‘Hybrid Protein Model’ for optimally defining 3D protein structure fragments | Zendy

Alexandre G. de Brevern | Zendy; S. Hazout | Zendy

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‘Hybrid Protein Model’ for optimally defining 3D protein structure fragments

Author(s) -

Alexandre G. de Brevern,

S. Hazout

Publication year - 2003

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/btf859

Subject(s) - computer science , protein structure , structural alignment , loop modeling , protein structure prediction , homology modeling , threading (protein sequence) , alphabet , computational biology , algorithm , artificial intelligence , sequence alignment , biology , genetics , peptide sequence , gene , biochemistry , linguistics , philosophy , enzyme

Our aim is to develop a process that automatically defines a repertory of contiguous 3D protein structure fragments and can be used in homology modeling. We present here improvements to the method we introduced previously: the 'hybrid protein model' (de Brevern and Hazout, THEOR: Chem. Acc., 106, 36-47, (2001)) The hybrid protein learns a non-redundant databank encoded in a structural alphabet composed of 16 Protein Blocks (PBs; de Brevern et al., Proteins, 41, 271-287, (2000)). Every local fold is learned by looking for the most similar pattern present in the hybrid protein and modifying it slightly. Finally each position corresponds to a cluster of similar 3D local folds.

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