DSP: a protein shape string and its profile prediction server.

Nucleic Acids Research
Jiangming SunTonghua Li

Abstract

Many studies have demonstrated that shape string is an extremely important structure representation, since it is more complete than the classical secondary structure. The shape string provides detailed information also in the regions denoted random coil. But few services are provided for systematic analysis of protein shape string. To fill this gap, we have developed an accurate shape string predictor based on two innovative technologies: a knowledge-driven sequence alignment and a sequence shape string profile method. The performance on blind test data demonstrates that the proposed method can be used for accurate prediction of protein shape string. The DSP server provides both predicted shape string and sequence shape string profile for each query sequence. Using this information, the users can compare protein structure or display protein evolution in shape string space. The DSP server is available at both http://cheminfo.tongji.edu.cn/dsp/ and its main mirror http://chemcenter.tongji.edu.cn/dsp/.

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Citations

Nov 13, 2012·PloS One·Qi SongShengnan Tang
Nov 3, 2012·Biochimie·Duo-Duo WangSheng-Nan Tang
Nov 29, 2017·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Cong ShenFei Guo
May 9, 2014·The Journal of Biological Chemistry·Dustin T KingNatalie C J Strynadka

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Methods Mentioned

BETA
X-ray

Software Mentioned

OS X
DSP
Frag1D
Linux
PHI
BLAST

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