Eintrag weiter verarbeiten
iAlign: a method for the structural comparison of protein–protein interfaces
Gespeichert in:
| Zeitschriftentitel: | Bioinformatics |
|---|---|
| Personen und Körperschaften: | , |
| In: | Bioinformatics, 26, 2010, 18, S. 2259-2265 |
| Format: | E-Article |
| Sprache: | Englisch |
| veröffentlicht: |
Oxford University Press (OUP)
|
| Schlagwörter: |
| author_facet |
Gao, Mu Skolnick, Jeffrey Gao, Mu Skolnick, Jeffrey |
|---|---|
| author |
Gao, Mu Skolnick, Jeffrey |
| spellingShingle |
Gao, Mu Skolnick, Jeffrey Bioinformatics iAlign: a method for the structural comparison of protein–protein interfaces Computational Mathematics Computational Theory and Mathematics Computer Science Applications Molecular Biology Biochemistry Statistics and Probability |
| author_sort |
gao, mu |
| spelling |
Gao, Mu Skolnick, Jeffrey 1367-4811 1367-4803 Oxford University Press (OUP) Computational Mathematics Computational Theory and Mathematics Computer Science Applications Molecular Biology Biochemistry Statistics and Probability http://dx.doi.org/10.1093/bioinformatics/btq404 <jats:title>Abstract</jats:title> <jats:p>Motivation: Protein–protein interactions play an essential role in many cellular processes. The rapid accumulation of protein–protein complex structures provides an unprecedented opportunity for comparative studies of protein–protein interactions. To facilitate such studies, it is necessary to develop an accurate and efficient computational algorithm for the comparison of protein–protein interaction modes. While there are many structural comparison approaches developed for individual proteins, very few methods are available for protein–protein complexes.</jats:p> <jats:p>Results: We present a novel interface alignment method, iAlign, for the structural alignment of protein–protein interfaces. New scoring schemes for measuring interface similarity are introduced, and an iterative dynamic programming algorithm is implemented. We find that the similarity scores follow extreme value distributions. Using statistical models, we empirically estimate their statistical significance, which is in good agreement with manual classifications by human experts. Large-scale tests of iAlign were conducted on both artificial docking models and experimental structures. In a benchmark test on 1517 dimers, iAlign successfully detects biologically related, structurally similar protein–protein interfaces at a coverage percentage of 90% and an error per query of 0.05. When compared against previously published methods, iAlign is substantially more accurate and efficient.</jats:p> <jats:p>Availability: The iAlign software package is freely available at http://cssb.biology.gatech.edu/iAlign</jats:p> <jats:p>Contact: skolnick@gatech.edu</jats:p> <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.</jats:p> iAlign: a method for the structural comparison of protein–protein interfaces Bioinformatics |
| doi_str_mv |
10.1093/bioinformatics/btq404 |
| facet_avail |
Online Free |
| finc_class_facet |
Informatik Biologie Chemie und Pharmazie Mathematik |
| format |
ElectronicArticle |
| fullrecord |
blob:ai-49-aHR0cDovL2R4LmRvaS5vcmcvMTAuMTA5My9iaW9pbmZvcm1hdGljcy9idHE0MDQ |
| id |
ai-49-aHR0cDovL2R4LmRvaS5vcmcvMTAuMTA5My9iaW9pbmZvcm1hdGljcy9idHE0MDQ |
| institution |
DE-Ch1 DE-L229 DE-D275 DE-Bn3 DE-Brt1 DE-Zwi2 DE-D161 DE-Gla1 DE-Zi4 DE-15 DE-Pl11 DE-Rs1 DE-105 DE-14 |
| imprint |
Oxford University Press (OUP), 2010 |
| imprint_str_mv |
Oxford University Press (OUP), 2010 |
| issn |
1367-4811 1367-4803 |
| issn_str_mv |
1367-4811 1367-4803 |
| language |
English |
| mega_collection |
Oxford University Press (OUP) (CrossRef) |
| match_str |
gao2010ialignamethodforthestructuralcomparisonofproteinproteininterfaces |
| publishDateSort |
2010 |
| publisher |
Oxford University Press (OUP) |
| recordtype |
ai |
| record_format |
ai |
| series |
Bioinformatics |
| source_id |
49 |
| title |
iAlign: a method for the structural comparison of protein–protein interfaces |
| title_unstemmed |
iAlign: a method for the structural comparison of protein–protein interfaces |
| title_full |
iAlign: a method for the structural comparison of protein–protein interfaces |
| title_fullStr |
iAlign: a method for the structural comparison of protein–protein interfaces |
| title_full_unstemmed |
iAlign: a method for the structural comparison of protein–protein interfaces |
| title_short |
iAlign: a method for the structural comparison of protein–protein interfaces |
| title_sort |
ialign: a method for the structural comparison of protein–protein interfaces |
| topic |
Computational Mathematics Computational Theory and Mathematics Computer Science Applications Molecular Biology Biochemistry Statistics and Probability |
| url |
http://dx.doi.org/10.1093/bioinformatics/btq404 |
| publishDate |
2010 |
| physical |
2259-2265 |
| description |
<jats:title>Abstract</jats:title>
