Mechanisms of transcription factor selectivity.

Absence of a simple code: how transcription factors read the genome. Trends Biochem Sci (2014) 1.84

Disentangling the many layers of eukaryotic transcriptional regulation. Annu Rev Genet (2012) 1.68

Exercise increases mitochondrial PGC-1alpha content and promotes nuclear-mitochondrial cross-talk to coordinate mitochondrial biogenesis. J Biol Chem (2011) 1.46

Integrated approaches reveal determinants of genome-wide binding and function of the transcription factor Pho4. Mol Cell (2011) 1.38

Coregulation of transcription factor binding and nucleosome occupancy through DNA features of mammalian enhancers. Mol Cell (2014) 1.36

MIR@NT@N: a framework integrating transcription factors, microRNAs and their targets to identify sub-network motifs in a meta-regulation network model. BMC Bioinformatics (2011) 1.33

Toward the identification and regulation of the Arabidopsis thaliana ABI3 regulon. Nucleic Acids Res (2012) 1.25

Genome-wide analysis of WRKY transcription factors in Solanum lycopersicum. Mol Genet Genomics (2012) 1.19

CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human. Bioinformatics (2012) 1.07

Understanding biomolecular motion, recognition, and allostery by use of conformational ensembles. Eur Biophys J (2011) 1.06

Interaction between p53 and estradiol pathways in transcriptional responses to chemotherapeutics. Cell Cycle (2013) 0.98

Principles of allosteric interactions in cell signaling. J Am Chem Soc (2014) 0.97

ASD v2.0: updated content and novel features focusing on allosteric regulation. Nucleic Acids Res (2013) 0.94

Restricted leucine zipper dimerization and specificity of DNA recognition of the melanocyte master regulator MITF. Genes Dev (2012) 0.91

Genomic analysis reveals a novel nuclear factor-κB (NF-κB)-binding site in Alu-repetitive elements. J Biol Chem (2011) 0.90

Gene profiling of MTA1 identifies novel gene targets and functions. PLoS One (2011) 0.88

The role of allostery in the ubiquitin-proteasome system. Crit Rev Biochem Mol Biol (2012) 0.87

The spatial structure of cell signaling systems. Phys Biol (2013) 0.86

Formation of stress-specific p53 binding patterns is influenced by chromatin but not by modulation of p53 binding affinity to response elements. Nucleic Acids Res (2010) 0.84

Cooperativity of stress-responsive transcription factors in core hypoxia-inducible factor binding regions. PLoS One (2012) 0.83

ToxR Antagonizes H-NS Regulation of Horizontally Acquired Genes to Drive Host Colonization. PLoS Pathog (2016) 0.83

Transcription factor networks as targets for therapeutic intervention of cancer: the breast cancer paradigm. Mol Med (2011) 0.83

Benchmarks for flexible and rigid transcription factor-DNA docking. BMC Struct Biol (2011) 0.82

The role of response elements organization in transcription factor selectivity: the IFN-β enhanceosome example. PLoS Comput Biol (2011) 0.82

Why does binding of proteins to DNA or proteins to proteins not necessarily spell function? ACS Chem Biol (2010) 0.82

Learning transcriptional regulation on a genome scale: a theoretical analysis based on gene expression data. Brief Bioinform (2011) 0.82

A role for insulator elements in the regulation of gene expression response to hypoxia. Nucleic Acids Res (2011) 0.81

Lysine120 interactions with p53 response elements can allosterically direct p53 organization. PLoS Comput Biol (2010) 0.81

The patterns of histone modifications in the vicinity of transcription factor binding sites in human lymphoblastoid cell lines. PLoS One (2013) 0.80

High performance transcription factor-DNA docking with GPU computing. Proteome Sci (2012) 0.78

TFinDit: transcription factor-DNA interaction data depository. BMC Bioinformatics (2012) 0.78

Cooperative activation of Xenopus rhodopsin transcription by paired-like transcription factors. BMC Mol Biol (2014) 0.78

A dynamic checkpoint in oxidative lesion discrimination by formamidopyrimidine-DNA glycosylase. Nucleic Acids Res (2015) 0.77

