Partner-Aware Prediction of Interacting Residues in Protein-Protein Complexes from Sequence Data
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{"title"=>"Partner-aware prediction of interacting residues in protein-protein complexes from sequence data", "type"=>"journal", "authors"=>[{"first_name"=>"Shandar", "last_name"=>"Ahmad", "scopus_author_id"=>"7401993307"}, {"first_name"=>"Kenji", "last_name"=>"Mizuguchi", "scopus_author_id"=>"7101693768"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"doi"=>"10.1371/journal.pone.0029104", "sgr"=>"83355170696", "pmid"=>"22194998", "issn"=>"19326203", "scopus"=>"2-s2.0-83355170696", "pui"=>"363076158"}, "id"=>"270fb952-0d4a-380e-bcba-a52222271ca6", "abstract"=>"Computational prediction of residues that participate in protein-protein interactions is a difficult task, and state of the art methods have shown only limited success in this arena. One possible problem with these methods is that they try to predict interacting residues without incorporating information about the partner protein, although it is unclear how much partner information could enhance prediction performance. To address this issue, the two following comparisons are of crucial significance: (a) comparison between the predictability of inter-protein residue pairs, i.e., predicting exactly which residue pairs interact with each other given two protein sequences; this can be achieved by either combining conventional single-protein predictions or making predictions using a new model trained directly on the residue pairs, and the performance of these two approaches may be compared: (b) comparison between the predictability of the interacting residues in a single protein (irrespective of the partner residue or protein) from conventional methods and predictions converted from the pair-wise trained model. Using these two streams of training and validation procedures and employing similar two-stage neural networks, we showed that the models trained on pair-wise contacts outperformed the partner-unaware models in predicting both interacting pairs and interacting single-protein residues. Prediction performance decreased with the size of the conformational change upon complex formation; this trend is similar to docking, even though no structural information was used in our prediction. An example application that predicts two partner-specific interfaces of a protein was shown to be effective, highlighting the potential of the proposed approach. Finally, a preliminary attempt was made to score docking decoy poses using prediction of interacting residue pairs; this analysis produced an encouraging result.", "link"=>"http://www.mendeley.com/research/partneraware-prediction-interacting-residues-proteinprotein-complexes-sequence-data", "reader_count"=>33, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>3, "Researcher"=>4, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>14, "Student > Master"=>8, "Student > Bachelor"=>2, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>3, "Researcher"=>4, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>14, "Student > Master"=>8, "Student > Bachelor"=>2, "Professor"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>6, "Mathematics"=>2, "Agricultural and Biological Sciences"=>13, "Medicine and Dentistry"=>2, "Arts and Humanities"=>1, "Chemistry"=>1, "Computer Science"=>7}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Chemistry"=>{"Chemistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>13}, "Computer Science"=>{"Computer Science"=>7}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>6}, "Mathematics"=>{"Mathematics"=>2}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "reader_count_by_country"=>{"Poland"=>1, "Australia"=>1}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/703844"], "description"=>"<p>Even though there are few data points in high RMSD category making the statistical point only suggestive in nature, poorer prediction performance for complexes undergoing large conformational change is consistent with the arguments in the discussion.</p>", "links"=>[], "tags"=>["rmsd", "bound", "unbound"], "article_id"=>374208, "categories"=>["Biological Sciences", "Biochemistry", "Biophysics"], "users"=>["Shandar Ahmad", "Kenji Mizuguchi"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0029104.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relationship_between_prediction_performance_and_the_RMSD_between_bound_and_unbound_complexes_/374208", "title"=>"Relationship between prediction performance and the RMSD between bound and unbound complexes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-12-14 01:10:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/703535"], "description"=>"<p>Each plot corresponds to interface propensity of a residue with all of the 20 possible partner residues. Single residue propensity values for the target residue are shown by a horizontal dashed line. See <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029104#pone-0029104-t001\" target=\"_blank\">Table 1</a> for comments and <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029104#pone.0029104.s003\" target=\"_blank\">Table S1</a> for additional details.</p>", "links"=>[], "tags"=>["residue-pair", "propensities", "logarithmic", "protein-protein"], "article_id"=>373901, "categories"=>["Biological Sciences", "Biochemistry", "Biophysics"], "users"=>["Shandar Ahmad", "Kenji Mizuguchi"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0029104.g003"], "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sequence_based_residue_pair_contact_propensities_natural_logarithmic_values_in_a_protein_protein_interface_/373901", "title"=>"Sequence-based residue-pair contact propensities (natural logarithmic values) in a protein-protein interface.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-12-14 01:05:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/703361"], "description"=>"<p>Overall prediction of interacting pairs of residues in two stages.</p>", "links"=>[], "tags"=>["interacting", "pairs", "residues"], "article_id"=>373737, "categories"=>["Biological Sciences", "Biochemistry", "Biophysics"], "users"=>["Shandar Ahmad", "Kenji Mizuguchi"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0029104.