GARN: Sampling RNA 3D Structure Space with Game Theory and Knowledge-Based Scoring Strategies
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{"title"=>"GARN: Sampling RNA 3D structure space with game theory and knowledge-based scoring strategies", "type"=>"journal", "authors"=>[{"first_name"=>"Mélanie", "last_name"=>"Boudard", "scopus_author_id"=>"56035924500"}, {"first_name"=>"Julie", "last_name"=>"Bernauer", "scopus_author_id"=>"8584012600"}, {"first_name"=>"Dominique", "last_name"=>"Barth", "scopus_author_id"=>"7102201205"}, {"first_name"=>"Johanne", "last_name"=>"Cohen", "scopus_author_id"=>"36652396300"}, {"first_name"=>"Alain", "last_name"=>"Denise", "scopus_author_id"=>"6602851578"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "pui"=>"606225811", "sgr"=>"84943328936", "doi"=>"10.1371/journal.pone.0136444", "scopus"=>"2-s2.0-84943328936", "pmid"=>"26313379"}, "id"=>"bb8c65b5-d677-3fe2-9c7a-acab45135a58", "abstract"=>"Cellular processes involve large numbers of RNA molecules. The functions of these RNA molecules and their binding to molecular machines are highly dependent on their 3D structures. One of the key challenges in RNA structure prediction and modeling is predicting the spatial arrangement of the various structural elements of RNA. As RNA folding is generally hierarchical, methods involving coarse-grained models hold great promise for this purpose. We present here a novel coarse-grained method for sampling, based on game theory and knowledge-based potentials. This strategy, GARN (Game Algorithm for RNa sampling), is often much faster than previously described techniques and generates large sets of solutions closely resembling the native structure. GARN is thus a suitable starting point for the molecular modeling of large RNAs, particularly those with experimental constraints. GARN is available from: http://garn.lri.fr/.", "link"=>"http://www.mendeley.com/research/garn-sampling-rna-3d-structure-space-game-theory-knowledgebased-scoring-strategies", "reader_count"=>9, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Researcher"=>2, "Student > Ph. D. Student"=>2, "Student > Postgraduate"=>1, "Student > Master"=>2, "Student > Bachelor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Researcher"=>2, "Student > Ph. D. Student"=>2, "Student > Postgraduate"=>1, "Student > Master"=>2, "Student > Bachelor"=>1}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>4, "Materials Science"=>1, "Mathematics"=>1, "Agricultural and Biological Sciences"=>3}, "reader_count_by_subdiscipline"=>{"Materials Science"=>{"Materials Science"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}, "Mathematics"=>{"Mathematics"=>1}}, "reader_count_by_country"=>{"Poland"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2230512"], "description"=>"<p>Results from GARN runs with default parameters for full structures were compared with those for iFoldRNA, MCSym, FARNA and NAST. Not all servers can handle the ten structures of the <i>test set</i>, either due to the complexity of sampling or because the fragment templates are not available. For iFoldRNA, the only input provided to the server is the sequence. For NAST, only the secondary structure is used. The results obtained with NAST and iFoldRNA are therefore less accurate than those obtained with other techniques. NAST performs well on molecules of fewer than 50 nucleotides, but information about tertiary interactions is required to improve the results obtained. Our procedure not only yields better overall results for the minimal RMSD structure, it also provides several structures close to that of the native sample to choose from.</p>", "links"=>[], "tags"=>["Sampling RNA 3 D Structure Space", "RNA structure prediction", "GARN", "RNA molecules", "3 D structures"], "article_id"=>1525472, "categories"=>["Uncategorised"], "users"=>["Mélanie Boudard", "Julie Bernauer", "Dominique Barth", "Johanne Cohen", "Alain Denise"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0136444.t001", "stats"=>{"downloads"=>2, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_with_other_methods_/1525472", "title"=>"Comparison with other methods.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-08-27 03:07:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/2230510"], "description"=>"<p>The top left panel shows the structure and its associated GARN graph. Panel (1) shows the best three-way junction obtained with GARN (in pink) superimposed on the native structure graph (in white). Panels (2) and (3) show the second-best three-way junctions (in pink) superimposed on the native structure graph (in white).</p>", "links"=>[], "tags"=>["Sampling RNA 3 D Structure Space", "RNA structure prediction", "GARN", "RNA molecules", "3 D structures"], "article_id"=>1525470, "categories"=>["Uncategorised"], "users"=>["Mélanie Boudard", "Julie Bernauer", "Dominique Barth", "Johanne Cohen", "Alain Denise"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0136444.g004", "stats"=>{"downloads"=>3, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Three_way_junction_structure_results_for_the_7S_RNA_of_human_SRP_PDB_ID_1MFQ_/1525470", "title"=>"Three-way junction structure results for the 7S RNA of human SRP (PDB ID 1MFQ).