Combinatorial control of gene expression. Biomed Res Int (2013) 0.77

Predicting protein-DNA interactions by full search computational docking. Proteins (2013) 0.77

p53 dynamics upon response element recognition explored by molecular simulations. Sci Rep (2015) 0.76

ePIANNO: ePIgenomics ANNOtation tool. PLoS One (2016) 0.75

Nucleosome organization in the vicinity of transcription factor binding sites in the human genome. BMC Genomics (2014) 0.75

PatchDock and SymmDock: servers for rigid and symmetric docking. Nucleic Acids Res (2005) 7.66

The role of dynamic conformational ensembles in biomolecular recognition. Nat Chem Biol (2009) 7.36

Principles of docking: An overview of search algorithms and a guide to scoring functions. Proteins (2002) 5.79

Is allostery an intrinsic property of all dynamic proteins? Proteins (2004) 4.99

A method for simultaneous alignment of multiple protein structures. Proteins (2004) 3.45

Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proc Natl Acad Sci U S A (2003) 3.42

Allostery: absence of a change in shape does not imply that allostery is not at play. J Mol Biol (2008) 3.24

Hot regions in protein--protein interactions: the organization and contribution of structurally conserved hot spot residues. J Mol Biol (2004) 3.10

Stabilities and conformations of Alzheimer's beta -amyloid peptide oligomers (Abeta 16-22, Abeta 16-35, and Abeta 10-35): Sequence effects. Proc Natl Acad Sci U S A (2002) 3.06

Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations. Protein Sci (2002) 3.01

Induced fit, conformational selection and independent dynamic segments: an extended view of binding events. Trends Biochem Sci (2010) 2.97

Principles of protein-protein interactions: what are the preferred ways for proteins to interact? Chem Rev (2008) 2.96

FireDock: fast interaction refinement in molecular docking. Proteins (2007) 2.90

Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. Pharmacol Ther (2013) 2.64

Close-range electrostatic interactions in proteins. Chembiochem (2002) 2.42

FireDock: a web server for fast interaction refinement in molecular docking. Nucleic Acids Res (2008) 2.39

The origin of allosteric functional modulation: multiple pre-existing pathways. Structure (2009) 2.33

Recognition of functional sites in protein structures. J Mol Biol (2004) 2.32

Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms. Mol Biosyst (2009) 2.18

Extended disordered proteins: targeting function with less scaffold. Trends Biochem Sci (2003) 2.12

A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications. Protein Sci (2004) 2.11

PRISM: protein interactions by structural matching. Nucleic Acids Res (2005) 2.11

Protein-protein interactions; coupling of structurally conserved residues and of hot spots across interfaces. Implications for docking. Structure (2004) 2.06

Residues crucial for maintaining short paths in network communication mediate signaling in proteins. Mol Syst Biol (2006) 1.98

Taking geometry to its edge: fast unbound rigid (and hinge-bent) docking. Proteins (2003) 1.95

Geometry-based flexible and symmetric protein docking. Proteins (2005) 1.95

Flexible protein alignment and hinge detection. Proteins (2002) 1.93

Relationship between ion pair geometries and electrostatic strengths in proteins. Biophys J (2002) 1.91

HingeProt: automated prediction of hinges in protein structures. Proteins (2008) 1.86

Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM. Nat Protoc (2011) 1.84

Synonymous mutations and ribosome stalling can lead to altered folding pathways and distinct minima. J Mol Biol (2008) 1.80

Allostery in disease and in drug discovery. Cell (2013) 1.77

Principles of flexible protein-protein docking. Proteins (2008) 1.71

Simulations as analytical tools to understand protein aggregation and predict amyloid conformation. Curr Opin Chem Biol (2006) 1.70

ARTS: alignment of RNA tertiary structures. Bioinformatics (2005) 1.67

Protein-protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking. J Mol Biol (2004) 1.64

Polymorphism in Alzheimer Abeta amyloid organization reflects conformational selection in a rugged energy landscape. Chem Rev (2010) 1.62

Enzyme dynamics point to stepwise conformational selection in catalysis. Curr Opin Chem Biol (2010) 1.61

Similar binding sites and different partners: implications to shared proteins in cellular pathways. Structure (2007) 1.60

Molecular dynamics simulations of alanine rich beta-sheet oligomers: Insight into amyloid formation. Protein Sci (2002) 1.59

Dynamic allostery: linkers are not merely flexible. Structure (2011) 1.58

Correlated mutations: advances and limitations. A study on fusion proteins and on the Cohesin-Dockerin families. Proteins (2006) 1.58

