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

Toward the Rational Design of p53-Stabilizing Drugs: Probing the Surface of the Oncogenic Y220C Mutant

(2010) Nicolas Basse et al.   CHEMISTRY & BIOLOGY

Clinical and molecular aspects of aniridia

(2010) H Kokotas et al.   CLINICAL GENETICS

Exploring the sequence determinants of amyloid structure using position-specific scoring matrices

(2010) Sebastian Maurer-Stroh et al.   NATURE METHODS

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

(2009) Christian A. Grove et al.   CELL

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

(2009) Michael F Berger et al.   Nature Protocols

Identification of Pax6-Dependent Gene Regulatory Networks in the Mouse Lens

(2009) Louise V. Wolf et al.   PLoS One

Predicting DNA recognition by Cys2His2 zinc finger proteins

(2008) Anton V. Persikov et al.   BIOINFORMATICS

Prediction of TF target sites based on atomistic models of protein-DNA complexes

(2008) Vladimir Angarica et al.   BMC BIOINFORMATICS

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

Molecular basis of xeroderma pigmentosum group C DNA recognition by engineered meganucleases

(2008) Pilar Redondo et al.   NATURE

Predicting transcription factor specificity with all-atom models

(2008) S. Jamal Rahi et al.   NUCLEIC ACIDS RESEARCH

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 I-DmoI in complex with its target DNA provides new insights into meganuclease engineering

(2008) M. J. Marcaida et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Concise Review: Pax6 Transcription Factor Contributes to both Embryonic and Adult Neurogenesis as a Multifunctional Regulator

(2008) Noriko Osumi et al.   STEM CELLS