Published in Curr Opin Struct Biol on July 13, 2012
Absence of a simple code: how transcription factors read the genome. Trends Biochem Sci (2014) 1.84
Quantitative modeling of transcription factor binding specificities using DNA shape. Proc Natl Acad Sci U S A (2015) 1.46
Specificity and nonspecificity in RNA-protein interactions. Nat Rev Mol Cell Biol (2015) 1.08
Sequence based prediction of DNA-binding proteins based on hybrid feature selection using random forest and Gaussian naïve Bayes. PLoS One (2014) 0.97
Kinase-mediated changes in nucleosome conformation trigger chromatin decondensation via poly(ADP-ribosyl)ation. Mol Cell (2014) 0.84
Coarse-Grained Models for Protein-Cell Membrane Interactions. Polymers (Basel) (2015) 0.80
Probing the role of interfacial waters in protein-DNA recognition using a hybrid implicit/explicit solvation model. Proteins (2013) 0.78
Prediction of DNA binding motifs from 3D models of transcription factors; identifying TLX3 regulated genes. Nucleic Acids Res (2014) 0.78
Solvated protein-DNA docking using HADDOCK. J Biomol NMR (2013) 0.76
Structure-based prediction of transcription factor binding specificity using an integrative energy function. Bioinformatics (2016) 0.76
An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system. BMC Bioinformatics (2015) 0.75
Mapping specificity landscapes of RNA-protein interactions by high throughput sequencing. Methods (2017) 0.75
Sequence logos: a new way to display consensus sequences. Nucleic Acids Res (1990) 36.74
Breaking the code of DNA binding specificity of TAL-type III effectors. Science (2009) 22.33
A simple cipher governs DNA recognition by TAL effectors. Science (2009) 19.99
Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol (2002) 9.74
Exploring protein native states and large-scale conformational changes with a modified generalized born model. Proteins (2004) 9.15
DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc Natl Acad Sci U S A (1998) 8.14
ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol (2011) 7.33
The role of DNA shape in protein-DNA recognition. Nature (2009) 5.52
A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat. J Biomol Struct Dyn (1999) 5.14
Additivity in protein-DNA interactions: how good an approximation is it? Nucleic Acids Res (2002) 5.04
Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming. Dev Cell (2010) 4.50
The crystal structure of TAL effector PthXo1 bound to its DNA target. Science (2012) 3.69
DNA bending: the prevalence of kinkiness and the virtues of normality. Nucleic Acids Res (1998) 3.67
Structural basis for sequence-specific recognition of DNA by TAL effectors. Science (2012) 3.64
Non-independence of Mnt repressor-operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay. Nucleic Acids Res (2001) 3.63
Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument. Nat Biotechnol (2011) 2.60
Protein-DNA binding specificity predictions with structural models. Nucleic Acids Res (2005) 2.45
Determining the specificity of protein-DNA interactions. Nat Rev Genet (2010) 2.38
Molecular basis of xeroderma pigmentosum group C DNA recognition by engineered meganucleases. Nature (2008) 2.37
Structural and energetic origins of sequence-specific DNA bending: Monte Carlo simulations of papillomavirus E2-DNA binding sites. Structure (2005) 2.17
UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions. Nucleic Acids Res (2010) 2.16
DNA basepair step deformability inferred from molecular dynamics simulations. Biophys J (2003) 2.12
A simple physical model for the prediction and design of protein-DNA interactions. J Mol Biol (2004) 1.90
Bind-n-Seq: high-throughput analysis of in vitro protein-DNA interactions using massively parallel sequencing. Nucleic Acids Res (2009) 1.88
Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs. Nucleic Acids Res (2010) 1.58
Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry. Nucleic Acids Res (2007) 1.40
Extensive protein and DNA backbone sampling improves structure-based specificity prediction for C2H2 zinc fingers. Nucleic Acids Res (2011) 1.27
Energetics of protein-DNA interactions. Nucleic Acids Res (2007) 1.26
A threading-based method for the prediction of DNA-binding proteins with application to the human genome. PLoS Comput Biol (2009) 1.19
Using protein design algorithms to understand the molecular basis of disease caused by protein-DNA interactions: the Pax6 example. Nucleic Acids Res (2010) 1.16
The Protein-DNA Interface database. BMC Bioinformatics (2010) 1.15
3D-footprint: a database for the structural analysis of protein-DNA complexes. Nucleic Acids Res (2009) 1.12