Analysis of ordered and disordered protein complexes reveals structural features discriminating between stable and unstable monomers. J Mol Biol (2004) 1.54

MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions. Nucleic Acids Res (2008) 1.52

Architectures and functional coverage of protein-protein interfaces. J Mol Biol (2008) 1.51

Truncated beta-amyloid peptide channels provide an alternative mechanism for Alzheimer's Disease and Down syndrome. Proc Natl Acad Sci U S A (2010) 1.48

FiberDock: Flexible induced-fit backbone refinement in molecular docking. Proteins (2010) 1.47

A survey of available tools and web servers for analysis of protein-protein interactions and interfaces. Brief Bioinform (2009) 1.47

Modeling the Alzheimer Abeta17-42 fibril architecture: tight intermolecular sheet-sheet association and intramolecular hydrated cavities. Biophys J (2007) 1.44

Models of beta-amyloid ion channels in the membrane suggest that channel formation in the bilayer is a dynamic process. Biophys J (2007) 1.44

New structures help the modeling of toxic amyloidbeta ion channels. Trends Biochem Sci (2008) 1.43

Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering molecular dynamics simulation: significant role of Asn ladder. Proc Natl Acad Sci U S A (2005) 1.43

Atomic-level description of amyloid beta-dimer formation. J Am Chem Soc (2006) 1.41

The ARTS web server for aligning RNA tertiary structures. Nucleic Acids Res (2006) 1.37

Short peptide amyloid organization: stabilities and conformations of the islet amyloid peptide NFGAIL. Biophys J (2003) 1.33

Structural stability and dynamics of an amyloid-forming peptide GNNQQNY from the yeast prion sup-35. Biophys J (2006) 1.33

Multiple structural alignment by secondary structures: algorithm and applications. Protein Sci (2003) 1.32

Zinc ions promote Alzheimer Abeta aggregation via population shift of polymorphic states. Proc Natl Acad Sci U S A (2010) 1.32

Allostery and population shift in drug discovery. Curr Opin Pharmacol (2010) 1.32

Models of toxic beta-sheet channels of protegrin-1 suggest a common subunit organization motif shared with toxic alzheimer beta-amyloid ion channels. Biophys J (2008) 1.30

MolAxis: efficient and accurate identification of channels in macromolecules. Proteins (2008) 1.30

Nanoparticle-induced vascular blockade in human prostate cancer. Blood (2010) 1.30

The multiple common point set problem and its application to molecule binding pattern detection. J Comput Biol (2006) 1.28

Topological properties of protein interaction networks from a structural perspective. Biochem Soc Trans (2008) 1.28

Molecular-level examination of Cu2+ binding structure for amyloid fibrils of 40-residue Alzheimer's β by solid-state NMR spectroscopy. J Am Chem Soc (2011) 1.27

Protein-protein interactions: organization, cooperativity and mapping in a bottom-up Systems Biology approach. Phys Biol (2005) 1.26

Residue centrality, functionally important residues, and active site shape: analysis of enzyme and non-enzyme families. Protein Sci (2006) 1.26

How different are structurally flexible and rigid binding sites? Sequence and structural features discriminating proteins that do and do not undergo conformational change upon ligand binding. J Mol Biol (2006) 1.26

A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method. BMC Bioinformatics (2011) 1.25

FiberDock: a web server for flexible induced-fit backbone refinement in molecular docking. Nucleic Acids Res (2010) 1.25

Predicting molecular interactions in silico: II. Protein-protein and protein-drug docking. Curr Med Chem (2004) 1.25

PRISM: protein-protein interaction prediction by structural matching. Methods Mol Biol (2008) 1.24

Protein-protein interaction networks: how can a hub protein bind so many different partners? Trends Biochem Sci (2009) 1.24

Theoretical characterization of substrate access/exit channels in the human cytochrome P450 3A4 enzyme: involvement of phenylalanine residues in the gating mechanism. J Phys Chem B (2009) 1.23

Spatial chemical conservation of hot spot interactions in protein-protein complexes. BMC Biol (2007) 1.22

Sequence analysis of p53 response-elements suggests multiple binding modes of the p53 tetramer to DNA targets. Nucleic Acids Res (2007) 1.22

β-Barrel topology of Alzheimer's β-amyloid ion channels. J Mol Biol (2010) 1.21

How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues. Biophys J (2004) 1.21