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Identifying Protein-Protein Interaction Sites Using Covering Algorithm
Identification of protein-protein interface residues is crucial for structural biology. This paper proposes a covering algorithm for predicting protein-protein interface residues with features including protein sequence profile and residue accessible area. This method adequately utilizes the charact...
Autores principales: | , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
Molecular Diversity Preservation International (MDPI)
2009
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2695276/ https://www.ncbi.nlm.nih.gov/pubmed/19564948 http://dx.doi.org/10.3390/ijms10052190 |
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author | Du, Xiuquan Cheng, Jiaxing Song, Jie |
author_facet | Du, Xiuquan Cheng, Jiaxing Song, Jie |
author_sort | Du, Xiuquan |
collection | PubMed |
description | Identification of protein-protein interface residues is crucial for structural biology. This paper proposes a covering algorithm for predicting protein-protein interface residues with features including protein sequence profile and residue accessible area. This method adequately utilizes the characters of a covering algorithm which have simple, lower complexity and high accuracy for high dimension data. The covering algorithm can achieve a comparable performance (69.62%, Complete dataset; 60.86%, Trim dataset with overall accuracy) to a support vector machine and maximum entropy on our dataset, a correlation coefficient (CC) of 0.2893, 58.83% specificity, 56.12% sensitivity on the Complete dataset and 0.2144 (CC), 53.34% (specificity), 65.59% (sensitivity) on the Trim dataset in identifying interface residues by 5-fold cross-validation on 61 protein chains. This result indicates that the covering algorithm is a powerful and robust protein-protein interaction site prediction method that can guide biologists to make specific experiments on proteins. Examination of the predictions in the context of the 3-dimensional structures of proteins demonstrates the effectiveness of this method. |
format | Text |
id | pubmed-2695276 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2009 |
publisher | Molecular Diversity Preservation International (MDPI) |
record_format | MEDLINE/PubMed |
spelling | pubmed-26952762009-06-29 Identifying Protein-Protein Interaction Sites Using Covering Algorithm Du, Xiuquan Cheng, Jiaxing Song, Jie Int J Mol Sci Article Identification of protein-protein interface residues is crucial for structural biology. This paper proposes a covering algorithm for predicting protein-protein interface residues with features including protein sequence profile and residue accessible area. This method adequately utilizes the characters of a covering algorithm which have simple, lower complexity and high accuracy for high dimension data. The covering algorithm can achieve a comparable performance (69.62%, Complete dataset; 60.86%, Trim dataset with overall accuracy) to a support vector machine and maximum entropy on our dataset, a correlation coefficient (CC) of 0.2893, 58.83% specificity, 56.12% sensitivity on the Complete dataset and 0.2144 (CC), 53.34% (specificity), 65.59% (sensitivity) on the Trim dataset in identifying interface residues by 5-fold cross-validation on 61 protein chains. This result indicates that the covering algorithm is a powerful and robust protein-protein interaction site prediction method that can guide biologists to make specific experiments on proteins. Examination of the predictions in the context of the 3-dimensional structures of proteins demonstrates the effectiveness of this method. Molecular Diversity Preservation International (MDPI) 2009-05-15 /pmc/articles/PMC2695276/ /pubmed/19564948 http://dx.doi.org/10.3390/ijms10052190 Text en © 2009 by the authors; licensee Molecular Diversity Preservation International, Basel, Switzerland. http://creativecommons.org/licenses/by/3.0 This article is an open-access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/3.0/). |
spellingShingle | Article Du, Xiuquan Cheng, Jiaxing Song, Jie Identifying Protein-Protein Interaction Sites Using Covering Algorithm |
title | Identifying Protein-Protein Interaction Sites Using Covering Algorithm |
title_full | Identifying Protein-Protein Interaction Sites Using Covering Algorithm |
title_fullStr | Identifying Protein-Protein Interaction Sites Using Covering Algorithm |
title_full_unstemmed | Identifying Protein-Protein Interaction Sites Using Covering Algorithm |
title_short | Identifying Protein-Protein Interaction Sites Using Covering Algorithm |
title_sort | identifying protein-protein interaction sites using covering algorithm |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2695276/ https://www.ncbi.nlm.nih.gov/pubmed/19564948 http://dx.doi.org/10.3390/ijms10052190 |
work_keys_str_mv | AT duxiuquan identifyingproteinproteininteractionsitesusingcoveringalgorithm AT chengjiaxing identifyingproteinproteininteractionsitesusingcoveringalgorithm AT songjie identifyingproteinproteininteractionsitesusingcoveringalgorithm |