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-27 03:07:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/2230507"], "description"=>"<p>(I) Each game consists of several turns obeying a common set of rules. First, one or all the players choose a strategy (a direction on the grid) according to the relative probabilities of their choosing each strategy. The score is then updated by one or all the players, based on their distances from the other players, and the probabilities are then updated. Depending on the type of game, three schemes are possible (II): (a) in the AA game, all players apply a strategy and all players then calculate their scores, in two successive steps, (b) in the OA game, all players calculate their score each time a single player plays (the usual total number of turns <i>k</i> is thus divided by the number of players to allow for the same relative number of iterations), (c) in the OO game, each player applies a strategy and the score for that player is calculated before the next player plays.</p>", "links"=>[], "tags"=>["Sampling RNA 3 D Structure Space", "RNA structure prediction", "GARN", "RNA molecules", "3 D structures"], "article_id"=>1525467, "categories"=>["Uncategorised"], "users"=>["Mélanie Boudard", "Julie Bernauer", "Dominique Barth", "Johanne Cohen", "Alain Denise"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0136444.g002", "stats"=>{"downloads"=>3, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Overview_of_the_gameplay_/1525467", "title"=>"Overview of the gameplay.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-27 03:07:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/2230521", "https://ndownloader.figshare.com/files/2230522", "https://ndownloader.figshare.com/files/2230523", "https://ndownloader.figshare.com/files/2230524", "https://ndownloader.figshare.com/files/2230525", "https://ndownloader.figshare.com/files/2230526", "https://ndownloader.figshare.com/files/2230527", "https://ndownloader.figshare.com/files/2230528", "https://ndownloader.figshare.com/files/2230529", "https://ndownloader.figshare.com/files/2230530", "https://ndownloader.figshare.com/files/2230531", "https://ndownloader.figshare.com/files/2230532", "https://ndownloader.figshare.com/files/2230533", "https://ndownloader.figshare.com/files/2230534", "https://ndownloader.figshare.com/files/2230535", "https://ndownloader.figshare.com/files/2230536", "https://ndownloader.figshare.com/files/2230537", "https://ndownloader.figshare.com/files/2230538", "https://ndownloader.figshare.com/files/2230539", "https://ndownloader.figshare.com/files/2230540", "https://ndownloader.figshare.com/files/2230541", "https://ndownloader.figshare.com/files/2230542", "https://ndownloader.figshare.com/files/2230543", "https://ndownloader.figshare.com/files/2230544", "https://ndownloader.figshare.com/files/2230545"], "description"=>"<div><p>Cellular processes involve large numbers of RNA molecules. The functions of these RNA molecules and their binding to molecular machines are highly dependent on their 3D structures. One of the key challenges in RNA structure prediction and modeling is predicting the spatial arrangement of the various structural elements of RNA. As RNA folding is generally hierarchical, methods involving coarse-grained models hold great promise for this purpose. We present here a novel coarse-grained method for sampling, based on game theory and knowledge-based potentials. This strategy, GARN (Game Algorithm for RNa sampling), is often much faster than previously described techniques and generates large sets of solutions closely resembling the native structure. GARN is thus a suitable starting point for the molecular modeling of large RNAs, particularly those with experimental constraints. GARN is available from: <a href=\"http://garn.lri.fr/\" target=\"_blank\">http://garn.lri.fr/</a>.</p></div>", "links"=>[], "tags"=>["Sampling RNA 3 D Structure Space", "RNA structure prediction", "GARN", "RNA molecules", "3 D structures"], "article_id"=>1525481, "categories"=>["Uncategorised"], "users"=>["Mélanie Boudard", "Julie Bernauer", "Dominique Barth", "Johanne Cohen", "Alain Denise"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0136444.s001", "https://dx.doi.org/10.1371/journal.pone.0136444.s002", "https://dx.doi.org/10.1371/journal.pone.0136444.s003", "https://dx.doi.org/10.1371/journal.pone.0136444.s004", "https://dx.doi.org/10.1371/journal.pone.0136444.s005", "https://dx.doi.org/10.1371/journal.pone.0136444.s006", "https://dx.doi.org/10.1371/journal.pone.0136444.s007", "https://dx.doi.org/10.1371/journal.pone.0136444.s008", "https://dx.doi.org/10.1371/journal.pone.0136444.s009", "https://dx.doi.org/10.1371/journal.pone.0136444.s010", "https://dx.doi.org/10.1371/journal.pone.0136444.s011", "https://dx.doi.org/10.1371/journal.pone.0136444.s012", "https://dx.doi.org/10.1371/journal.pone.0136444.s013", "https://dx.doi.org/10.1371/journal.pone.0136444.s014", "https://dx.doi.org/10.1371/journal.pone.0136444.s015", "https://dx.doi.org/10.1371/journal.pone.0136444.s016", "https://dx.doi.org/10.1371/journal.pone.0136444.s017", "https://dx.doi.org/10.1371/journal.pone.0136444.s018", "https://dx.doi.org/10.1371/journal.pone.0136444.s019", "https://dx.doi.org/10.1371/journal.pone.0136444.s020", "https://dx.doi.org/10.1371/journal.pone.0136444.s021", "https://dx.doi.org/10.1371/journal.pone.0136444.s022", "https://dx.doi.org/10.1371/journal.pone.0136444.s023", "https://dx.doi.org/10.1371/journal.pone.0136444.s024", "https://dx.doi.org/10.1371/journal.pone.0136444.s025"], "stats"=>{"downloads"=>26, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_GARN_Sampling_RNA_3D_Structure_Space_with_Game_Theory_and_Knowledge_Based_Scoring_Strategies_/1525481", "title"=>"GARN: