A knowledge-based orientation potential for transcription factor-DNA docking | Zendy

Takako Takeda | Zendy; Rosario I. Corona | Zendy; Juntao Guo | Zendy

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A knowledge-based orientation potential for transcription factor-DNA docking

Author(s) -

Takako Takeda,

Rosario I. Corona,

Juntao Guo

Publication year - 2012

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/bts699

Subject(s) - docking (animal) , decoy , dna , computational biology , macromolecular docking , protein–ligand docking , computer science , transcription factor , biological system , biophysics , protein structure , biology , virtual screening , bioinformatics , drug discovery , biochemistry , medicine , receptor , nursing , gene

Computational modeling of protein-DNA complexes remains a challenging problem in structural bioinformatics. One of the key factors for a successful protein-DNA docking is a potential function that can accurately discriminate the near-native structures from decoy complexes and at the same time make conformational sampling more efficient. Here, we developed a novel orientation-dependent, knowledge-based, residue-level potential for improving transcription factor (TF)-DNA docking.

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