Published in Proteins on November 01, 2004
Protein-DNA binding specificity predictions with structural models. Nucleic Acids Res (2005) 2.45
DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces. Nucleic Acids Res (2007) 1.68
Ab initio prediction of transcription factor targets using structural knowledge. PLoS Comput Biol (2005) 1.64
Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry. Nucleic Acids Res (2007) 1.40
De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins. Nucleic Acids Res (2013) 1.28
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
An all-atom knowledge-based energy function for protein-DNA threading, docking decoy discrimination, and prediction of transcription-factor binding profiles. Proteins (2009) 1.07
Improved predictions of transcription factor binding sites using physicochemical features of DNA. Nucleic Acids Res (2012) 1.06
Using sequence-specific chemical and structural properties of DNA to predict transcription factor binding sites. PLoS Comput Biol (2010) 0.95
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
Using genome-wide measurements for computational prediction of SH2-peptide interactions. Nucleic Acids Res (2009) 0.92
Predicting target DNA sequences of DNA-binding proteins based on unbound structures. PLoS One (2012) 0.88
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
A structural-based strategy for recognition of transcription factor binding sites. PLoS One (2013) 0.84
Benchmarks for flexible and rigid transcription factor-DNA docking. BMC Struct Biol (2011) 0.82
An effective approach for generating a three-Cys2His2 zinc-finger-DNA complex model by docking. BMC Bioinformatics (2010) 0.78
DBD2BS: connecting a DNA-binding protein with its binding sites. Nucleic Acids Res (2012) 0.77
Mesoscopic model and free energy landscape for protein-DNA binding sites: analysis of cyanobacterial promoters. PLoS Comput Biol (2014) 0.75
Structure-based modeling of protein: DNA specificity. Brief Funct Genomics (2014) 0.75
Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors. PLoS Comput Biol (2017) 0.75
Direct Comparison of Amino Acid and Salt Interactions with Double-Stranded and Single-Stranded DNA from Explicit-Solvent Molecular Dynamics Simulations. J Chem Theory Comput (2017) 0.75
The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae. Cell (2004) 8.89
Chemosensing in Escherichia coli: two regimes of two-state receptors. Proc Natl Acad Sci U S A (2006) 3.12
Self-organization of the Escherichia coli chemotaxis network imaged with super-resolution light microscopy. PLoS Biol (2009) 3.07
The bacterial actin MreB rotates, and rotation depends on cell-wall assembly. Proc Natl Acad Sci U S A (2011) 2.61
Quantifying the integration of quorum-sensing signals with single-cell resolution. PLoS Biol (2009) 2.40
A quantitative comparison of sRNA-based and protein-based gene regulation. Mol Syst Biol (2008) 2.33
In vivo residue-specific histone methylation dynamics. J Biol Chem (2009) 2.33
Dynamic structures in Escherichia coli: spontaneous formation of MinE rings and MinD polar zones. Proc Natl Acad Sci U S A (2003) 2.19
Precise adaptation in bacterial chemotaxis through "assistance neighborhoods". Proc Natl Acad Sci U S A (2006) 2.13
Cell shape and cell-wall organization in Gram-negative bacteria. Proc Natl Acad Sci U S A (2008) 2.13
The Vibrio harveyi master quorum-sensing regulator, LuxR, a TetR-type protein is both an activator and a repressor: DNA recognition and binding specificity at target promoters. Mol Microbiol (2008) 2.11
Deducing receptor signaling parameters from in vivo analysis: LuxN/AI-1 quorum sensing in Vibrio harveyi. Cell (2008) 2.10
Responding to chemical gradients: bacterial chemotaxis. Curr Opin Cell Biol (2011) 2.00
Vibrio harveyi quorum sensing: a coincidence detector for two autoinducers controls gene expression. EMBO J (2003) 1.99
A curvature-mediated mechanism for localization of lipids to bacterial poles. PLoS Comput Biol (2006) 1.95
Mechanisms for maintaining cell shape in rod-shaped Gram-negative bacteria. Mol Microbiol (2011) 1.91
PSICIC: noise and asymmetry in bacterial division revealed by computational image analysis at sub-pixel resolution. PLoS Comput Biol (2008) 1.88
Accuracy of direct gradient sensing by single cells. Proc Natl Acad Sci U S A (2008) 1.81
Kinetic analysis of the assembly of the outer membrane protein LamB in Escherichia coli mutants each lacking a secretion or targeting factor in a different cellular compartment. J Bacteriol (2006) 1.66
Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli. Mol Syst Biol (2009) 1.57
Chemotaxis in Escherichia coli: a molecular model for robust precise adaptation. PLoS Comput Biol (2007) 1.56
Negative feedback loops involving small regulatory RNAs precisely control the Vibrio harveyi quorum-sensing response. Mol Cell (2010) 1.52
Receptor-receptor coupling in bacterial chemotaxis: evidence for strongly coupled clusters. Biophys J (2006) 1.43
Hourglass model for a protein-based circadian oscillator. Phys Rev Lett (2006) 1.43
α-Ketoglutarate coordinates carbon and nitrogen utilization via enzyme I inhibition. Nat Chem Biol (2011) 1.41
Information processing and signal integration in bacterial quorum sensing. Mol Syst Biol (2009) 1.39
Differences in signalling by directly and indirectly binding ligands in bacterial chemotaxis. EMBO J (2010) 1.32