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Overall_prediction_of_interacting_pairs_of_residues_in_two_stages_/373737", "title"=>"Overall prediction of interacting pairs of residues in two stages.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-12-14 01:02:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/357697", "https://ndownloader.figshare.com/files/357862", "https://ndownloader.figshare.com/files/358027", "https://ndownloader.figshare.com/files/358149"], "description"=>"<div><p>Computational prediction of residues that participate in protein-protein interactions is a difficult task, and state of the art methods have shown only limited success in this arena. One possible problem with these methods is that they try to predict interacting residues without incorporating information about the partner protein, although it is unclear how much partner information could enhance prediction performance. To address this issue, the two following comparisons are of crucial significance: (a) comparison between the predictability of inter-protein residue pairs, i.e., predicting exactly which residue pairs interact with each other given two protein sequences; this can be achieved by either combining conventional single-protein predictions or making predictions using a new model trained directly on the residue pairs, and the performance of these two approaches may be compared: (b) comparison between the predictability of the interacting residues in a single protein (irrespective of the partner residue or protein) from conventional methods and predictions converted from the pair-wise trained model. Using these two streams of training and validation procedures and employing similar two-stage neural networks, we showed that the models trained on pair-wise contacts outperformed the partner-unaware models in predicting both interacting pairs and interacting single-protein residues. Prediction performance decreased with the size of the conformational change upon complex formation; this trend is similar to docking, even though no structural information was used in our prediction. An example application that predicts two partner-specific interfaces of a protein was shown to be effective, highlighting the potential of the proposed approach. Finally, a preliminary attempt was made to score docking decoy poses using prediction of interacting residue pairs; this analysis produced an encouraging result.</p> </div>", "links"=>[], "tags"=>["partner-aware", "interacting", "residues", "protein-protein", "complexes"], "article_id"=>130704, "categories"=>["Biological Sciences", "Biochemistry", "Biophysics"], "users"=>["Shandar Ahmad", "Kenji Mizuguchi"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0029104.s001", "https://dx.doi.org/10.1371/journal.pone.0029104.s002", "https://dx.doi.org/10.1371/journal.pone.0029104.s003", "https://dx.doi.org/10.1371/journal.pone.0029104.s004"], "stats"=>{"downloads"=>0, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Partner_Aware_Prediction_of_Interacting_Residues_in_Protein_Protein_Complexes_from_Sequence_Data/130704", "title"=>"Partner-Aware Prediction of Interacting Residues in Protein-Protein Complexes from Sequence Data", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-12-14 00:11:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/703210"], "description"=>"<p>For each of the 124 complexes, the data sets were prepared by pairing residues from the ligand and receptor chains for a pair-wise prediction (as shown in the second part of the illustration). Single-residue data were also prepared for the whole complex. However, the residues were not encoded as pairs; they were taken from individual chains and partner information was discarded, and the contact data for all the chains were pooled together to obtain whole-complex data. In one training cycle, the contact and feature data from all but one of the complexes were used for training, and the left-out complex data were then used to evaluate prediction performance. Performance scores were calculated for one complex in one training cycle. The obtained set of 124 scores was then averaged to obtain an overall performance score.</p>", "links"=>[], "tags"=>["single-residue", "complexes", "dimeric", "ligand", "complexed", "receptor", "shown"], "article_id"=>373579, "categories"=>["Biological Sciences", "Biochemistry", "Biophysics"], "users"=>["Shandar Ahmad", "Kenji Mizuguchi"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0029104.g001"], "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Residue_pair_and_single_residue_contact_data_preparation_from_ligand_receptor_complexes_an_example_with_a_dimeric_ligand_complexed_with_a_dimeric_receptor_is_shown_here_/373579", "title"=>"Residue pair and single-residue contact data preparation from ligand/receptor complexes (an example with a dimeric ligand complexed with a dimeric receptor is shown here).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-12-14 00:59:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/703713"], "description"=>"<p>The left and right images were drawn from the top-scoring 20 predictions from single-protein trained models (solid red) and pair-wise trained models (solid green), respectively. Many false positive cases observed in the single-protein trained model were eliminated in the pair-wise model. (The false positive rate in the selected 20 residues is 75% and 50% with an overall AUC of ROC being 60% and 82%, respectively. Predictions are made from the models trained by excluding this complex from the training data.)</p>", "links"=>[], "tags"=>["predictions", "mapped", "three-dimensional", "acetylcholinesterase", "toxin", "f-vii", "fasciculin-2", "chains"], "article_id"=>374073, "categories"=>["Biological Sciences", "Biochemistry", "Biophysics"], "users"=>["Shandar Ahmad", "Kenji Mizuguchi"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0029104.g004"], "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Binding_site_predictions_mapped_to_the_three_dimensional_structure_of_Acetylcholinesterase_in_complex_with_Toxin_F_VII_Fasciculin_2_PDB_ID_1MAH_chains_A_and_F_respectively_in_red_and_blue_color_cartoons_/374073", "title"=>"Binding site predictions mapped to the three-dimensional structure of Acetylcholinesterase in complex with Toxin F-VII Fasciculin-2 (PDB ID: 1MAH, chains A and F respectively in red and blue color cartoons).