ProSeg: a database of local structures of protein segments |
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Authors: | Yoshito Sawada Shinya Honda |
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Institution: | (1) National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Tsukuba 305-8566, Japan |
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Abstract: | Integration of knowledge on the sequence-structure correlation of proteins provides a basis for the structural design of artificial
novel proteins. As one of strategies, it is effective to consider a short segment, whose size is in between an amino acid
and a domain, as a correlation unit for exploring the structure-to-sequence relationship. Here we report the development of
a database called ProSeg, which consists of two sub-databases, Segment DB and Cluster DB. Segment DB contains tens of thousands of segments that were
prepared by dividing the primary sequences of 370 proteins using a sliding L-residue window (L = 5, 9, 11, 15). These segments were classified into several thousands of clusters according to their three-dimensional structural
resemblance. Cluster DB contains much cluster-related information, which includes image, rank, frequency, secondary structure
assignment, sequence profile, etc. Users can search for a suitable cluster by inputting an appropriate parameter (i.e., PDB
ID, dihedral angles, or DSSP symbols), which identifies the backbone structure of a query segment. Analogous to a language,
ProSeg could be regarded as a ‘structure-sequence dictionary’ that contains over 10,000 ‘protein words’. ProSeg is freely accessible through the Internet (). |
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Keywords: | Sequence-structure correlation Database Short peptide segment Classification Clustering PDB Protein word Protein design |
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