Differential neutralization efficiency of hemagglutinin epitopes, antibody interference, and the design of influenza vaccines. Proc Natl Acad Sci U S A (2009) 1.31
Variable sizes of Escherichia coli chemoreceptor signaling teams. Mol Syst Biol (2008) 1.29
Lipid localization in bacterial cells through curvature-mediated microphase separation. Biophys J (2008) 1.25
Thermal robustness of signaling in bacterial chemotaxis. Cell (2011) 1.23
Active regulation of receptor ratios controls integration of quorum-sensing signals in Vibrio harveyi. Mol Syst Biol (2011) 1.19
Maximum likelihood and the single receptor. Phys Rev Lett (2009) 1.18
Probing bacterial transmembrane histidine kinase receptor-ligand interactions with natural and synthetic molecules. Proc Natl Acad Sci U S A (2010) 1.12
Measurement of the copy number of the master quorum-sensing regulator of a bacterial cell. Biophys J (2010) 1.11
Achieving optimal growth through product feedback inhibition in metabolism. PLoS Comput Biol (2010) 1.10
Self-organized periodicity of protein clusters in growing bacteria. Phys Rev Lett (2008) 1.08
Dynamics of cooperativity in chemical sensing among cell-surface receptors. Phys Rev Lett (2011) 1.08
Growth-induced instability in metabolic networks. Phys Rev Lett (2007) 1.08
Chemotaxis receptor complexes: from signaling to assembly. PLoS Comput Biol (2007) 1.04
Min-protein oscillations in round bacteria. Phys Biol (2004) 1.04
Limits of sensing temporal concentration changes by single cells. Phys Rev Lett (2010) 1.04
Exponential sensitivity of noise-driven switching in genetic networks. Phys Biol (2008) 1.04
Precision and kinetics of adaptation in bacterial chemotaxis. Biophys J (2010) 1.02
Designability of protein structures: a lattice-model study using the Miyazawa-Jernigan matrix. Proteins (2002) 1.00
Emergence of highly designable protein-backbone conformations in an off-lattice model. Proteins (2002) 1.00
Filament depolymerization can explain chromosome pulling during bacterial mitosis. PLoS Comput Biol (2011) 0.99
A dynamic-signaling-team model for chemotaxis receptors in Escherichia coli. Proc Natl Acad Sci U S A (2010) 0.98
Weight matrices for protein-DNA binding sites from a single co-crystal structure. Phys Rev E Stat Nonlin Soft Matter Phys (2006) 0.98
Flexibility of alpha-helices: results of a statistical analysis of database protein structures. J Mol Biol (2003) 0.97
Non-local interaction via diffusible resource prevents coexistence of cooperators and cheaters in a lattice model. PLoS One (2013) 0.97
Hydrophobic interaction and hydrogen-bond network for a methane pair in liquid water. Proc Natl Acad Sci U S A (2007) 0.96
How can vaccines against influenza and other viral diseases be made more effective? PLoS Biol (2010) 0.96
Accuracy of direct gradient sensing by cell-surface receptors. Prog Biophys Mol Biol (2009) 0.93
Flexibility of beta-sheets: principal component analysis of database protein structures. Proteins (2004) 0.92
Modeling torque versus speed, shot noise, and rotational diffusion of the bacterial flagellar motor. Phys Rev Lett (2009) 0.91
Evaluating gene expression dynamics using pairwise RNA FISH data. PLoS Comput Biol (2010) 0.91
An excitable cortex and memory model successfully predicts new pseudopod dynamics. PLoS One (2012) 0.90
Curvature and shape determination of growing bacteria. Phys Rev E Stat Nonlin Soft Matter Phys (2009) 0.89
Fast accurate evaluation of protein solvent exposure. Proteins (2004) 0.89
Pattern formation within Escherichia coli: diffusion, membrane attachment, and self-interaction of MinD molecules. Phys Rev Lett (2004) 0.89
Kondo model for the "0.7 anomaly" in transport through a quantum point contact. Phys Rev Lett (2002) 0.89
Evolution, interactions, and biological networks. PLoS Biol (2007) 0.88
An improved pairwise decomposable finite-difference Poisson-Boltzmann method for computational protein design. J Comput Chem (2008) 0.88
Predicting functionally informative mutations in Escherichia coli BamA using evolutionary covariance analysis. Genetics (2013) 0.86
Mechanics of membrane bulging during cell-wall disruption in gram-negative bacteria. Phys Rev E Stat Nonlin Soft Matter Phys (2011) 0.85
Steps in the bacterial flagellar motor. PLoS Comput Biol (2009) 0.84
Identifying proteins of high designability via surface-exposure patterns. Proteins (2002) 0.83
Modeling the role of covalent enzyme modification in Escherichia coli nitrogen metabolism. Phys Biol (2010) 0.82
Non-genetic individuality in Escherichia coli motor switching. Phys Biol (2011) 0.82
Designability of alpha-helical proteins. Proc Natl Acad Sci U S A (2002) 0.81
Cell shape can mediate the spatial organization of the bacterial cytoskeleton. Biophys J (2013) 0.81
Does the potential for chaos constrain the embryonic cell-cycle oscillator? PLoS Comput Biol (2011) 0.81
Turning to the cold. Nat Cell Biol (2007) 0.79
Gibbs sampling and helix-cap motifs. Nucleic Acids Res (2005) 0.79
Protein-level fluctuation correlation at the microcolony level and its application to the Vibrio harveyi quorum-sensing circuit. Biophys J (2011) 0.78
Local moment formation in quantum point contacts. Phys Rev Lett (2003) 0.78
Statistical mechanics of RNA folding: importance of alphabet size. Phys Rev E Stat Nonlin Soft Matter Phys (2003) 0.77
Active biopolymers confer fast reorganization kinetics. Phys Rev Lett (2011) 0.76
Ammonia Transport. Ecosal Plus (2004) 0.75
Working together at the interface of physics and biology. Phys Biol (2014) 0.75