Published in Proc Natl Acad Sci U S A on January 01, 1989
enoLOGOS: a versatile web tool for energy normalized sequence logos. Nucleic Acids Res (2005) 4.03
Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential. Biophys J (2004) 3.93
Non-independence of Mnt repressor-operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay. Nucleic Acids Res (2001) 3.63
Physical constraints and functional characteristics of transcription factor-DNA interaction. Proc Natl Acad Sci U S A (2002) 3.07
Inferring binding energies from selected binding sites. PLoS Comput Biol (2009) 2.66
Lambda repressor recognizes the approximately 2-fold symmetric half-operator sequences asymmetrically. Proc Natl Acad Sci U S A (1989) 2.61
Octamerization of lambda CI repressor is needed for effective repression of P(RM) and efficient switching from lysogeny. Genes Dev (2001) 2.53
Protein-DNA binding specificity predictions with structural models. Nucleic Acids Res (2005) 2.45
Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence. Proc Natl Acad Sci U S A (2010) 2.32
Quantitative parameters for amino acid-base interaction: implications for prediction of protein-DNA binding sites. Nucleic Acids Res (1998) 1.94
A consensus sequence for binding of Lrp to DNA. J Bacteriol (1995) 1.88
Functional borders, genetic fine structure, and distance requirements of cis elements mediating light responsiveness of the parsley chalcone synthase promoter. Proc Natl Acad Sci U S A (1990) 1.84
Calculating biological behaviors of epigenetic states in the phage lambda life cycle. Funct Integr Genomics (2004) 1.74
Protein-DNA conformational changes in the crystal structure of a lambda Cro-operator complex. Proc Natl Acad Sci U S A (1990) 1.63
Recognition of specific DNA sequences by the c-myb protooncogene product: role of three repeat units in the DNA-binding domain. Proc Natl Acad Sci U S A (1993) 1.55
Modeling the specificity of protein-DNA interactions. Quant Biol (2013) 1.50
Highly conserved residues in the bZIP domain of yeast GCN4 are not essential for DNA binding. Mol Cell Biol (1991) 1.42
Protein evolution on partially correlated landscapes. Proc Natl Acad Sci U S A (1995) 1.35
Thermodynamics of Cro protein-DNA interactions. Proc Natl Acad Sci U S A (1992) 1.35
Cro's role in the CI Cro bistable switch is critical for {lambda}'s transition from lysogeny to lytic development. Genes Dev (2007) 1.31
Contacts between steroid hormone receptors and thymines in DNA: an interference method. Proc Natl Acad Sci U S A (1990) 1.30
Identification and utilization of arbitrary correlations in models of recombination signal sequences. Genome Biol (2002) 1.29
Predicting strength and function for promoters of the Escherichia coli alternative sigma factor, sigmaE. Proc Natl Acad Sci U S A (2010) 1.23
Additive, cooperative and anti-cooperative effects between identity nucleotides of a tRNA. EMBO J (1993) 1.22
Tuning promoter strength through RNA polymerase binding site design in Escherichia coli. PLoS Comput Biol (2012) 1.19
Multilevel autoregulation of λ repressor protein CI by DNA looping in vitro. Proc Natl Acad Sci U S A (2011) 1.18
Identification of base and backbone contacts used for DNA sequence recognition and high-affinity binding by LAC9, a transcription activator containing a C6 zinc finger. Mol Cell Biol (1991) 1.14
Consistencies of individual DNA base-amino acid interactions in structures and sequences. Nucleic Acids Res (1995) 1.13
Prediction of TF target sites based on atomistic models of protein-DNA complexes. BMC Bioinformatics (2008) 1.07
How Cro and lambda-repressor distinguish between operators: the structural basis underlying a genetic switch. Proc Natl Acad Sci U S A (1998) 1.07
Stability and instability in the lysogenic state of phage lambda. J Bacteriol (2010) 1.03
Differences between EcoRI nonspecific and "star" sequence complexes revealed by osmotic stress. Biophys J (2004) 1.01
Genetic analysis of the Tn21 mer operator-promoter. J Bacteriol (1992) 0.99
Binding site analysis of c-Myb: screening of potential binding sites by using the mutation matrix derived from systematic binding affinity measurements. Nucleic Acids Res (1996) 0.97
Saturation mutagenesis of the DNA site bound by the small carboxy-terminal domain of gamma delta resolvase. EMBO J (1990) 0.96
Lac repressor with the helix-turn-helix motif of lambda cro binds to lac operator. EMBO J (1992) 0.95
