Predicting DNA recognition by Cys2His2 zinc finger proteins.

ABSTRACT:

Motivation

Cys(2)His(2) zinc finger (ZF) proteins represent the largest class of eukaryotic transcription factors. Their modular structure and well-conserved protein-DNA interface allow the development of computational approaches for predicting their DNA-binding preferences even when no binding sites are known for a particular protein. The 'canonical model' for ZF protein-DNA interaction consists of only four amino acid nucleotide contacts per zinc finger domain.

Results

We present an approach for predicting ZF binding based on support vector machines (SVMs). While most previous computational approaches have been based solely on examples of known ZF protein-DNA interactions, ours additionally incorporates information about protein-DNA pairs known to bind weakly or not at all

SUBMITTER: Persikov AV 

PROVIDER: S-EPMC2638941 | biostudies-literature | 2009 Jan

REPOSITORIES: biostudies-literature