scholarly journals Toward a detailed understanding of search trajectories in fragment assembly approaches to protein structure prediction

2016 ◽  
Vol 84 (4) ◽  
pp. 411-426 ◽  
Author(s):  
Shaun M. Kandathil ◽  
Julia Handl ◽  
Simon C. Lovell
Keyword(s):  
Protein Structure ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
Detailed Understanding ◽  
Fragment Assembly ◽  
Search Trajectories

scholarly journals The dual role of fragments in fragment-assembly methods for de novo protein structure prediction

2011 ◽  
Vol 80 (2) ◽  
pp. 490-504 ◽  
Author(s):  
Julia Handl ◽  
Joshua Knowles ◽  
Robert Vernon ◽  
David Baker ◽  
Simon C. Lovell
Keyword(s):  
Protein Structure ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
De Novo ◽  
Dual Role ◽  
Fragment Assembly

De novo protein structure prediction by dynamic fragment assembly and conformational space annealing

2011 ◽  
Vol 79 (8) ◽  
pp. 2403-2417 ◽  
Author(s):  
Juyong Lee ◽  
Jinhyuk Lee ◽  
Takeshi N. Sasaki ◽  
Masaki Sasai ◽  
Chaok Seok ◽  
...  
Keyword(s):  
Protein Structure ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
De Novo ◽  
Conformational Space ◽  
Fragment Assembly

scholarly journals Complementing sequence-derived features with structural information extracted from fragment libraries for protein structure prediction

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Siyuan Liu ◽  
Tong Wang ◽  
Qijiang Xu ◽  
Bin Shao ◽  
Jian Yin ◽  
...  
Keyword(s):  
Protein Folding ◽  
Protein Structure ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
Structural Information ◽  
Three Dimensional ◽  
Structural Features ◽  
Dimensional Structure ◽  
Fragment Assembly ◽  
Fragment Libraries

Abstract Background Fragment libraries play a key role in fragment-assembly based protein structure prediction, where protein fragments are assembled to form a complete three-dimensional structure. Rich and accurate structural information embedded in fragment libraries has not been systematically extracted and used beyond fragment assembly. Methods To better leverage the valuable structural information for protein structure prediction, we extracted seven types of structural information from fragment libraries. We broadened the usage of such structural information by transforming fragment libraries into protein-specific potentials for gradient-descent based protein folding and encoding fragment libraries as structural features for protein property prediction. Results Fragment libraires improved the accuracy of protein folding and outperformed state-of-the-art algorithms with respect to predicted properties, such as torsion angles and inter-residue distances. Conclusion Our work implies that the rich structural information extracted from fragment libraries can complement sequence-derived features to help protein structure prediction.

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