Predictions of Hot Spot Residues at Protein-Protein Interfaces Using Support Vector Machines
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{"title"=>"Predictions of hot spot residues at protein-protein interfaces using support vector machines", "type"=>"journal", "authors"=>[{"first_name"=>"Stefano", "last_name"=>"Lise", "scopus_author_id"=>"6701624432"}, {"first_name"=>"Daniel", "last_name"=>"Buchan", "scopus_author_id"=>"6701578325"}, {"first_name"=>"Massimiliano", "last_name"=>"Pontil", "scopus_author_id"=>"6603887035"}, {"first_name"=>"David T.", "last_name"=>"Jones", "scopus_author_id"=>"55718421500"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-79952205470", "sgr"=>"79952205470", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0016774", "pmid"=>"21386962", "isbn"=>"1932-6203 (Electronic)\\n1932-6203 (Linking)", "pui"=>"361364858"}, "id"=>"e17854ea-7245-3a61-a806-384daf0af4f1", "abstract"=>"Protein-protein interactions are critically dependent on just a few 'hot spot' residues at the interface. Hot spots make a dominant contribution to the free energy of binding and they can disrupt the interaction if mutated to alanine. Here, we present HSPred, a support vector machine(SVM)-based method to predict hot spot residues, given the structure of a complex. HSPred represents an improvement over a previously described approach (Lise et al, BMC Bioinformatics 2009, 10:365). It achieves higher accuracy by treating separately predictions involving either an arginine or a glutamic acid residue. These are the amino acid types on which the original model did not perform well. We have therefore developed two additional SVM classifiers, specifically optimised for these cases. HSPred reaches an overall precision and recall respectively of 61% and 69%, which roughly corresponds to a 10% improvement. An implementation of the described method is available as a web server at http://bioinf.cs.ucl.ac.uk/hspred. It is free to non-commercial users.", "link"=>"http://www.mendeley.com/research/predictions-hot-spot-residues-proteinprotein-interfaces-using-support-vector-machines", "reader_count"=>79, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>6, "Researcher"=>22, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>26, "Student > Postgraduate"=>2, "Other"=>3, "Student > Master"=>9, "Student > Bachelor"=>3, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>6, "Researcher"=>22, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>26, "Student > Postgraduate"=>2, "Other"=>3, "Student > Master"=>9, "Student > Bachelor"=>3, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>11, "Agricultural and Biological Sciences"=>36, "Medicine and Dentistry"=>1, "Arts and Humanities"=>2, "Physics and Astronomy"=>1, "Chemistry"=>16, "Social Sciences"=>1, "Computer Science"=>7}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Chemistry"=>{"Chemistry"=>16}, "Social Sciences"=>{"Social Sciences"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>36}, "Computer Science"=>{"Computer Science"=>7}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>11}, "Unspecified"=>{"Unspecified"=>3}, "Environmental Science"=>{"Environmental Science"=>1}, "Arts and Humanities"=>{"Arts and Humanities"=>2}}, "reader_count_by_country"=>{"Republic of Singapore"=>1, "Argentina"=>1, "Korea (South)"=>1, "United States"=>1, "China"=>1, "United Kingdom"=>4, "Australia"=>1, "France"=>1, "India"=>1, "Spain"=>1}, "group_count"=>1}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/794642"], "description"=>"<p>We report the absolute values of the correlation coefficients between energy features and the observed (values greater than 0.2 are in bold).</p>", "links"=>[], "tags"=>["observed"], "article_id"=>465022, "categories"=>["Biological Sciences", "Biochemistry"], "users"=>["Stefano Lise", "Daniel Buchan", "Massimiliano Pontil", "David T. Jones"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016774.t003", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Correlation_of_energy_terms_with_observed_values_/465022", "title"=>"Correlation of energy terms with observed values.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 20:13:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/794359"], "description"=>"<p>Mapping of HSPred predictions onto the the complex (PDB code: 1LFD). The monomers have been rotated to display the interface. Red residues are correctly predicted hot spots (true positives); blue residues are correctly predicted non hot spots (true negatives); yellow residues are non hot spots erroneously predicts as hot spots (false positives).</p>", "links"=>[], "tags"=>["Computational biology", "Biochemistry"], "article_id"=>464739, "categories"=>["Biological Sciences", "Biochemistry"], "users"=>["Stefano Lise", "Daniel Buchan", "Massimiliano Pontil", "David T. Jones"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016774.g003", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Ras_RalGDS_complex_/464739", "title"=>"Ras/RalGDS complex.