MP-T: improving membrane protein alignment for structure prediction.
MOTIVATION: Membrane proteins are clinically relevant, yet their crystal structures are rare. Models of membrane proteins are typically built from template structures with low sequence identity to the target sequence, using a sequence-structure alignment as a blueprint. This alignment is usually ma...
| Main Authors: | , |
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| Format: | Journal article |
| Language: | English |
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2013
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| _version_ | 1797088740961681408 |
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| author | Hill, JR Deane, C |
| author_facet | Hill, JR Deane, C |
| author_sort | Hill, JR |
| collection | OXFORD |
| description | MOTIVATION: Membrane proteins are clinically relevant, yet their crystal structures are rare. Models of membrane proteins are typically built from template structures with low sequence identity to the target sequence, using a sequence-structure alignment as a blueprint. This alignment is usually made with programs designed for use on soluble proteins. Biological membranes have layers of varying hydrophobicity, and membrane proteins have different amino-acid substitution preferences from their soluble counterparts. Here we include these factors into an alignment method to improve alignments and consequently improve membrane protein models. RESULTS: We developed Membrane Protein Threader (MP-T), a sequence-structure alignment tool for membrane proteins based on multiple sequence alignment. Alignment accuracy is tested against seven other alignment methods over 165 non-redundant alignments of membrane proteins. MP-T produces more accurate alignments than all other methods tested (δF(M) from +0.9 to +5.5%). Alignments generated by MP-T also lead to significantly better models than those of the best alternative alignment tool (one-fourth of models see an increase in GDT_TS of ≥4%). AVAILABILITY: All source code, alignments and models are available at http://www.stats.ox.ac.uk/proteins/resources |
| first_indexed | 2024-03-07T02:54:25Z |
| format | Journal article |
| id | oxford-uuid:aecb04f7-0d38-4b78-9338-1c7e4f88178a |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T02:54:25Z |
| publishDate | 2013 |
| record_format | dspace |
| spelling | oxford-uuid:aecb04f7-0d38-4b78-9338-1c7e4f88178a2022-03-27T03:45:04ZMP-T: improving membrane protein alignment for structure prediction.Journal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:aecb04f7-0d38-4b78-9338-1c7e4f88178aEnglishSymplectic Elements at Oxford2013Hill, JRDeane, C MOTIVATION: Membrane proteins are clinically relevant, yet their crystal structures are rare. Models of membrane proteins are typically built from template structures with low sequence identity to the target sequence, using a sequence-structure alignment as a blueprint. This alignment is usually made with programs designed for use on soluble proteins. Biological membranes have layers of varying hydrophobicity, and membrane proteins have different amino-acid substitution preferences from their soluble counterparts. Here we include these factors into an alignment method to improve alignments and consequently improve membrane protein models. RESULTS: We developed Membrane Protein Threader (MP-T), a sequence-structure alignment tool for membrane proteins based on multiple sequence alignment. Alignment accuracy is tested against seven other alignment methods over 165 non-redundant alignments of membrane proteins. MP-T produces more accurate alignments than all other methods tested (δF(M) from +0.9 to +5.5%). Alignments generated by MP-T also lead to significantly better models than those of the best alternative alignment tool (one-fourth of models see an increase in GDT_TS of ≥4%). AVAILABILITY: All source code, alignments and models are available at http://www.stats.ox.ac.uk/proteins/resources |
| spellingShingle | Hill, JR Deane, C MP-T: improving membrane protein alignment for structure prediction. |
| title | MP-T: improving membrane protein alignment for structure prediction. |
| title_full | MP-T: improving membrane protein alignment for structure prediction. |
| title_fullStr | MP-T: improving membrane protein alignment for structure prediction. |
| title_full_unstemmed | MP-T: improving membrane protein alignment for structure prediction. |
| title_short | MP-T: improving membrane protein alignment for structure prediction. |
| title_sort | mp t improving membrane protein alignment for structure prediction |
| work_keys_str_mv | AT hilljr mptimprovingmembraneproteinalignmentforstructureprediction AT deanec mptimprovingmembraneproteinalignmentforstructureprediction |