Structural Constraints on the Covariance Matrix Derived from Multiple Aligned Protein Sequences
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Mendeley | Further Information

{"title"=>"Structural constraints on the covariance matrix derived from multiple aligned protein sequences", "type"=>"journal", "authors"=>[{"first_name"=>"William R.", "last_name"=>"Taylor", "scopus_author_id"=>"7402890169"}, {"first_name"=>"Michael I.", "last_name"=>"Sadowski", "scopus_author_id"=>"8686419200"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"isbn"=>"1932-6203 (Electronic)\\n1932-6203 (Linking)", "sgr"=>"82655183567", "pui"=>"363029633", "scopus"=>"2-s2.0-82655183567", "issn"=>"19326203", "pmid"=>"22194819", "doi"=>"10.1371/journal.pone.0028265"}, "id"=>"0b355a2d-6dfc-3d04-aed0-9dc90cece611", "abstract"=>"Residue contact predictions were calculated based on the mutual information observed between pairs of positions in large multiple protein sequence alignments. Where previously only the statistical properties of these data have been considered important, we introduce new measures to impose constraints that make the contact map more consistent with a three dimensional structure. These included global (bulk) properties and local secondary structure properties. The latter allowed the contact constraints to be employed at the level of filtering pairs of secondary structure contacts which led to a more efficient (lower-level) implementation in the PLATO structure prediction server. Where previously the measure of success with this method had been whether the correct fold was predicted in the top 10 ranked models, with the current implementation, our summary statistic is the number of correct folds included in the top 10 models--which is on average over 50 percent.", "link"=>"http://www.mendeley.com/research/structural-constraints-covariance-matrix-derived-multiple-aligned-protein-sequences", "reader_count"=>22, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>4, "Researcher"=>7, "Student > Ph. D. Student"=>6, "Student > Master"=>3, "Other"=>1, "Student > Bachelor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>4, "Researcher"=>7, "Student > Ph. D. Student"=>6, "Student > Master"=>3, "Other"=>1, "Student > Bachelor"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>4, "Agricultural and Biological Sciences"=>12, "Business, Management and Accounting"=>1, "Chemistry"=>1, "Computer Science"=>3}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Chemistry"=>{"Chemistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>12}, "Computer Science"=>{"Computer Science"=>3}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}}, "reader_count_by_country"=>{"United States"=>1, "United Kingdom"=>2, "Germany"=>1, "India"=>1}, "group_count"=>2}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/706249"], "description"=>"<p>Pseudo-centroid contacts under 8 Å are plotted in green.</p>", "links"=>[], "tags"=>["contacts", "re-balancing", "correction"], "article_id"=>376612, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Physics", "Biochemistry", "Biophysics"], "users"=>["William R. Taylor", "Michael I. Sadowski"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0028265.g004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Contact_map_for_1f4pA_showing_predicted_contacts_before_re_balancing_lower_right_and_after_correction_upper_left_/376612", "title"=>"Contact map for 1f4pA showing predicted contacts before re-balancing (lower-right) and after correction (upper-left).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-12-05 01:50:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/705929"], "description"=>"<p>The number of contacts between pseudo-centroids for the domains included in the SCOP40 database is plotted against the number of residues in the domain (Protein length). The green line is the best-fit to the data over the plotted range.</p>", "links"=>[], "tags"=>["contacts"], "article_id"=>376294, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Physics", "Biochemistry", "Biophysics"], "users"=>["William R. Taylor", "Michael I. Sadowski"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0028265.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_contacts_with_protein_length_/376294", "title"=>"Number of contacts with protein length.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-12-05 01:44:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/706334"], "description"=>"<p>The cumulative total number of true folds is plotted against the log(rank) of the model in the ranked list of decoys, up to a maximum of 10,000 models (4). As less than this number were sometimes constructed, the plots can end in ‘mid-air’. The result for the basic PLATO method is plotted in bold cyan. The models constructed by the contact augmented method were ranked by three scores: red, using just the basic PLATO score; green, using just the predicted contacts, and blue, using their combined score. The plots in dashed lines are the results after re-balancing the contact matrix with the structural constraints described in the text, using the same colour assignments.</p>", "links"=>[], "tags"=>["2trxa", "1f4pa", "3chya", "folds"], "article_id"=>376692, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Physics", "Biochemistry", "Biophysics"], "users"=>["William R. Taylor", "Michael I. Sadowski"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0028265.g005", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_parts_a_2trxA_b_1f4pA_c_3chyA_d_5p21A_True_folds_against_log_rank_/376692", "title"=>"[parts: (a) 2trxA (b) 1f4pA (c) 3chyA (d) 5p21A]: True folds against (log) rank.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-12-05 01:51:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/706493"], "description"=>"<p>Of the five proteins considered, one (1cozA) did not produce models and is not tabulated. For each of the other proteins (PDB) the number of decoys constructed by the basic PLATO method is tabulated in the leftmost column along with those using the PLATO method with direct contact (DC) information and, in parenthes, the number after applying structural constraints to the contact matrix. The computer execution time is roughly proportional to these numbers. The number of true folds (defined by topology string) found in the top 5 and top 10 ranked positions is tabulated for the basic PLATO method and the DC augmented method ranked by the PLATO score and the DC score combined as their geometric mean as used previously (with the arithmetic mean in parenthes). The number of hits over larger subsets is more easily seen in the plots in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0028265#pone-0028265-g005\" target=\"_blank\">Figure 5</a>. In the rightmost column, the root mean square (RMS) deviation was calculated over the number of residues (CA atoms) shown in parentheses for the top model. These values are slightly higher than some reported previously as the current models were not selected using residue-level contact data.