RNA base-amino acid interaction strengths derived from structures and sequences. Nucleic Acids Res (1997) 0.95
Modeling the quantitative specificity of DNA-binding proteins from example binding sites. PLoS One (2009) 0.91
ACTIVITY: a database on DNA/RNA sites activity adapted to apply sequence-activity relationships from one system to another. Nucleic Acids Res (2001) 0.90
Synthesis of isotope labeled oligonucleotides and their use in an NMR study of a protein-DNA complex. Nucleic Acids Res (1992) 0.89
Evolutionary meandering of intermolecular interactions along the drift barrier. Proc Natl Acad Sci U S A (2014) 0.89
Specificity of the Mnt protein determined by binding to randomized operators. Proc Natl Acad Sci U S A (1991) 0.88
High-resolution specificity from DNA sequencing highlights alternative modes of Lac repressor binding. Genetics (2014) 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
Non-additivity of sequence-specific enzyme-DNA interactions in the EcoRI DNA methyltransferase. Nucleic Acids Res (1991) 0.85
Reprogramming homing endonuclease specificity through computational design and directed evolution. Nucleic Acids Res (2013) 0.84
Molecular simulation uncovers the conformational space of the λ Cro dimer in solution. Biophys J (2011) 0.80
Packing interface energetics in different crystal forms of the λ Cro dimer. Proteins (2013) 0.79
Structure based sequence dependent stiffness scale for trinucleotides: a direct method. J Biol Phys (2000) 0.78
Synthetic biology outside the cell: linking computational tools to cell-free systems. Front Bioeng Biotechnol (2014) 0.78
Determinants of bacteriophage 933W repressor DNA binding specificity. PLoS One (2012) 0.78
Simple Biophysical Model Predicts Faster Accumulation of Hybrid Incompatibilities in Small Populations Under Stabilizing Selection. Genetics (2015) 0.77
High-affinity quasi-specific sites in the genome: how the DNA-binding proteins cope with them. Biophys J (2011) 0.77
The challenge-phage assay reveals differences in the binding equilibria of mutant Escherichia coli Trp super-repressors in vivo. Nucleic Acids Res (1993) 0.77
Thermodynamic Additivity for Impacts of Base-Pair Substitutions on Association of the Egr-1 Zinc-Finger Protein with DNA. Biochemistry (2016) 0.75
Indirect read-out of the promoter DNA by RNA polymerase in the closed complex. Nucleic Acids Res (2012) 0.75
Temperature and osmotic stress dependence of the thermodynamics for binding linker histone H1(0), Its carboxyl domain (H1(0)-C) or globular domain (H1(0)-G) to B-DNA. Biochem Biophys Rep (2017) 0.75
A new method for sequencing DNA. Proc Natl Acad Sci U S A (1977) 250.51
Protein-DNA recognition. Annu Rev Biochem (1984) 22.02
Lac repressor-operator interaction. I. Equilibrium studies. J Mol Biol (1970) 13.32
Sequence-specific recognition of double helical nucleic acids by proteins. Proc Natl Acad Sci U S A (1976) 13.30
The lac repressor-operator interaction. 3. Kinetic studies. J Mol Biol (1970) 10.07
Saturation mutagenesis of the yeast his3 regulatory site: requirements for transcriptional induction and for binding by GCN4 activator protein. Science (1986) 6.36
Structure of the cro repressor from bacteriophage lambda and its interaction with DNA. Nature (1981) 5.24
Interactions between DNA-bound repressors govern regulation by the lambda phage repressor. Proc Natl Acad Sci U S A (1979) 5.02
Structure of the DNA-Eco RI endonuclease recognition complex at 3 A resolution. Science (1986) 4.89
Mechanism of action of the cro protein of bacteriophage lambda. Proc Natl Acad Sci U S A (1978) 4.34
Recognition sequences of repressor and polymerase in the operators of bacteriophage lambda. Cell (1975) 4.28
DNA-binding proteins. Science (1983) 3.56
The molecular basis of DNA-protein recognition inferred from the structure of cro repressor. Nature (1982) 3.56
Effect of non-contacted bases on the affinity of 434 operator for 434 repressor and Cro. Nature (1987) 2.49
How lac repressor recognizes lac operator. Proc Natl Acad Sci U S A (1978) 2.15
A new-specificity mutant of 434 repressor that defines an amino acid-base pair contact. Nature (1987) 2.13
DNA twisting and the affinity of bacteriophage 434 operator for bacteriophage 434 repressor. Proc Natl Acad Sci U S A (1988) 2.08
Kinetic studies on Cro repressor-operator DNA interaction. J Mol Biol (1987) 1.85