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-12-14 01:07:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/704099"], "description"=>"<p>The two partners are shown in transparent colors (chain A, which is the beta-adrenergic receptor kinase-1, is shown in red, and chain G, which is the guanine nucleotide binding protein's gamma-2 subunit, is shown in green). Predictions from the pair-wise model for each partner chain were converted into single chain predictions and displayed on chain B. Common binding sites, predicted with both partners, were removed and residues exclusively predicted with each partner are shown in the corresponding partner color. Out of the 30 top-scoring residues after removing common predictions, most residues have been assigned to the correct partner.</p>", "links"=>[], "tags"=>["interfaces", "beta", "subunit", "guanine", "nucleotide", "binding", "shown"], "article_id"=>374455, "categories"=>["Biological Sciences", "Biochemistry", "Biophysics"], "users"=>["Shandar Ahmad", "Kenji Mizuguchi"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0029104.g006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Partner_specific_prediction_of_two_interfaces_for_the_beta_subunit_of_the_guanine_nucleotide_binding_protein_transducin_beta_chain_1_PDB_ID_3PSC_chain_B_is_shown_as_the_blue_cartoon_/374455", "title"=>"Partner-specific prediction of two interfaces for the beta subunit of the guanine nucleotide binding protein (transducin beta chain 1) (PDB ID: 3PSC, chain B is shown as the blue cartoon).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-12-14 01:14:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/704288"], "description"=>"<p>Complete data for the performance of each protein complex and other measures of performance (e.g., precision, recall and F-measure) are provided in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029104#pone.0029104.s003\" target=\"_blank\">Table S1</a>. The classification was taken from the original curators <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029104#pone.0029104-Hwang1\" target=\"_blank\">[39]</a>.</p>", "links"=>[], "tags"=>["pair-wise", "predictions", "grouped", "reported", "structure-based"], "article_id"=>374646, "categories"=>["Biological Sciences", "Biochemistry", "Biophysics"], "users"=>["Shandar Ahmad", "Kenji Mizuguchi"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0029104.t003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Performance_of_pair_wise_predictions_grouped_by_reported_difficulty_level_in_structure_based_predictions_and_functional_class_/374646", "title"=>"Performance of pair-wise predictions grouped by reported difficulty level in structure-based predictions and functional class.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-12-14 01:17:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/704257"], "description"=>"<p>The results from the current model are based on a 7-residue window from the protein and contain information from the sequence PSSM and global amino acid composition of the protein (for stage 2 models, the predictions from all window sizes from 1 to 7 were averaged). The p-values were computed by taking protein-wise performance scores and applying the paired Student's t-test over a set of values in the two models being compared.</p><p>*These online predictions (PSIVER and SPPIDER) are based on a single model and are optimized for binding site definitions and data sets that are different from those used in this study. Although our performance appears to be higher than those of these web servers, the choice of data sets, contact definitions and performance evaluation method used were not extensively examined because the main objective of this work was to establish the point that was made in the top two rows of this table. The performance scores from the online web servers are provided only as a record (see also the results and discussion).</p>", "links"=>[], "tags"=>["levels"], "article_id"=>374628, "categories"=>["Biological Sciences", "Biochemistry", "Biophysics"], "users"=>["Shandar Ahmad", "Kenji Mizuguchi"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0029104.t002"], "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_between_the_performance_levels_of_the_various_models_/374628", "title"=>"Comparison between the performance levels of the various models.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-12-14 01:17:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/704229"], "description"=>"<p>The residue pairs presenting most significant p-values (top 10 from the favored and excluded categories each) are listed here. It should be noted that the data were derived from all residues of the complex, and that the surface propensity of the residues is implicitly included. Near absence of the hydrophobic residues in the top scoring pairs highlights the fact that from a purely sequence point of view hydrophobic pairs may not be the best interface candidates. However, if only the surface residues were considered (using structure information), situation might be different.</p>", "links"=>[], "tags"=>["occurrences", "protein-protein", "interfaces", "derived"], "article_id"=>374591, "categories"=>["Biological Sciences", "Biochemistry", "Biophysics"], "users"=>["Shandar Ahmad", "Kenji Mizuguchi"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0029104.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_most_significant_contact_occurrences_in_protein_protein_interfaces_derived_from_protein_protein_complexes_/374591", "title"=>"The most significant contact occurrences in protein-protein interfaces derived from protein-protein complexes.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-12-14 01:16:31"}

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Relative Metric

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