Literature DB >> 17599940

POODLE-S: web application for predicting protein disorder by using physicochemical features and reduced amino acid set of a position-specific scoring matrix.

Kana Shimizu1, Shuichi Hirose, Tamotsu Noguchi.   

Abstract

UNLABELLED: Protein disorder is characterized by a lack of a stable 3D structure, and is considered to be involved in a number of important protein functions such as regulatory and signalling events. We developed a web application, the POODLE-S, which predicts the disordered region from amino acid sequences by using physicochemical features and reduced amino acid set of a position-specific scoring matrix. AVAILABILITY: POODLE-S is available from http://mbs.cbrc.jp/poodle/poodle-s.html and can be used by both academic and commercial users.

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Year:  2007        PMID: 17599940     DOI: 10.1093/bioinformatics/btm330

Source DB:  PubMed          Journal:  Bioinformatics        ISSN: 1367-4803            Impact factor:   6.937


  45 in total

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2.  Bivalent binding drives the formation of the Grb2-Gab1 signaling complex in a noncooperative manner.

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3.  An optimized Npro-based method for the expression and purification of intrinsically disordered proteins for an NMR study.

Authors:  Natsuko Goda; Naoki Matsuo; Takeshi Tenno; Sonoko Ishino; Yoshizumi Ishino; Satoshi Fukuchi; Motonori Ota; Hidekazu Hiroaki
Journal:  Intrinsically Disord Proteins       Date:  2015-02-23

4.  Multivalent binding and facilitated diffusion account for the formation of the Grb2-Sos1 signaling complex in a cooperative manner.

Authors:  Caleb B McDonald; Jordan E Balke; Vikas Bhat; David C Mikles; Brian J Deegan; Kenneth L Seldeen; Amjad Farooq
Journal:  Biochemistry       Date:  2012-03-02       Impact factor: 3.162

5.  Casein Kinase 1 Regulates Cytorhabdovirus Replication and Transcription by Phosphorylating a Phosphoprotein Serine-Rich Motif.

Authors:  Qiang Gao; Teng Yan; Zhen-Jia Zhang; Song-Yu Liu; Xiao-Dong Fang; Dong-Min Gao; Yi-Zhou Yang; Wen-Ya Xu; Ji-Hui Qiao; Qing Cao; Zhi-Hang Ding; Ying Wang; Jialin Yu; Xian-Bing Wang
Journal:  Plant Cell       Date:  2020-07-08       Impact factor: 11.277

6.  SPINE-D: accurate prediction of short and long disordered regions by a single neural-network based method.

Authors:  Tuo Zhang; Eshel Faraggi; Bin Xue; A Keith Dunker; Vladimir N Uversky; Yaoqi Zhou
Journal:  J Biomol Struct Dyn       Date:  2012

7.  Evaluation of disorder predictions in CASP9.

Authors:  Bohdan Monastyrskyy; Krzysztof Fidelis; John Moult; Anna Tramontano; Andriy Kryshtafovych
Journal:  Proteins       Date:  2011-09-16

Review 8.  A comprehensive overview of computational protein disorder prediction methods.

Authors:  Xin Deng; Jesse Eickholt; Jianlin Cheng
Journal:  Mol Biosyst       Date:  2011-08-26

9.  Development of an accurate classification system of proteins into structured and unstructured regions that uncovers novel structural domains: its application to human transcription factors.

Authors:  Satoshi Fukuchi; Keiichi Homma; Yoshiaki Minezaki; Takashi Gojobori; Ken Nishikawa
Journal:  BMC Struct Biol       Date:  2009-04-30

10.  Predicting disordered regions in proteins using the profiles of amino acid indices.

Authors:  Pengfei Han; Xiuzhen Zhang; Zhi-Ping Feng
Journal:  BMC Bioinformatics       Date:  2009-01-30       Impact factor: 3.169

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