MRFalign: Protein Homology Detection through Alignment of Markov Random Fields
Publication Date
March 27, 2014
Journal
PLOS Computational Biology
Authors
Jianzhu Ma, Sheng Wang, Zhiyong Wang & Jinbo Xu
Volume
10
Issue
3
Pages
e1003500
DOI
https://dx.plos.org/10.1371/journal.pcbi.1003500
Publisher URL
http://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1003500
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/24675572
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3967925
Europe PMC
http://europepmc.org/abstract/MED/24675572
Web of Science
000336509000021
Scopus
84897393474
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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1439385"], "description"=>"<p>Homology detection performance for mainly beta proteins at the superfamily level.</p>", "links"=>[], "tags"=>["Computational biology", "detection", "beta", "proteins", "superfamily"], "article_id"=>977664, "categories"=>["Biological Sciences"], "users"=>["Jianzhu Ma", "Sheng Wang", "Zhiyong Wang", "Jinbo Xu"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003500.t009", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Homology_detection_performance_for_mainly_beta_proteins_at_the_superfamily_level_/977664", "title"=>"Homology detection performance for mainly beta proteins at the superfamily level.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-03-27 04:19:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/1439383"], "description"=>"<p>Three structure alignment tools (TMalign, Matt and DeepAlign) are used to generate reference alignments. “4-offset” means that 4-position off the exact match is allowed. The bold indicates the best results.</p>", "links"=>[], "tags"=>["Computational biology", "alignment", "precision"], "article_id"=>977662, "categories"=>["Biological Sciences"], "users"=>["Jianzhu Ma", "Sheng Wang", "Zhiyong Wang", "Jinbo Xu"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003500.t004", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Reference_dependent_alignment_precision_on_Se3_6K_/977662", "title"=>"Reference-dependent alignment precision on Se3.6K.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-03-27 04:19:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/1439380"], "description"=>"<p>Homology detection performance at the superfamily level.</p>", "links"=>[], "tags"=>["Computational biology", "detection", "superfamily"], "article_id"=>977659, "categories"=>["Biological Sciences"], "users"=>["Jianzhu Ma", "Sheng Wang", "Zhiyong Wang", "Jinbo Xu"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003500.t007", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Homology_detection_performance_at_the_superfamily_level_/977659", "title"=>"Homology detection performance at the superfamily level.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-03-27 04:19:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/1439379"], "description"=>"<p>Three structure alignment tools (TMalign, Matt and DeepAlign) are used to generate reference alignments. “4-offset” means that 4-position off the exact match is allowed. The bold indicates the best results.</p>", "links"=>[], "tags"=>["Computational biology", "alignment"], "article_id"=>977658, "categories"=>["Biological Sciences"], "users"=>["Jianzhu Ma", "Sheng Wang", "Zhiyong Wang", "Jinbo Xu"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003500.t001", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Reference_dependent_alignment_recall_on_Set3_6K_/977658", "title"=>"Reference-dependent alignment recall on Set3.6K.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-03-27 04:19:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/1439374"], "description"=>"<p>Model a multiple sequence alignment (left) by a Markov Random Fields (right).</p>", "links"=>[], "tags"=>["Computational biology", "alignment", "markov", "fields"], "article_id"=>977653, "categories"=>["Biological Sciences"], "users"=>["Jianzhu Ma", "Sheng Wang", "Zhiyong Wang", "Jinbo Xu"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003500.g003", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Model_a_multiple_sequence_alignment_left_by_a_Markov_Random_Fields_right_/977653", "title"=>"Model a multiple sequence alignment (left) by a Markov Random Fields (right).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-27 04:19:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/1439373"], "description"=>"<p>One point represents two models generated by our method (x-axis) and HHpred (y-axis).</p>", "links"=>[], "tags"=>["Computational biology", "hhpred", "36", "casp10"], "article_id"=>977652, "categories"=>["Biological Sciences"], "users"=>["Jianzhu Ma", "Sheng Wang", "Zhiyong Wang", "Jinbo Xu"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003500.g002", "stats"=>{"downloads"=>3, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_model_quality_measured_by_TM_score_of_our_method_and_HHpred_for_the_36_CASP10_hard_targets_/977652", "title"=>"The model quality, measured by TM-score, of our method and HHpred for the 36 CASP10 hard targets.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-27 04:19:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/1439387"], "description"=>"<p>The structure alignments generated by DeepAlign are used as reference alignments.</p>", "links"=>[], "tags"=>["Computational biology", "alignment", "benchmarks"], "article_id"=>977666, "categories"=>["Biological Sciences"], "users"=>["Jianzhu Ma", "Sheng Wang", "Zhiyong Wang", "Jinbo Xu"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003500.t011", "stats"=>{"downloads"=>2, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Contribution_of_edge_alignment_potential_and_mutual_information_measured_by_alignment_recall_improvement_on_two_benchmarks_Set3_6K_and_Set2_6K_/977666", "title"=>"Contribution of edge alignment potential and mutual information, measured by alignment recall improvement on two benchmarks Set3.6K and Set2.6K.