JOY: protein sequence-structure representation and analysis

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JOY: protein sequence-structure representation and analysis

MOTIVATION JOY is a program to annotate protein sequence alignments with three-dimensional (3D) structural features. It was developed to display 3D structural information in a sequence alignment and to help understand the conservation of amino acids in their specific local environments. RESULTS : The JOY representation now constitutes an essential part of the two databases of protein structur...

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Analysis of protein sequence/structure similarity relationships.

Current analyses of protein sequence/structure relationships have focused on expected similarity relationships for structurally similar proteins. To survey and explore the basis of these relationships, we present a general sequence/structure map that covers all combinations of similarity/dissimilarity relationships and provide novel energetic analyses of these relationships. To aid our analysis...

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Protein sequence randomness and sequence/structure correlations.

We investigated protein sequence/structure correlation by constructing a space of protein sequences, based on methods developed previously for constructing a space of protein structures. The space is constructed by using a representation of the amino acids as vectors of 10 property factors that encode almost all of their physical properties. Each sequence is represented by a distribution of ove...

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Protein Sequence and Structure Analysis of Antibody Variable Domains

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ژورنال

عنوان ژورنال: Bioinformatics

سال: 1998

ISSN: 1367-4803,1460-2059

DOI: 10.1093/bioinformatics/14.7.617