Predicting protein interaction sites from residue spatial sequence profile and evolution rate

This paper proposes a novel method that can predict protein interaction sites in heterocomplexes using residue spatial sequence profile and evolution rate approaches. The former represents the information of multiple sequence alignments while the latter corresponds to a residue’s evolutionary conser...

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Bibliographic Details
Published in:FEBS letters 2006-01, Vol.580 (2), p.380-384
Main Authors: Wang, Bing, Chen, Peng, Huang, De-Shuang, Li, Jing-jing, Lok, Tat-Ming, Lyu, Michael R.
Format: Article
Language:English
Subjects:
Algorithms
Amino Acid Sequence
Evolution, Molecular
Evolutionary rate
Macromolecular Substances
Models, Molecular
Molecular Sequence Data
Multiple sequence alignments
Phylogenetic tree
Protein Conformation
Protein Interaction Mapping
Protein interaction sites
Proteins - chemistry
Proteins - genetics
Proteins - metabolism
Sequence Analysis, Protein
Spatial sequence profile
Support vector machines
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Summary:This paper proposes a novel method that can predict protein interaction sites in heterocomplexes using residue spatial sequence profile and evolution rate approaches. The former represents the information of multiple sequence alignments while the latter corresponds to a residue’s evolutionary conservation score based on a phylogenetic tree. Three predictors using a support vector machines algorithm are constructed to predict whether a surface residue is a part of a protein–protein interface. The efficiency and the effectiveness of our proposed approach is verified by its better prediction performance compared with other models. The study is based on a non-redundant data set of heterodimers consisting of 69 protein chains.
ISSN:0014-5793
1873-3468
DOI:10.1016/j.febslet.2005.11.081