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-03-27 04:19:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/1439382"], "description"=>"<p>See <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003500#pcbi-1003500-t004\" target=\"_blank\">Table 4</a> for explanation.</p>", "links"=>[], "tags"=>["Computational biology", "alignment", "precision"], "article_id"=>977661, "categories"=>["Biological Sciences"], "users"=>["Jianzhu Ma", "Sheng Wang", "Zhiyong Wang", "Jinbo Xu"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003500.t005", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Reference_dependent_alignment_precision_on_Set2_6K_/977661", "title"=>"Reference-dependent alignment precision on Set2.6K.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-03-27 04:19:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/1439381"], "description"=>"<p>The protein pairs are divided into 3 groups based upon the SCOP classification. The bold indicates the best results.</p>", "links"=>[], "tags"=>["Computational biology", "alignment", "precision", "benchmark"], "article_id"=>977660, "categories"=>["Biological Sciences"], "users"=>["Jianzhu Ma", "Sheng Wang", "Zhiyong Wang", "Jinbo Xu"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003500.t006", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Reference_dependent_alignment_precision_exact_match_on_the_large_benchmark_Set60K_/977660", "title"=>"Reference-dependent alignment precision (exact match) on the large benchmark Set60K.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-03-27 04:19:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/1439378"], "description"=>"<p>See <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003500#pcbi-1003500-t001\" target=\"_blank\">Table 1</a> for explanation.</p>", "links"=>[], "tags"=>["Computational biology", "alignment"], "article_id"=>977657, "categories"=>["Biological Sciences"], "users"=>["Jianzhu Ma", "Sheng Wang", "Zhiyong Wang", "Jinbo Xu"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003500.t002", "stats"=>{"downloads"=>2, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Reference_dependent_alignment_recall_on_Set2_6K_/977657", "title"=>"Reference-dependent alignment recall on Set2.6K.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-03-27 04:19:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/1439376"], "description"=>"<p>Fold recognition rate of our method on SCOP40, with respect to the similarity (measured by E-value) between the test data and the training data.</p>", "links"=>[], "tags"=>["Computational biology"], "article_id"=>977655, "categories"=>["Biological Sciences"], "users"=>["Jianzhu Ma", "Sheng Wang", "Zhiyong Wang", "Jinbo Xu"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003500.t012", "stats"=>{"downloads"=>7, "page_views"=>30, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Fold_recognition_rate_of_our_method_on_SCOP40_with_respect_to_the_similarity_measured_by_E_value_between_the_test_data_and_the_training_data_/977655", "title"=>"Fold recognition rate of our method on SCOP40, with respect to the similarity (measured by E-value) between the test data and the training data.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-03-27 04:19:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/1439377"], "description"=>"<p>The protein pairs are divided into 3 groups based upon the SCOP classification. The bold indicates the best results.</p>", "links"=>[], "tags"=>["Computational biology", "alignment", "benchmark"], "article_id"=>977656, "categories"=>["Biological Sciences"], "users"=>["Jianzhu Ma", "Sheng Wang", "Zhiyong Wang", "Jinbo Xu"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003500.t003", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Reference_dependent_alignment_recall_exact_match_on_the_large_benchmark_Set60K_/977656", "title"=>"Reference-dependent alignment recall (exact match) on the large benchmark Set60K.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-03-27 04:19:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/1439375"], "description"=>"<p>(A) Represented as a sequence of states. (B) Each alignment is a path in the alignment matrix.</p>", "links"=>[], "tags"=>["Computational biology"], "article_id"=>977654, "categories"=>["Biological Sciences"], "users"=>["Jianzhu Ma", "Sheng Wang", "Zhiyong Wang", "Jinbo Xu"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003500.g004", "stats"=>{"downloads"=>1, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Representation_of_protein_alignment_/977654", "title"=>"Representation of protein alignment.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-27 04:19:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/1439372"], "description"=>"<p>The X-axis is the geometric mean of the two protein lengths in a protein pair. The Y-axis is the running time in seconds.</p>", "links"=>[], "tags"=>["Computational biology", "viterbi", "algorithm", "admm"], "article_id"=>977651, "categories"=>["Biological Sciences"], "users"=>["Jianzhu Ma", "Sheng Wang", "Zhiyong Wang", "Jinbo Xu"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003500.g001", "stats"=>{"downloads"=>1, "page_views"=>29, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Running_time_of_the_Viterbi_algorithm_and_our_ADMM_algorithm_/977651", "title"=>"Running time of the Viterbi algorithm and our ADMM algorithm.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-27 04:19:27"}
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Relative Metric

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