3DRobot: automated generation of diverse and well-packed protein structure decoys | Zendy

Haiyou Deng | Zendy; Ya Jia | Zendy; Yang Zhang | Zendy

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3DRobot: automated generation of diverse and well-packed protein structure decoys

Author(s) -

Haiyou Deng,

Ya Jia,

Yang Zhang

Publication year - 2015

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btv601

Subject(s) - decoy , protein structure prediction , computer science , folding (dsp implementation) , protein folding , algorithm , protein structure , data mining , chemistry , engineering , biochemistry , receptor , electrical engineering

Computationally generated non-native protein structure conformations (or decoys) are often used for designing protein folding simulation methods and force fields. However, almost all the decoy sets currently used in literature suffer from uneven root mean square deviation (RMSD) distribution with bias to non-protein like hydrogen-bonding and compactness patterns. Meanwhile, most protein decoy sets are pre-calculated and there is a lack of methods for automated generation of high-quality decoys for any target proteins.

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