CPORT: A Consensus Interface Predictor and Its Performance in Prediction-Driven Docking with HADDOCK
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{"title"=>"Cport: A consensus interface predictor and its performance in prediction-driven docking with HADDOCK", "type"=>"journal", "authors"=>[{"first_name"=>"Sjoerd J.", "last_name"=>"de Vries", "scopus_author_id"=>"8608761200"}, {"first_name"=>"Alexandre M.J.J.", "last_name"=>"Bonvin", "scopus_author_id"=>"7003870500"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"361500799", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0017695", "scopus"=>"2-s2.0-79953040045", "pmid"=>"21464987", "sgr"=>"79953040045"}, "id"=>"be41bc89-0823-3d61-9189-f75e1e1379f9", "abstract"=>"BACKGROUND Macromolecular complexes are the molecular machines of the cell. Knowledge at the atomic level is essential to understand and influence their function. However, their number is huge and a significant fraction is extremely difficult to study using classical structural methods such as NMR and X-ray crystallography. Therefore, the importance of large-scale computational approaches in structural biology is evident. This study combines two of these computational approaches, interface prediction and docking, to obtain atomic-level structures of protein-protein complexes, starting from their unbound components. METHODOLOGY/PRINCIPAL FINDINGS Here we combine six interface prediction web servers into a consensus method called CPORT (Consensus Prediction Of interface Residues in Transient complexes). We show that CPORT gives more stable and reliable predictions than each of the individual predictors on its own. A protocol was developed to integrate CPORT predictions into our data-driven docking program HADDOCK. For cases where experimental information is limited, this prediction-driven docking protocol presents an alternative to ab initio docking, the docking of complexes without the use of any information. Prediction-driven docking was performed on a large and diverse set of protein-protein complexes in a blind manner. Our results indicate that the performance of the HADDOCK-CPORT combination is competitive with ZDOCK-ZRANK, a state-of-the-art ab initio docking/scoring combination. Finally, the original interface predictions could be further improved by interface post-prediction (contact analysis of the docking solutions). CONCLUSIONS/SIGNIFICANCE The current study shows that blind, prediction-driven docking using CPORT and HADDOCK is competitive with ab initio docking methods. This is encouraging since prediction-driven docking represents the absolute bottom line for data-driven docking: any additional biological knowledge will greatly improve the results obtained by prediction-driven docking alone. Finally, the fact that original interface predictions could be further improved by interface post-prediction suggests that prediction-driven docking has not yet been pushed to the limit. A web server for CPORT is freely available at http://haddock.chem.uu.nl/services/CPORT.", "link"=>"http://www.mendeley.com/research/cport-consensus-interface-predictor-performance-predictiondriven-docking-haddock", "reader_count"=>101, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Professor > Associate Professor"=>3, "Student > Doctoral Student"=>3, "Researcher"=>21, "Student > Ph. D. Student"=>29, "Student > Postgraduate"=>4, "Student > Master"=>14, "Other"=>4, "Student > Bachelor"=>15, "Lecturer"=>1, "Professor"=>4}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Professor > Associate Professor"=>3, "Student > Doctoral Student"=>3, "Researcher"=>21, "Student > Ph. D. Student"=>29, "Student > Postgraduate"=>4, "Student > Master"=>14, "Other"=>4, "Student > Bachelor"=>15, "Lecturer"=>1, "Professor"=>4}, "reader_count_by_subject_area"=>{"Engineering"=>3, "Unspecified"=>4, "Biochemistry, Genetics and Molecular Biology"=>23, "Mathematics"=>3, "Agricultural and Biological Sciences"=>49, "Medicine and Dentistry"=>4, "Arts and Humanities"=>1, "Physics and Astronomy"=>1, "Chemistry"=>7, "Computer Science"=>6}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>3}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>4}, "Chemistry"=>{"Chemistry"=>7}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>49}, "Computer Science"=>{"Computer Science"=>6}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>23}, "Mathematics"=>{"Mathematics"=>3}, "Unspecified"=>{"Unspecified"=>4}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "reader_count_by_country"=>{"United States"=>1, "Ireland"=>1, "Japan"=>1, "United Kingdom"=>1, "Italy"=>1, "Australia"=>1, "France"=>1, "Portugal"=>1, "Germany"=>1}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/788323"], "description"=>"<p>The table indicates the percentage of cases for which at least one correct structure is selected in the top 400, and the percentage of complexes of which the number of correct structures is higher than random selection (enrichment) or lower than random selection (depletion). Significance (p<0.05) was determined using the hypergeometric distribution.