i-Patch: interprotein contact prediction using local network information.
Biological processes are commonly controlled by precise protein-protein interactions. These connections rely on specific amino acids at the binding interfaces. Here we predict the binding residues of such interprotein complexes. We have developed a suite of methods, i-Patch, which predict the interp...
| Main Authors: | , , , , |
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| Format: | Journal article |
| Language: | English |
| Published: |
2010
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| _version_ | 1797075188687306752 |
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| author | Hamer, R Luo, Q Armitage, J Reinert, G Deane, C |
| author_facet | Hamer, R Luo, Q Armitage, J Reinert, G Deane, C |
| author_sort | Hamer, R |
| collection | OXFORD |
| description | Biological processes are commonly controlled by precise protein-protein interactions. These connections rely on specific amino acids at the binding interfaces. Here we predict the binding residues of such interprotein complexes. We have developed a suite of methods, i-Patch, which predict the interprotein contact sites by considering the two proteins as a network, with residues as nodes and contacts as edges. i-Patch starts with two proteins, A and B, which are assumed to interact, but for which the structure of the complex is not available. However, we assume that for each protein, we have a reference structure and a multiple sequence alignment of homologues. i-Patch then uses the propensities of patches of residues to interact, to predict interprotein contact sites. i-Patch outperforms several other tested algorithms for prediction of interprotein contact sites. It gives 59% precision with 20% recall on a blind test set of 31 protein pairs. Combining the i-Patch scores with an existing correlated mutation algorithm, McBASC, using a logistic model gave little improvement. Results from a case study, on bacterial chemotaxis protein complexes, demonstrate that our predictions can identify contact residues, as well as suggesting unknown interfaces in multiprotein complexes. |
| first_indexed | 2024-03-06T23:46:50Z |
| format | Journal article |
| id | oxford-uuid:71361f9e-757e-47e9-8710-f02a2975fca1 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-06T23:46:50Z |
| publishDate | 2010 |
| record_format | dspace |
| spelling | oxford-uuid:71361f9e-757e-47e9-8710-f02a2975fca12022-03-26T19:42:11Zi-Patch: interprotein contact prediction using local network information.Journal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:71361f9e-757e-47e9-8710-f02a2975fca1EnglishSymplectic Elements at Oxford2010Hamer, RLuo, QArmitage, JReinert, GDeane, CBiological processes are commonly controlled by precise protein-protein interactions. These connections rely on specific amino acids at the binding interfaces. Here we predict the binding residues of such interprotein complexes. We have developed a suite of methods, i-Patch, which predict the interprotein contact sites by considering the two proteins as a network, with residues as nodes and contacts as edges. i-Patch starts with two proteins, A and B, which are assumed to interact, but for which the structure of the complex is not available. However, we assume that for each protein, we have a reference structure and a multiple sequence alignment of homologues. i-Patch then uses the propensities of patches of residues to interact, to predict interprotein contact sites. i-Patch outperforms several other tested algorithms for prediction of interprotein contact sites. It gives 59% precision with 20% recall on a blind test set of 31 protein pairs. Combining the i-Patch scores with an existing correlated mutation algorithm, McBASC, using a logistic model gave little improvement. Results from a case study, on bacterial chemotaxis protein complexes, demonstrate that our predictions can identify contact residues, as well as suggesting unknown interfaces in multiprotein complexes. |
| spellingShingle | Hamer, R Luo, Q Armitage, J Reinert, G Deane, C i-Patch: interprotein contact prediction using local network information. |
| title | i-Patch: interprotein contact prediction using local network information. |
| title_full | i-Patch: interprotein contact prediction using local network information. |
| title_fullStr | i-Patch: interprotein contact prediction using local network information. |
| title_full_unstemmed | i-Patch: interprotein contact prediction using local network information. |
| title_short | i-Patch: interprotein contact prediction using local network information. |
| title_sort | i patch interprotein contact prediction using local network information |
| work_keys_str_mv | AT hamerr ipatchinterproteincontactpredictionusinglocalnetworkinformation AT luoq ipatchinterproteincontactpredictionusinglocalnetworkinformation AT armitagej ipatchinterproteincontactpredictionusinglocalnetworkinformation AT reinertg ipatchinterproteincontactpredictionusinglocalnetworkinformation AT deanec ipatchinterproteincontactpredictionusinglocalnetworkinformation |