Using a structural and logics systems approach to infer bHLH–DNA binding specificity determinants

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 Multiparameter Network Reveals Extensive Divergence between C. elegans bHLH Transcription Factors

(2009) Christian A. Grove et al.   CELL

Nuance in the double-helix and its role in protein–DNA recognition

(2009) Remo Rohs et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors

(2009) Michael F Berger et al.   Nature Protocols

Experimental determination of the evolvability of a transcription factor

(2009) S. J. Maerkl et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparison of DNA binding across protein superfamilies

(2009) Bruno Contreras-Moreira et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

From Nonspecific DNA–Protein Encounter Complexes to the Prediction of DNA–Protein Interactions

(2009) Mu Gao et al.   PLoS Computational Biology

Variation in Homeodomain DNA Binding Revealed by High-Resolution Analysis of Sequence Preferences

(2008) Michael F. Berger et al.   CELL

Analysis of Homeodomain Specificities Allows the Family-wide Prediction of Preferred Recognition Sites

(2008) Marcus B. Noyes et al.   CELL

Transcription factor functionality and transcription regulatory networks

(2008) Christian A. Grove et al.   Molecular BioSystems

UniPROBE: an online database of protein binding microarray data on protein-DNA interactions

(2008) D. E. Newburger et al.   NUCLEIC ACIDS RESEARCH

Crystal Structure of E47−NeuroD1/Beta2 bHLH Domain−DNA Complex:  Heterodimer Selectivity and DNA Recognition†,‡

(2007) Antonella Longo et al.   BIOCHEMISTRY