<jats:p>Motivation: Protein–protein interactions play an essential role in many cellular processes. The rapid accumulation of protein–protein complex structures provides an unprecedented opportunity for comparative studies of protein–protein interactions. To facilitate such studies, it is necessary to develop an accurate and efficient computational algorithm for the comparison of protein–protein interaction modes. While there are many structural comparison approaches developed for individual proteins, very few methods are available for protein–protein complexes.</jats:p>
<jats:p>Results: We present a novel interface alignment method, iAlign, for the structural alignment of protein–protein interfaces. New scoring schemes for measuring interface similarity are introduced, and an iterative dynamic programming algorithm is implemented. We find that the similarity scores follow extreme value distributions. Using statistical models, we empirically estimate their statistical significance, which is in good agreement with manual classifications by human experts. Large-scale tests of iAlign were conducted on both artificial docking models and experimental structures. In a benchmark test on 1517 dimers, iAlign successfully detects biologically related, structurally similar protein–protein interfaces at a coverage percentage of 90% and an error per query of 0.05. When compared against previously published methods, iAlign is substantially more accurate and efficient.</jats:p>
<jats:p>Availability: The iAlign software package is freely available at http://cssb.biology.gatech.edu/iAlign</jats:p>
<jats:p>Contact: skolnick@gatech.edu</jats:p>
<jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.</jats:p> |
| container_issue |
18 |
| container_start_page |
2259 |
| container_title |
Bioinformatics |
| container_volume |
26 |
| format_de105 |
Article, E-Article |
| format_de14 |
Article, E-Article |
| format_de15 |
Article, E-Article |
| format_de520 |
Article, E-Article |
| format_de540 |
Article, E-Article |
| format_dech1 |
Article, E-Article |
| format_ded117 |
Article, E-Article |
| format_degla1 |
E-Article |
| format_del152 |
Buch |
| format_del189 |
Article, E-Article |
| format_dezi4 |
Article |
| format_dezwi2 |
Article, E-Article |
| format_finc |
Article, E-Article |
| format_nrw |
Article, E-Article |
| _version_ |
1792347430463733761 |
| geogr_code |
not assigned |
| last_indexed |
2024-03-01T17:55:08.906Z |
| geogr_code_person |
not assigned |
| openURL |
url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fvufind.svn.sourceforge.net%3Agenerator&rft.title=iAlign%3A+a+method+for+the+structural+comparison+of+protein%E2%80%93protein+interfaces&rft.date=2010-09-15&genre=article&issn=1367-4803&volume=26&issue=18&spage=2259&epage=2265&pages=2259-2265&jtitle=Bioinformatics&atitle=iAlign%3A+a+method+for+the+structural+comparison+of+protein%E2%80%93protein+interfaces&aulast=Skolnick&aufirst=Jeffrey&rft_id=info%3Adoi%2F10.1093%2Fbioinformatics%2Fbtq404&rft.language%5B0%5D=eng |
| SOLR | |
| _version_ | 1792347430463733761 |
| author | Gao, Mu, Skolnick, Jeffrey |
| author_facet | Gao, Mu, Skolnick, Jeffrey, Gao, Mu, Skolnick, Jeffrey |
| author_sort | gao, mu |
| container_issue | 18 |
| container_start_page | 2259 |
| container_title | Bioinformatics |
| container_volume | 26 |
| description | <jats:title>Abstract</jats:title> <jats:p>Motivation: Protein–protein interactions play an essential role in many cellular processes. The rapid accumulation of protein–protein complex structures provides an unprecedented opportunity for comparative studies of protein–protein interactions. To facilitate such studies, it is necessary to develop an accurate and efficient computational algorithm for the comparison of protein–protein interaction modes. While there are many structural comparison approaches developed for individual proteins, very few methods are available for protein–protein complexes.</jats:p> <jats:p>Results: We present a novel interface alignment method, iAlign, for the structural alignment of protein–protein interfaces. New scoring schemes for measuring interface similarity are introduced, and an iterative dynamic programming algorithm is implemented. We find that the similarity scores follow extreme value distributions. Using statistical models, we empirically estimate their statistical significance, which is in good agreement with manual classifications by human experts. Large-scale tests of iAlign were conducted on both artificial docking models and experimental structures. In a benchmark test on 1517 dimers, iAlign successfully detects biologically related, structurally similar protein–protein interfaces at a coverage percentage of 90% and an error per query of 0.05. When compared against previously published methods, iAlign is substantially more accurate and efficient.</jats:p> <jats:p>Availability: The iAlign software package is freely available at http://cssb.biology.gatech.edu/iAlign</jats:p> <jats:p>Contact: skolnick@gatech.edu</jats:p> <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.</jats:p> |
