Mining of protein contact maps for protein fold prediction
نویسندگان
چکیده
Contact maps have been used in ab initio methods for the problem of protein structure prediction problem. Secondary structures and contacts made by the residues are clearly visible in the contact maps where helices are seen as thick bands and the beta sheets are seen as orthogonal to the diagonal. This paper explores the idea of extracting rules from contact maps to represent “protein fold” information.
منابع مشابه
Evolution and similarity evaluation of protein structures in contact map space.
Prediction of fold from amino acid sequence of a protein has been an active area of research in the past few years, but the limited accuracy of existing techniques emphasizes the need to develop newer approaches to tackle this task. In this study, we use contact map prediction as an intermediate step in fold prediction from sequence. Contact map is a reduced graph-theoretic representation of pr...
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The 3D conformation of a protein may be compactly represented in a symmetrical, square, boolean matrix of pairwise, inter-residue contacts, or “contact map”. The contact map provides a host of useful information about the protein’s structure. In this paper we describe how data mining can be used to extract valuable information from contact maps. For example, clusters of contacts represent certa...
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MOTIVATION Accurate prediction of protein contact maps is an important step in computational structural proteomics. Because contact maps provide a translation and rotation invariant topological representation of a protein, they can be used as a fundamental intermediary step in protein structure prediction. RESULTS We develop a new set of flexible machine learning architectures for the predict...
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ورودعنوان ژورنال:
- Wiley Interdisc. Rew.: Data Mining and Knowledge Discovery
دوره 1 شماره
صفحات -
تاریخ انتشار 2011