Cro regulatory protein specified by bacteriophage lambda. Structure, DNA-binding, and repression of RNA synthesis. J Biol Chem (1977) 1.78
How lambda repressor and lambda Cro distinguish between OR1 and OR3. Cell (1986) 1.68
Completed DNA sequences and organization of repressor-binding sites in the operators of phage lambda. J Mol Biol (1977) 1.66
Homologous interactions of lambda repressor and lambda Cro with the lambda operator. Cell (1986) 1.58
Recognition of nucleotide sequences. Annu Rev Biochem (1969) 1.56
DNA sequence determinants of lambda repressor binding in vivo. Genetics (1988) 1.23
Specific recognition of guanine bases in protein-nucleic acid complexes. FEBS Lett (1977) 1.06
Different interactions used by Cro repressor in specific and nonspecific DNA binding. J Biol Chem (1986) 1.05
Altered Cro repressors from engineered mutagenesis of a synthetic cro gene. Proc Natl Acad Sci U S A (1985) 0.95
A phase 2 trial of ponatinib in Philadelphia chromosome-positive leukemias. N Engl J Med (2013) 6.67
Solution structure of a specific DNA complex of the Myb DNA-binding domain with cooperative recognition helices. Cell (1994) 3.74
The utility of MRI in suspected MS: report of the Therapeutics and Technology Assessment Subcommittee of the American Academy of Neurology. Neurology (2003) 3.21
Structure-based prediction of DNA target sites by regulatory proteins. Proteins (1999) 2.31
Unique mode of GCC box recognition by the DNA-binding domain of ethylene-responsive element-binding factor (ERF domain) in plant. J Biol Chem (1998) 2.23
Solution structure of a DNA-binding unit of Myb: a helix-turn-helix-related motif with conserved tryptophans forming a hydrophobic core. Proc Natl Acad Sci U S A (1992) 2.23
A versatile synthetic dimerizer for the regulation of protein-protein interactions. Proc Natl Acad Sci U S A (1997) 2.04
ProTherm: Thermodynamic Database for Proteins and Mutants. Nucleic Acids Res (1999) 1.85
The tryptophan cluster: a hypothetical structure of the DNA-binding domain of the myb protooncogene product. J Biol Chem (1990) 1.80
Megavesicles implicated in the rapid transport of intracisternal aggregates across the Golgi stack. Cell (2000) 1.70
Role of structural and sequence information in the prediction of protein stability changes: comparison between buried and partially buried mutations. Protein Eng (1999) 1.61
3DinSight: an integrated relational database and search tool for the structure, function and properties of biomolecules. Bioinformatics (1998) 1.59
Regulated delivery of therapeutic proteins after in vivo somatic cell gene transfer. Science (1999) 1.57
Recognition of specific DNA sequences by the c-myb protooncogene product: role of three repeat units in the DNA-binding domain. Proc Natl Acad Sci U S A (1993) 1.55
Important amino acid properties for enhanced thermostability from mesophilic to thermophilic proteins. Biophys Chem (1999) 1.55
Comparison of the free and DNA-complexed forms of the DNA-binding domain from c-Myb. Nat Struct Biol (1995) 1.46
Use of pentoxifylline therapy for patients with AIDS-related wasting: pilot study. Clin Infect Dis (1994) 1.44
A ligand-reversible dimerization system for controlling protein-protein interactions. Proc Natl Acad Sci U S A (2000) 1.38
Thermodynamics of specific and non-specific DNA binding by the c-Myb DNA-binding domain. J Mol Biol (1998) 1.29
Genetic reclassification of porcine enteroviruses. J Gen Virol (2001) 1.28
Double-blind evaluation of glycerol therapy in acute cerebral infarction. Lancet (1972) 1.25
ProTherm, version 2.0: thermodynamic database for proteins and mutants. Nucleic Acids Res (2000) 1.23
Transcriptional squelching re-examined. Nature (1997) 1.23
The serum response factor is extensively modified by phosphorylation following its synthesis in serum-stimulated fibroblasts. Mol Cell Biol (1991) 1.21
Transactivation and transformation by Myb are negatively regulated by a leucine-zipper structure. Proc Natl Acad Sci U S A (1992) 1.21
Delivery of a stringent dimerizer-regulated gene expression system in a single retroviral vector. Proc Natl Acad Sci U S A (2000) 1.16
A possible role of the C-terminal domain of the RecA protein. A gateway model for double-stranded DNA binding. J Biol Chem (1996) 1.16
L-type voltage-sensitive calcium channel activation stimulates gene expression by a serum response factor-dependent pathway. J Biol Chem (1994) 1.10
