 3369, 3424, 3471, 3521, 3583, 3625, 3687, 3743, 3788, 3838, 3896, 3953, 4015, 4075, 4148, 4201, 4275, 4347, 4420, 4486, 4535, 4592, 4660, 4731, 4792, 4845, 4901, 4971, 5027, 5089, 5148, 5200, 5261, 5318, 5374]}, {"subject_area"=>"/Biology and life sciences/Biochemistry", "average_usage"=>[303, 640, 835, 987, 1125, 1245, 1347, 1439, 1513, 1610, 1694, 1763, 1823, 1883, 1949, 2011, 2076, 2137, 2198, 2258, 2326, 2372, 2430, 2512, 2565, 2617, 2681, 2735, 2795, 2850, 2907, 2966, 3033, 3081, 3129, 3177, 3224, 3279, 3334, 3382, 3435, 3489, 3547, 3587, 3634, 3695, 3756, 3810, 3861, 3912, 3984, 4046, 4109, 4169, 4236, 4288, 4346, 4417, 4463, 4536, 4587, 4681, 4731, 4787, 4858, 4910, 4993, 5046, 5100, 5168, 5233, 5283, 5351]}]}
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