Sampling RNA 3D Structure Space with Game Theory and Knowledge-Based Scoring Strategies", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-08-27 03:07:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/2230501"], "description"=>"<p>Nodes (players) are built from the secondary structure representation in which base-paired nucleotides are shown in blue and free nucleotides are shown in yellow. Blue nodes correspond to helices and yellow nodes to junctions. Each element, except the three-way junction is represented by one node (shown as a sphere), taken to be the geometric center of the heavy atoms. The three-way junction contains two nodes, accounting for helical stacking and branching, respectively.</p>", "links"=>[], "tags"=>["Sampling RNA 3 D Structure Space", "RNA structure prediction", "GARN", "RNA molecules", "3 D structures"], "article_id"=>1525461, "categories"=>["Uncategorised"], "users"=>["Mélanie Boudard", "Julie Bernauer", "Dominique Barth", "Johanne Cohen", "Alain Denise"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0136444.g001", "stats"=>{"downloads"=>2, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Graph_representation_of_the_xpt_pbuX_guanine_riboswitch_aptamer_domain_PDB_ID_4FE5_/1525461", "title"=>"Graph representation of the xpt-pbuX guanine riboswitch aptamer domain (PDB ID: 4FE5).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-27 03:07:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/2230509"], "description"=>"<p>The native structure graph is superimposed on the X-ray structure in the top panel. This superimposition indicates that the native structure graph (in blue and yellow) represents the native X-ray structure well. From top to bottom, the graphs most closely matching the native graphs are shown in gray (the darker the gray, the closer the match), superimposed on the native structure graph. These graphs show a good range of samples that could be used for reconstruction: the global shape of the molecule is recovered and the geometry of the junction is of interest.</p>", "links"=>[], "tags"=>["Sampling RNA 3 D Structure Space", "RNA structure prediction", "GARN", "RNA molecules", "3 D structures"], "article_id"=>1525469, "categories"=>["Uncategorised"], "users"=>["Mélanie Boudard", "Julie Bernauer", "Dominique Barth", "Johanne Cohen", "Alain Denise"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0136444.g003", "stats"=>{"downloads"=>3, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Visualization_of_five_near_native_samples_for_the_7S_RNA_of_human_SRP_PDB_ID_1MFQ_/1525469", "title"=>"Visualization of five near-native samples for the 7S RNA of human SRP (PDB ID 1MFQ).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-27 03:07:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/2230513"], "description"=>"<p>The RNAJAG results are taken from [<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0136444#pone.0136444.ref030\" target=\"_blank\">30</a>] and were obtained with a different graph model. The RMSD values are, therefore, not directly comparable. Missing data indicate that the default server settings were unable to handle the request. The 4GXY four-way junction is represented by two three-way junctions. For each technique, 50 samples were requested.</p>", "links"=>[], "tags"=>["Sampling RNA 3 D Structure Space", "RNA structure prediction", "GARN", "RNA molecules", "3 D structures"], "article_id"=>1525473, "categories"=>["Uncategorised"], "users"=>["Mélanie Boudard", "Julie Bernauer", "Dominique Barth", "Johanne Cohen", "Alain Denise"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0136444.t002", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_with_other_prediction_methods_for_three_way_junctions_/1525473", "title"=>"Comparison with other prediction methods for three-way junctions.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-08-27 03:07:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/2230511"], "description"=>"<p>The best model generated by GARN (in pink) and the equivalent coarse-grained models obtained with other techniques are superimposed on the native structure graph (in black). The GARN technique does not enforce packing, but frequently provides the solution closest to the native structure.</p>", "links"=>[], "tags"=>["Sampling RNA 3 D Structure Space", "RNA structure prediction", "GARN", "RNA molecules", "3 D structures"], "article_id"=>1525471, "categories"=>["Uncategorised"], "users"=>["Mélanie Boudard", "Julie Bernauer", "Dominique Barth", "Johanne Cohen", "Alain Denise"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0136444.g005", "stats"=>{"downloads"=>6, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_with_other_RNA_structure_prediction_methods_for_the_7S_RNA_of_human_SRP_PDB_ID_1MFQ_/1525471", "title"=>"Comparison with other RNA structure prediction methods for the 7S RNA of human SRP (PDB ID 1MFQ).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-27 03:07:10"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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