2009年3月
ProSeg: a database of local structures of protein segments
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- ,
- 巻
- 23
- 号
- 3
- 開始ページ
- 163
- 終了ページ
- 169
- 記述言語
- 英語
- 掲載種別
- 研究論文(学術雑誌)
- DOI
- 10.1007/s10822-008-9248-x
- 出版者・発行元
- SPRINGER
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 (http://riodb.ibase.aist.go.jp/proseg/).
- リンク情報
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- DOI
- https://doi.org/10.1007/s10822-008-9248-x
- CiNii Articles
- http://ci.nii.ac.jp/naid/80020107980
- PubMed
- https://www.ncbi.nlm.nih.gov/pubmed/18931918
- Web of Science
- https://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=JSTA_CEL&SrcApp=J_Gate_JST&DestLinkType=FullRecord&KeyUT=WOS:000262987300004&DestApp=WOS_CPL
- ID情報
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- DOI : 10.1007/s10822-008-9248-x
- ISSN : 0920-654X
- CiNii Articles ID : 80020107980
- PubMed ID : 18931918
- Web of Science ID : WOS:000262987300004