Direct inference of protein-DNA interactions using compressed sensing methods. Proc Natl Acad Sci U S A (2011) 1.08
Prediction of TF target sites based on atomistic models of protein-DNA complexes. BMC Bioinformatics (2008) 1.07
Pushing the limits of what is achievable in protein-DNA docking: benchmarking HADDOCK's performance. Nucleic Acids Res (2010) 1.04
Creating PWMs of transcription factors using 3D structure-based computation of protein-DNA free binding energies. BMC Bioinformatics (2010) 1.00
Experimentally based contact energies decode interactions responsible for protein-DNA affinity and the role of molecular waters at the binding interface. Nucleic Acids Res (2009) 0.93
ADAPT: a molecular mechanics approach for studying the structural properties of long DNA sequences. Biopolymers (2001) 0.93
Ab initio prediction of transcription factor binding sites. Pac Symp Biocomput (2007) 0.91
Structural modeling of TAL effector-DNA interactions. Protein Sci (2012) 0.91
Protein-DNA binding specificity: a grid-enabled computational approach applied to single and multiple protein assemblies. Phys Chem Chem Phys (2009) 0.87
Predicting transcription factor specificity with all-atom models. Nucleic Acids Res (2008) 0.86
Identification of DNA-binding protein target sequences by physical effective energy functions: free energy analysis of lambda repressor-DNA complexes. BMC Struct Biol (2007) 0.85
Towards computational specificity screening of DNA-binding proteins. Nucleic Acids Res (2011) 0.85
ParaDock: a flexible non-specific DNA--rigid protein docking algorithm. Nucleic Acids Res (2011) 0.84
Structure-based DNA-binding prediction and design. Methods Mol Biol (2010) 0.81
Predicting the effects of basepair mutations in DNA-protein complexes by thermodynamic integration. Biophys J (2011) 0.79
Structure-based ab initio prediction of transcription factor-binding sites. Methods Mol Biol (2009) 0.79
High-resolution structure prediction and the crystallographic phase problem. Nature (2007) 7.67
ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol (2011) 7.33
Protein-protein docking with backbone flexibility. J Mol Biol (2007) 4.32
The crystal structure of TAL effector PthXo1 bound to its DNA target. Science (2012) 3.69
Automated prediction of CASP-5 structures using the Robetta server. Proteins (2003) 3.41
Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home. Proteins (2007) 3.01
Prediction of the structure of symmetrical protein assemblies. Proc Natl Acad Sci U S A (2007) 2.35
The kinase mTOR modulates the antibody response to provide cross-protective immunity to lethal infection with influenza virus. Nat Immunol (2013) 1.66
Emergence of symmetry in homooligomeric biological assemblies. Proc Natl Acad Sci U S A (2008) 1.43
Sampling bottlenecks in de novo protein structure prediction. J Mol Biol (2009) 1.40
Targeting G with TAL effectors: a comparison of activities of TALENs constructed with NN and NK repeat variable di-residues. PLoS One (2012) 1.38
Extensive protein and DNA backbone sampling improves structure-based specificity prediction for C2H2 zinc fingers. Nucleic Acids Res (2011) 1.27
Combined covalent-electrostatic model of hydrogen bonding improves structure prediction with Rosetta. J Chem Theory Comput (2015) 1.15
RosettaDock in CAPRI rounds 6-12. Proteins (2007) 1.08
TAL effectors: function, structure, engineering and applications. Curr Opin Struct Biol (2012) 0.99
Adding diverse noncanonical backbones to rosetta: enabling peptidomimetic design. PLoS One (2013) 0.94
Structure-based prediction of protein-peptide specificity in Rosetta. Proteins (2010) 0.92
Large-scale characterization of peptide-MHC binding landscapes with structural simulations. Proc Natl Acad Sci U S A (2011) 0.92
Rosetta in CAPRI rounds 13-19. Proteins (2010) 0.90
TAL effector specificity for base 0 of the DNA target is altered in a complex, effector- and assay-dependent manner by substitutions for the tryptophan in cryptic repeat -1. PLoS One (2013) 0.87
Improved modeling of side-chain--base interactions and plasticity in protein--DNA interface design. J Mol Biol (2012) 0.80
Probing the role of interfacial waters in protein-DNA recognition using a hybrid implicit/explicit solvation model. Proteins (2013) 0.78
Inferring PDZ domain multi-mutant binding preferences from single-mutant data. PLoS One (2010) 0.78
Classification Models for Predicting Cytochrome P450 Enzyme-Substrate Selectivity. Mol Inform (2012) 0.77
The Rosetta all-atom energy function for macromolecular modeling and design. J Chem Theory Comput (2017) 0.76
Structure-based modeling of protein: DNA specificity. Brief Funct Genomics (2014) 0.75