The cavity in the hydrophobic core of Myb DNA-binding domain is reserved for DNA recognition and trans-activation. Nat Struct Biol (1996) 1.09
Thermodynamic database for protein-nucleic acid interactions (ProNIT). Bioinformatics (2001) 1.09
Synthesis and activity of bivalent FKBP12 ligands for the regulated dimerization of proteins. Bioorg Med Chem (1998) 1.08
Importance of surrounding residues for protein stability of partially buried mutations. J Biomol Struct Dyn (2000) 1.05
Missense mutations in the Bacillus subtilis gnt repressor that diminish operator binding ability. J Mol Biol (1993) 1.04
Filling a cavity dramatically increases pressure stability of the c-Myb R2 subdomain. Proteins (2001) 1.03
Thermodynamic and kinetic studies of DNA triplex formation of an oligohomopyrimidine and a matched duplex by filter binding assay. Biochemistry (1993) 1.02
Pharmacologic control of a humanized gene therapy system implanted into nude mice. J Clin Invest (1997) 1.01
Treatment with glycerol of cerebral oedema due to acute cerebral infarction. Lancet (1971) 1.00
Relationship between amino acid properties and protein stability: buried mutations. J Protein Chem (1999) 1.00
Solvent density and long-range dipole field around a DNA-binding protein studied by molecular dynamics. Proteins (2000) 1.00
Hydrophobic interactions in the major groove can influence DNA local structure. J Biomol Struct Dyn (1986) 1.00
Comparative thermodynamic analyses of the Fv, Fab* and Fab fragments of anti-dansyl mouse monoclonal antibody. FEBS Lett (1995) 0.99
Preferential recognition of TCR hypervariable regions by human anti-idiotypic T cells induced by T cell vaccination. J Immunol (2000) 0.99
Orally administered betahistine and regional cerebral blood flow in cerebrovascular disease. J Clin Pharmacol (1974) 0.98
[The context organization of functional regions in yeast genes with high-level expression]. Mol Biol (Mosk) (2002) 0.98
Binding site analysis of c-Myb: screening of potential binding sites by using the mutation matrix derived from systematic binding affinity measurements. Nucleic Acids Res (1996) 0.97
Rapamycin control of transgene expression from a single AAV vector in mouse salivary glands. Gene Ther (2006) 0.96
T cell responses to myelin basic protein in patients with spinal cord injury and multiple sclerosis. J Neuroimmunol (1999) 0.96
Two consecutive zinc fingers in Sp1 and in MAZ are essential for interactions with cis-elements. J Biol Chem (2001) 0.96
Neurologic deficit in patients at high risk with thoracoabdominal aortic aneurysms: the role of cerebral spinal fluid drainage and distal aortic perfusion. J Vasc Surg (1994) 0.95
Interferon beta induces T-helper 2 immune deviation in MS. Neurology (1999) 0.95
Vertebrobasilar arterial insufficiency with dementia. Controlled trials of treatment with betahistine hydrochloride. J Am Geriatr Soc (1974) 0.94
rSNP_Guide, a database system for analysis of transcription factor binding to target sequences: application to SNPs and site-directed mutations. Nucleic Acids Res (2001) 0.94
Urodynamic pattern changes in multiple sclerosis. Urology (2001) 0.94
Immunoregulation and blocking antibodies induced by interferon beta treatment in MS. Neurology (2000) 0.94
Antigenic properties of porcine teschovirus 1 (PTV-1) Talfan strain and molecular strategy for serotyping of PTVs. Arch Virol (2007) 0.93
Regulation of gene expression with synthetic dimerizers. Methods Enzymol (1999) 0.93
Sequence dependence of the B-A conformational transition of DNA. Biopolymers (1989) 0.93
A backflow of electrons around photosystem II in Chlorella cells. Biochim Biophys Acta (1979) 0.93
Constitutive and regulated expression of processed insulin following in vivo hepatic gene transfer. Gene Ther (2002) 0.93
Letter: Glycerol-induced haemolysis. Lancet (1974) 0.92
The mutant RecA proteins, RecAR243Q and RecAK245N, exhibit defective DNA binding in homologous pairing. Arch Biochem Biophys (1999) 0.92
Phase Ib study of weekly mammalian target of rapamycin inhibitor ridaforolimus (AP23573; MK-8669) with weekly paclitaxel. Ann Oncol (2009) 0.92
Negative autoregulation of c-Myb activity by homodimer formation through the leucine zipper. J Biol Chem (1993) 0.92
A general strategy to enhance the potency of chimeric transcriptional activators. Proc Natl Acad Sci U S A (1999) 0.92
Aberrant T cell migration toward RANTES and MIP-1 alpha in patients with multiple sclerosis. Overexpression of chemokine receptor CCR5. Brain (2000) 0.91