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 20:11:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/794669"], "description"=>"<p>We report the absolute value of the weight associated to each feature in the scoring functions, together with the threshold that defines the decision boundary. Energy terms which are not included in the scoring function are denoted with the symbol.</p>", "links"=>[], "tags"=>["scoring"], "article_id"=>465044, "categories"=>["Biological Sciences", "Biochemistry"], "users"=>["Stefano Lise", "Daniel Buchan", "Massimiliano Pontil", "David T. Jones"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016774.t002", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Weight_of_energy_terms_in_the_scoring_functions_/465044", "title"=>"Weight of energy terms in the scoring functions.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 20:13:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/794209"], "description"=>"<p>Only the most frequent amino acid in the database are reported. In (a) are the results for SVM, in (b) for HSPred, which includes SVM and SVM.</p>", "links"=>[], "tags"=>["amino"], "article_id"=>464591, "categories"=>["Biological Sciences", "Biochemistry"], "users"=>["Stefano Lise", "Daniel Buchan", "Massimiliano Pontil", "David T. Jones"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016774.g002", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Predictions_results_for_different_amino_acids_/464591", "title"=>"Predictions results for different amino acids.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 20:10:59"}
  • {"files"=>["https://ndownloader.figshare.com/files/794506"], "description"=>"<p>Screenshot of the results page for the IL-4/IL-4R complex (PDB code: 1IAR). On top, predictions are visualised using a Jmol applet. On the left is IL-4 (chain A), on the right IL-4R (chain B). Predicted hot spots are in red, non hot spots in white. Residues not part of the interface are in blue. Below, predictions scores for each interface residues (excluding Pro and Gly amino acids) are reported (note that only the first few residues are displayed here). Scores greater than zero corresponds to predicted hot spots.</p>", "links"=>[], "tags"=>["hspred"], "article_id"=>464878, "categories"=>["Biological Sciences", "Biochemistry"], "users"=>["Stefano Lise", "Daniel Buchan", "Massimiliano Pontil", "David T. Jones"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016774.g004", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sample_output_for_the_HSPred_server_/464878", "title"=>"Sample output for the HSPred server.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 20:12:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/794695"], "description"=>"<p>Cross-validated estimates of performances for SVM and HSPred. MCC is the Matthews correlation coefficient (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0016774#s3\" target=\"_blank\">Methods</a> section for definition of the various performance measures).</p>", "links"=>[], "tags"=>["Computational biology", "Biochemistry"], "article_id"=>465071, "categories"=>["Biological Sciences", "Biochemistry"], "users"=>["Stefano Lise", "Daniel Buchan", "Massimiliano Pontil", "David T. Jones"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016774.t001", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_results_/465071", "title"=>"Summary of results.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 20:13:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/794051"], "description"=>"<p>The red filled area, (a), corresponds to side-chain atoms of the mutated residue; the red and blue striped regions, (b) and (c) respectively, correspond to atoms within of the of the mutated residue. We distinguish types of interactions: <i>side-chain inter-molecular</i> between (a) and (c), <i>environment inter-molecular</i> between (b) and (c), <i>side-chain intra-molecular</i> between (a) and (b).</p>", "links"=>[], "tags"=>["overview", "regions"], "article_id"=>464417, "categories"=>["Biological Sciences", "Biochemistry"], "users"=>["Stefano Lise", "Daniel Buchan", "Massimiliano Pontil", "David T. Jones"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016774.g001", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_overview_of_protein_structural_regions_which_define_the_different_energy_contributions_/464417", "title"=>"Schematic overview of protein structural regions which define the different energy contributions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 20:09:57"}

PMC Usage Stats | Further Information

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Relative Metric

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