</p><p>One-star and two-star criteria correspond to the CAPRI <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017695#pone.0017695-Mendez1\" target=\"_blank\">[18]</a> definitions (see Material & Methods). For one-star structures, only those complexes are considered with at least 10 one-star solutions among the 10 000 (63% of all complexes). For two-star structures, only those complexes are considered with at least one two-star solution (44% of all complexes). The fnat criterion is not taken into account.</p>", "links"=>[], "tags"=>["docking", "solutions", "rigid", "cport"], "article_id"=>458694, "categories"=>["Biochemistry", "Biophysics", "Information And Computing Sciences", "Biological Sciences", "Chemistry", "Genetics"], "users"=>["Sjoerd J. de Vries", "Alexandre M. J. J. Bonvin"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0017695.t003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Scoring_of_docking_solutions_at_the_rigid_body_stage_of_the_CPORT_docking_runs_/458694", "title"=>"Scoring of docking solutions at the rigid body stage of the CPORT docking runs.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-03-25 02:24:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/394705", "https://ndownloader.figshare.com/files/394707", "https://ndownloader.figshare.com/files/394713", "https://ndownloader.figshare.com/files/394717", "https://ndownloader.figshare.com/files/394723", "https://ndownloader.figshare.com/files/394729", "https://ndownloader.figshare.com/files/394739"], "description"=>"<div><h3>Background</h3><p>Macromolecular complexes are the molecular machines of the cell. Knowledge at the atomic level is essential to understand and influence their function. However, their number is huge and a significant fraction is extremely difficult to study using classical structural methods such as NMR and X-ray crystallography. Therefore, the importance of large-scale computational approaches in structural biology is evident. This study combines two of these computational approaches, interface prediction and docking, to obtain atomic-level structures of protein-protein complexes, starting from their unbound components.</p> <h3>Methodology/Principal Findings</h3><p>Here we combine six interface prediction web servers into a consensus method called CPORT (Consensus Prediction Of interface Residues in Transient complexes). We show that CPORT gives more stable and reliable predictions than each of the individual predictors on its own. A protocol was developed to integrate CPORT predictions into our data-driven docking program HADDOCK. For cases where experimental information is limited, this prediction-driven docking protocol presents an alternative to <em>ab initio</em> docking, the docking of complexes without the use of any information. Prediction-driven docking was performed on a large and diverse set of protein-protein complexes in a blind manner. Our results indicate that the performance of the HADDOCK-CPORT combination is competitive with ZDOCK-ZRANK, a state-of-the-art <em>ab initio</em> docking/scoring combination. Finally, the original interface predictions could be further improved by interface post-prediction (contact analysis of the docking solutions).</p> <h3>Conclusions/Significance</h3><p>The current study shows that blind, prediction-driven docking using CPORT and HADDOCK is competitive with <em>ab initio</em> docking methods. This is encouraging since prediction-driven docking represents the absolute bottom line for data-driven docking: any additional biological knowledge will greatly improve the results obtained by prediction-driven docking alone. Finally, the fact that original interface predictions could be further improved by interface post-prediction suggests that prediction-driven docking has not yet been pushed to the limit. A web server for CPORT is freely available at <a href=\"http://haddock.chem.uu.nl/services/CPORT\">http://haddock.chem.uu.nl/services/CPORT</a>.