Structure-based prediction of transcription factor binding specificity using an integrative energy function

DNA–protein π-interactions in nature: abundance, structure, composition and strength of contacts between aromatic amino acids and DNA nucleobases or deoxyribose sugar

(2014) Katie A. Wilson et al.   NUCLEIC ACIDS RESEARCH

De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins

(2013) Anton V. Persikov et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

(2013) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Takako Takeda et al.   BIOINFORMATICS

Atomistic modeling of protein–DNA interaction specificity: progress and applications

(2012) Limin Angela Liu et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Using protein design algorithms to understand the molecular basis of disease caused by protein–DNA interactions: the Pax6 example

(2010) Andreu Alibés et al.   NUCLEIC ACIDS RESEARCH

A Novel Alignment-Free Method for Comparing Transcription Factor Binding Site Motifs

(2010) Minli Xu et al.   PLoS One

Structure-based prediction of transcription factor binding sites using a protein-DNA docking approach

(2008) Zhijie Liu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS