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24 April 2024 |
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Article overview
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Locating the Long-range Contact Centers with B-factors and Hydrophobic Cores | | Peng Chen
; Bing Wang
; Hau-San Wong
; De-Shuang Huang
; | | Date: |
26 Dec 2006 | | Subject: | Biomolecules | | Abstract: | It is well known that contact map is one key to representing a specific protein structure. To simplify the complex problem of the contact map prediction, instead we predict the long-range contact centers centered at groups of neighboring contacts. Here, we propose a novel contact prediction method that combines two SVM predictors; each one contains input information from sequence profile, from evolutionary rate, and from prediction of secondary structure. One SVM predictor relies on the local lowest B-factor (attribute for representing the thermal motion of a given atom in protein), which can directly proportional to a local maximal contact density around one residue and in this case this site also may be a clustering centre of long-range contacts between residues. Another SVM predictor is based on hydrophobic cores, each one of which may be considered as a set of neighboring long-range contacts between residues. Incorporated these two SVM predictors by a fusion technique, the clustering centers of long-range contacts can be accurately predicted. | | Source: | arXiv, q-bio/0612048 | | Services: | Forum | Review | PDF | Favorites | |
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