</p> </div>", "links"=>[], "tags"=>["interface", "predictor", "prediction-driven", "docking", "haddock"], "article_id"=>137960, "categories"=>["Biochemistry", "Biophysics", "Information And Computing Sciences", "Biological Sciences", "Chemistry", "Genetics"], "users"=>["Sjoerd J. de Vries", "Alexandre M. J. J. Bonvin"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0017695.s001", "https://dx.doi.org/10.1371/journal.pone.0017695.s002", "https://dx.doi.org/10.1371/journal.pone.0017695.s003", "https://dx.doi.org/10.1371/journal.pone.0017695.s004", "https://dx.doi.org/10.1371/journal.pone.0017695.s005", "https://dx.doi.org/10.1371/journal.pone.0017695.s006", "https://dx.doi.org/10.1371/journal.pone.0017695.s007"], "stats"=>{"downloads"=>49, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/CPORT_A_Consensus_Interface_Predictor_and_Its_Performance_in_Prediction_Driven_Docking_with_HADDOCK/137960", "title"=>"CPORT: A Consensus Interface Predictor and Its Performance in Prediction-Driven Docking with HADDOCK", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-03-25 02:12:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/788292"], "description"=>"<p>CPORT made on average 45 predictions per protein chain; shown is the comparison between CPORT and the top 45 PINUP predictions for the 37 new targets of the protein-protein docking benchmark 3.0 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017695#pone.0017695-Hwang1\" target=\"_blank\">[17]</a>.</p>", "links"=>[], "tags"=>["cport", "pinup", "benchmark"], "article_id"=>458666, "categories"=>["Biochemistry", "Biophysics", "Information And Computing Sciences", "Biological Sciences", "Chemistry", "Genetics"], "users"=>["Sjoerd J. de Vries", "Alexandre M. J. J. Bonvin"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0017695.t002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_between_CPORT_and_PINUP_on_the_benchmark_3_0_/458666", "title"=>"Comparison between CPORT and PINUP on the benchmark 3.0.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-03-25 02:24:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/788226"], "description"=>"<p>Success rate of HADDOCK-CPORT compared to ZDOCK-ZRANK among 59 “enzyme” and “other” complexes from the protein-protein docking benchmark. Shown is the number of successful complexes for each method.</p>", "links"=>[], "tags"=>["haddock-cport"], "article_id"=>458604, "categories"=>["Biochemistry", "Biophysics", "Information And Computing Sciences", "Biological Sciences", "Chemistry", "Genetics"], "users"=>["Sjoerd J. de Vries", "Alexandre M. J. J. Bonvin"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0017695.t004", "stats"=>{"downloads"=>4, "page_views"=>25, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_between_HADDOCK_CPORT_and_ZDOCK_ZRANK_/458604", "title"=>"Comparison between HADDOCK-CPORT and ZDOCK-ZRANK.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-03-25 02:23:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/788268"], "description"=>"<p>CPORT made on average 50 predictions per protein chain; shown is the comparison between CPORT and the top 50 PINUP predictions on the protein-protein docking benchmark 2.0 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017695#pone.0017695-Mintseris1\" target=\"_blank\">[5]</a>.</p>", "links"=>[], "tags"=>["cport", "pinup", "predictions", "benchmark"], "article_id"=>458637, "categories"=>["Biochemistry", "Biophysics", "Information And Computing Sciences", "Biological Sciences", "Chemistry", "Genetics"], "users"=>["Sjoerd J. de Vries", "Alexandre M. J. J. Bonvin"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0017695.t001", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_between_CPORT_and_PINUP_predictions_on_the_benchmark_2_0_/458637", "title"=>"Comparison between CPORT and PINUP predictions on the benchmark 2.0.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-03-25 02:23:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/788138"], "description"=>"<p>Docking results for CPORT-driven docking using HADDOCK (top), compared to HADDOCK <i>ab initio</i> docking (bottom). The figure shows the percentage of cases for which at least one structure of that quality was generated during the rigid body stage (10 000 structures), and the top 400 (all refined structures), 100, 10 and 1 of the refinement stage. One-star and two-star criteria correspond to the CAPRI <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017695#pone.0017695-Mendez1\" target=\"_blank\">[18]</a> definitions (see Methods). For the rigid body stage, the fnat criterion is not taken into account.</p>", "links"=>[], "tags"=>["genetics and genomics", "chemistry", "Computational biology", "biophysics", "computer science", "Biochemistry"], "article_id"=>458510, "categories"=>["Biochemistry", "Biophysics", "Information And Computing Sciences", "Biological Sciences", "Chemistry", "Genetics"], "users"=>["Sjoerd J. de Vries", "Alexandre M. J. J. Bonvin"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0017695.g001", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Docking_results_/458510", "title"=>"Docking results.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-03-25 02:21:50"}

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Relative Metric

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