</p>", "links"=>[], "tags"=>["decoy"], "article_id"=>376862, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Physics", "Biochemistry", "Biophysics"], "users"=>["William R. Taylor", "Michael I. Sadowski"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0028265.t001", "stats"=>{"downloads"=>3, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Fold_recognition_over_the_test_decoy_sets_/376862", "title"=>"Fold recognition over the test decoy sets.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-12-05 01:54:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/706420"], "description"=>"<p>The <b>Target sequence</b> to be predicted is matched against the sequence database to generate a multiple <b>Sequence alignment</b> which is used both to predict secondary structure (<b>Predicted Sec. Str.s</b>) and residue contacts (<b>Predicted contacts</b>). These two derived data sets are combined to estimate pairwise packing interactions at the secondary structure element (SSE) level (<b>Sec. Str. packings</b>) which are used in the PLATO method firstly to select the structural class of the protein via <b>2D SSE layouts</b> of the secondary structures. The corresponding stick models (<b>3D ‘stick’ Forms</b>) provide the framework over which different protein folds are combinatorially generated with pairings of secondary structures being evaluated by their predicted packing score. The ‘stick’ folds are then constructed at the residue (α-carbon) level giving the final set of <b>Ca ranked Folds</b>.</p>", "links"=>[], "tags"=>["decoy"], "article_id"=>376791, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Physics", "Biochemistry", "Biophysics"], "users"=>["William R. Taylor", "Michael I. Sadowski"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0028265.g006", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Overview_of_decoy_model_construction_/376791", "title"=>"Overview of decoy model construction.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-12-05 01:53:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/358237", "https://ndownloader.figshare.com/files/358247"], "description"=>"<div><p>Residue contact predictions were calculated based on the mutual information observed between pairs of positions in large multiple protein sequence alignments. Where previously only the statistical properties of these data have been considered important, we introduce new measures to impose constraints that make the contact map more consistent with a three dimensional structure. These included global (bulk) properties and local secondary structure properties. The latter allowed the contact constraints to be employed at the level of filtering pairs of secondary structure contacts which led to a more efficient (lower-level) implementation in the PLATO structure prediction server. Where previously the measure of success with this method had been whether the correct fold was predicted in the top 10 ranked models, with the current implementation, our summary statistic is the number of correct folds included in the top 10 models — which is on average over 50 percent.</p> </div>", "links"=>[], "tags"=>["constraints", "covariance", "matrix", "derived", "aligned", "sequences"], "article_id"=>130808, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Physics", "Biochemistry", "Biophysics"], "users"=>["William R. Taylor", "Michael I. Sadowski"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0028265.s001", "https://dx.doi.org/10.1371/journal.pone.0028265.s002"], "stats"=>{"downloads"=>23, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Structural_Constraints_on_the_Covariance_Matrix_Derived_from_Multiple_Aligned_Protein_Sequences/130808", "title"=>"Structural Constraints on the Covariance Matrix Derived from Multiple Aligned Protein Sequences", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-12-05 00:13:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/706111"], "description"=>"<p>(<i>a</i>) The number of pseudo-centroid contacts is plotted against the fractional sequence separation of the pair with 0 = adjacent to 1 = terminal residues. The red lines each represent data from the SCOP40 database in ten length bins spanning 100 to 200 residues. The green line is a fitted curve (described in the text). Note: it is coincidental that this curve is similar to that plotted in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0028265#pone-0028265-g002\" target=\"_blank\">Figure 2</a>. (<i>b</i>) Individual data for 1f4pA plotted using the same colours as <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0028265#pone-0028265-g002\" target=\"_blank\">Figure 2</a>.</p>", "links"=>[], "tags"=>["contacts"], "article_id"=>376477, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Physics", "Biochemistry", "Biophysics"], "users"=>["William R. Taylor", "Michael I. Sadowski"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0028265.g003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_contacts_with_sequence_separation_/376477", "title"=>"Number of contacts with sequence separation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-12-05 01:47:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/705977"], "description"=>"<p>(<i>a</i>) The number of pseudo-centroid contacts is plotted against the fractional rank of the residues in the protein where 0 is most dense and 1 least dense. The red lines each represent data from the SCOP40 database in ten length bins spanning 100 to 200 residues. The green line is a fitted curve (described in the text). (<i>b</i>) Predicted contacts for 1f4p before correction (cyan) and after correction (red) are plotted along with the observed contacts (green) and the theoretical curve from part <i>a</i> (blue).</p>", "links"=>[], "tags"=>["contacts"], "article_id"=>376350, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Physics", "Biochemistry", "Biophysics"], "users"=>["William R. Taylor", "Michael I. Sadowski"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0028265.g002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_contacts_per_residue_/376350", "title"=>"Number of contacts per residue.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-12-05 01:45:50"}

PMC Usage Stats | Further Information

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Relative Metric

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