Recovery of protein structure from contact maps

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Recovery of protein structure from contact maps.

BACKGROUND Prediction of a protein's structure from its amino acid sequence is a key issue in molecular biology. While dynamics, performed in the space of two-dimensional contact maps, eases the necessary conformational search, it may also lead to maps that do not correspond to any real three-dimensional structure. To remedy this, an efficient procedure is needed to reconstruct three-dimensiona...

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Protein Structure from Contact Maps: A Case-Based Reasoning Approach

Determining the three-dimensional structure of a protein is an important step in understanding biological function. Despite advances in experimental methods (crystallography and NMR) and protein structure prediction techniques, the gap between the number of known protein sequences and determined structures continues to grow. Approaches to protein structure prediction vary from those that apply ...

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Mining Protein Contact Maps

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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Selecting protein fuzzy contact maps through information and structure measures

Protein contact maps are representations of the proteins three dimensional folding topology. A fuzzy generalization of contact maps (FGCM) provides to the researcher flexibility not present in standard (i.e. crisp) contact maps but it also changes the information content of the data. To aid in the rationale –rather than ad-hocselection of generalized contact maps parameters we introduce some un...

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Evolutionary Protein Contact Maps Prediction

In this study, a novel residue-residue contacts prediction approach based on evolutionary computation is presented. The prediction is based on four amino acids properties. In particular, we consider the hydrophobicity, the polarity, the charge and size of residues of amino acids. The prediction model consists of a set of rules that identifies contacts between amino acids. Results obtained confi...

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ژورنال

عنوان ژورنال: Folding and Design

سال: 1997

ISSN: 1359-0278

DOI: 10.1016/s1359-0278(97)00041-2