Computational protocol: The Transcription Factor Encyclopedia

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Protocol publication

[…] In summary, DNA binding transcription factors have been extensively studied and can be grouped according to a structural classification system []. For each of the small set of structural domains known to facilitate sequence-specific protein-DNA interactions, solved protein structures have been reported. Thus, it is feasible to produce homology-based models for many DNA-binding domains of proteins represented in TFe by using these solved protein structures as templates.We generated a set of 202 predicted protein structures--homology-based predictions of the DNA binding domains of TFs. To do this, we developed a custom pipeline, written in Python, that incorporates two tools well-known in the realm of protein studies: HMMER [] and Modeller []. Our protocol is based on the work of Morozov and Siggia [], in which templates are selected to optimize similarity of DNA-binding residues. This method has been shown to increase modeling accuracy at the DNA-binding interface.There are three main steps in generating the structural predictions: (1) building the template library; (2) finding a suitable template for each unsolved structure we would like to model; and (3) creating the structural prediction using the template as a guide. […]

Pipeline specifications

Software tools HMMER, MODELLER
Application Protein structure analysis
Organisms Mus musculus, Rattus norvegicus, Homo sapiens