Codon-level information improves predictions of inter-residue contacts in proteins by correlated mutation analysis
Methods for analysing correlated mutations in proteins are becoming an increasingly powerful tool for predicting contacts within and between proteins. Nevertheless, limitations remain due to the requirement for large multiple sequence alignments (MSA) and the fact that, in general, only the relative...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2015-09-01
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| Series: | eLife |
| Subjects: | |
| Online Access: | https://elifesciences.org/articles/08932 |
| _version_ | 1811180461965180928 |
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| author | Etai Jacob Ron Unger Amnon Horovitz |
| author_facet | Etai Jacob Ron Unger Amnon Horovitz |
| author_sort | Etai Jacob |
| collection | DOAJ |
| description | Methods for analysing correlated mutations in proteins are becoming an increasingly powerful tool for predicting contacts within and between proteins. Nevertheless, limitations remain due to the requirement for large multiple sequence alignments (MSA) and the fact that, in general, only the relatively small number of top-ranking predictions are reliable. To date, methods for analysing correlated mutations have relied exclusively on amino acid MSAs as inputs. Here, we describe a new approach for analysing correlated mutations that is based on combined analysis of amino acid and codon MSAs. We show that a direct contact is more likely to be present when the correlation between the positions is strong at the amino acid level but weak at the codon level. The performance of different methods for analysing correlated mutations in predicting contacts is shown to be enhanced significantly when amino acid and codon data are combined. |
| first_indexed | 2024-04-11T09:03:33Z |
| format | Article |
| id | doaj.art-20fcd743a0f543a08d542531d80e4c86 |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-11T09:03:33Z |
| publishDate | 2015-09-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-20fcd743a0f543a08d542531d80e4c862022-12-22T04:32:42ZengeLife Sciences Publications LtdeLife2050-084X2015-09-01410.7554/eLife.08932Codon-level information improves predictions of inter-residue contacts in proteins by correlated mutation analysisEtai Jacob0Ron Unger1Amnon Horovitz2The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel; Department of Structural Biology, Weizmann Institute of Science, Rehovot, IsraelThe Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, IsraelDepartment of Structural Biology, Weizmann Institute of Science, Rehovot, IsraelMethods for analysing correlated mutations in proteins are becoming an increasingly powerful tool for predicting contacts within and between proteins. Nevertheless, limitations remain due to the requirement for large multiple sequence alignments (MSA) and the fact that, in general, only the relatively small number of top-ranking predictions are reliable. To date, methods for analysing correlated mutations have relied exclusively on amino acid MSAs as inputs. Here, we describe a new approach for analysing correlated mutations that is based on combined analysis of amino acid and codon MSAs. We show that a direct contact is more likely to be present when the correlation between the positions is strong at the amino acid level but weak at the codon level. The performance of different methods for analysing correlated mutations in predicting contacts is shown to be enhanced significantly when amino acid and codon data are combined.https://elifesciences.org/articles/08932protein evolutioncorrelated mutationsstructure prediction |
| spellingShingle | Etai Jacob Ron Unger Amnon Horovitz Codon-level information improves predictions of inter-residue contacts in proteins by correlated mutation analysis eLife protein evolution correlated mutations structure prediction |
| title | Codon-level information improves predictions of inter-residue contacts in proteins by correlated mutation analysis |
| title_full | Codon-level information improves predictions of inter-residue contacts in proteins by correlated mutation analysis |
| title_fullStr | Codon-level information improves predictions of inter-residue contacts in proteins by correlated mutation analysis |
| title_full_unstemmed | Codon-level information improves predictions of inter-residue contacts in proteins by correlated mutation analysis |
| title_short | Codon-level information improves predictions of inter-residue contacts in proteins by correlated mutation analysis |
| title_sort | codon level information improves predictions of inter residue contacts in proteins by correlated mutation analysis |
| topic | protein evolution correlated mutations structure prediction |
| url | https://elifesciences.org/articles/08932 |
| work_keys_str_mv | AT etaijacob codonlevelinformationimprovespredictionsofinterresiduecontactsinproteinsbycorrelatedmutationanalysis AT ronunger codonlevelinformationimprovespredictionsofinterresiduecontactsinproteinsbycorrelatedmutationanalysis AT amnonhorovitz codonlevelinformationimprovespredictionsofinterresiduecontactsinproteinsbycorrelatedmutationanalysis |