| doi_str_mv | 10.1093/bioinformatics/btq404 |
| facet_avail | Online, Free |
| finc_class_facet | Informatik, Biologie, Chemie und Pharmazie, Mathematik |
| format | ElectronicArticle |
| format_de105 | Article, E-Article |
| format_de14 | Article, E-Article |
| format_de15 | Article, E-Article |
| format_de520 | Article, E-Article |
| format_de540 | Article, E-Article |
| format_dech1 | Article, E-Article |
| format_ded117 | Article, E-Article |
| format_degla1 | E-Article |
| format_del152 | Buch |
| format_del189 | Article, E-Article |
| format_dezi4 | Article |
| format_dezwi2 | Article, E-Article |
| format_finc | Article, E-Article |
| format_nrw | Article, E-Article |
| geogr_code | not assigned |
| geogr_code_person | not assigned |
| id | ai-49-aHR0cDovL2R4LmRvaS5vcmcvMTAuMTA5My9iaW9pbmZvcm1hdGljcy9idHE0MDQ |
| imprint | Oxford University Press (OUP), 2010 |
| imprint_str_mv | Oxford University Press (OUP), 2010 |
| institution | DE-Ch1, DE-L229, DE-D275, DE-Bn3, DE-Brt1, DE-Zwi2, DE-D161, DE-Gla1, DE-Zi4, DE-15, DE-Pl11, DE-Rs1, DE-105, DE-14 |
| issn | 1367-4811, 1367-4803 |
| issn_str_mv | 1367-4811, 1367-4803 |
| language | English |
| last_indexed | 2024-03-01T17:55:08.906Z |
| match_str | gao2010ialignamethodforthestructuralcomparisonofproteinproteininterfaces |
| mega_collection | Oxford University Press (OUP) (CrossRef) |
| physical | 2259-2265 |
| publishDate | 2010 |
| publishDateSort | 2010 |
| publisher | Oxford University Press (OUP) |
| record_format | ai |
| recordtype | ai |
| series | Bioinformatics |
| source_id | 49 |
| spelling | Gao, Mu Skolnick, Jeffrey 1367-4811 1367-4803 Oxford University Press (OUP) Computational Mathematics Computational Theory and Mathematics Computer Science Applications Molecular Biology Biochemistry Statistics and Probability http://dx.doi.org/10.1093/bioinformatics/btq404 <jats:title>Abstract</jats:title> <jats:p>Motivation: Protein–protein interactions play an essential role in many cellular processes. The rapid accumulation of protein–protein complex structures provides an unprecedented opportunity for comparative studies of protein–protein interactions. To facilitate such studies, it is necessary to develop an accurate and efficient computational algorithm for the comparison of protein–protein interaction modes. While there are many structural comparison approaches developed for individual proteins, very few methods are available for protein–protein complexes.</jats:p> <jats:p>Results: We present a novel interface alignment method, iAlign, for the structural alignment of protein–protein interfaces. New scoring schemes for measuring interface similarity are introduced, and an iterative dynamic programming algorithm is implemented. We find that the similarity scores follow extreme value distributions. Using statistical models, we empirically estimate their statistical significance, which is in good agreement with manual classifications by human experts. Large-scale tests of iAlign were conducted on both artificial docking models and experimental structures. In a benchmark test on 1517 dimers, iAlign successfully detects biologically related, structurally similar protein–protein interfaces at a coverage percentage of 90% and an error per query of 0.05. When compared against previously published methods, iAlign is substantially more accurate and efficient.</jats:p> <jats:p>Availability: The iAlign software package is freely available at http://cssb.biology.gatech.edu/iAlign</jats:p> <jats:p>Contact: skolnick@gatech.edu</jats:p> <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.</jats:p> iAlign: a method for the structural comparison of protein–protein interfaces Bioinformatics |
| spellingShingle | Gao, Mu, Skolnick, Jeffrey, Bioinformatics, iAlign: a method for the structural comparison of protein–protein interfaces, Computational Mathematics, Computational Theory and Mathematics, Computer Science Applications, Molecular Biology, Biochemistry, Statistics and Probability |
| title | iAlign: a method for the structural comparison of protein–protein interfaces |
| title_full | iAlign: a method for the structural comparison of protein–protein interfaces |
| title_fullStr | iAlign: a method for the structural comparison of protein–protein interfaces |
| title_full_unstemmed | iAlign: a method for the structural comparison of protein–protein interfaces |
| title_short | iAlign: a method for the structural comparison of protein–protein interfaces |
| title_sort | ialign: a method for the structural comparison of protein–protein interfaces |
| title_unstemmed | iAlign: a method for the structural comparison of protein–protein interfaces |
| topic | Computational Mathematics, Computational Theory and Mathematics, Computer Science Applications, Molecular Biology, Biochemistry, Statistics and Probability |
| url | http://dx.doi.org/10.1093/bioinformatics/btq404 |