Impaired apoptotic deletion of myelin basic protein-reactive T cells in patients with multiple sclerosis. Eur J Immunol (1999) 0.91
ACTIVITY: a database on DNA/RNA sites activity adapted to apply sequence-activity relationships from one system to another. Nucleic Acids Res (2001) 0.90
Reactivity pattern and cytokine profile of T cells primed by myelin peptides in multiple sclerosis and healthy individuals. Eur J Immunol (2001) 0.90
Phase I/IIa trial of the mammalian target of rapamycin inhibitor ridaforolimus (AP23573; MK-8669) administered orally in patients with refractory or advanced malignancies and sarcoma. Ann Oncol (2012) 0.89
Hereditary myoclonus and progressive distal muscular atrophy. Ann Neurol (1979) 0.88
Accuracy of clinical detection of INO in MS: corroboration with quantitative infrared oculography. Neurology (2003) 0.88
Cerebral embolization: prospective clinical analysis of 42 cases. Stroke (1974) 0.88
Narcolepsy following cerebral hypoxic ischemia. Ann Neurol (1986) 0.88
Human A-myb gene encodes a transcriptional activator containing the negative regulatory domains. FEBS Lett (1995) 0.87
Kinetic analysis of DNA binding by the c-Myb DNA-binding domain using surface plasmon resonance. FEBS Lett (1999) 0.87
Evaluation of free energy landscape for base-amino acid interactions using ab initio force field and extensive sampling. Biopolymers (2002) 0.87
Th2 immune regulation induced by T cell vaccination in patients with multiple sclerosis. Eur J Immunol (2000) 0.87
Pentoxifylline aggravates impairment in tumor necrosis factor-alpha secretion and increases mycobacterial load in macrophages from AIDS patients with disseminated Mycobacterium avium-intracellulare complex infection. J Infect Dis (1994) 0.87
Possible role of protein in photosynthetic electron transfer. Biochim Biophys Acta (1980) 0.86
Identification and differential expression of yeast SEC23-related gene (Msec23) in mouse tissues. FEBS Lett (1993) 0.86
Solution structures of Myb DNA-binding domain and its complex with DNA. Nucleic Acids Symp Ser (1993) 0.85
A common TCR V-D-J sequence in V beta 13.1 T cells recognizing an immunodominant peptide of myelin basic protein in multiple sclerosis. J Immunol (1999) 0.85
Regulation of chemokine receptor CCR5 and production of RANTES and MIP-1alpha by interferon-beta. J Neuroimmunol (2001) 0.84
Shape and energetics of a cavity in c-Myb probed by natural and non-natural amino acid mutations. J Mol Biol (1999) 0.84
DNA fingerprinting involving fluorescence-labeled termini of any enzymatically generated fragments of DNA. Jpn J Hum Genet (1994) 0.83
Interrelations between the efficiency of translation start sites and other sequence features of yeast mRNAs. Mol Genet Genomics (2003) 0.83
Identification of the location of antigenic sites of swine vesicular disease virus with neutralization-resistant mutants. J Gen Virol (1995) 0.83
Relationship between curved DNA conformations and slow gel migration. J Biomol Struct Dyn (1987) 0.82
Anti-viral properties of interferon beta treatment in patients with multiple sclerosis. Mult Scler (2002) 0.82
Reactivity and regulatory properties of human anti-idiotypic antibodies induced by T cell vaccination. J Immunol (2000) 0.82
The affinity maturation of anti-4-hydroxy-3-nitrophenylacetyl mouse monoclonal antibody. A calorimetric study of the antigen-antibody interaction. J Biol Chem (1995) 0.82
Temperature dependence of electron transfer between bacteriopheophytin and ubiquinone in protonated and deuterated reaction centers of Rhodopseudomonas sphaeroides. Biophys J (1981) 0.82
Orientational changes of the transition dipole moment of retinal chromophore on the disk membrane due to the conversion of rhodopsin to bathorhodopsin and to isorhodopsin. Vision Res (1979) 0.81
T cell recognition motifs of an immunodominant peptide of myelin basic protein in patients with multiple sclerosis: structural requirements and clinical implications. Eur J Immunol (1998) 0.81
Good response of membranous lupus nephritis to tacrolimus. Clin Nephrol (2006) 0.81
Th1 and Th2 deviation of myelin-autoreactive T cells by altered peptide ligands is associated with reciprocal regulation of Lck, Fyn, and ZAP-70. J Immunol (1999) 0.80
Triplex formation of chemically modified homopyrimidine oligonucleotides: thermodynamic and kinetic studies. Biochemistry (1999) 0.80
Neurologic manifestations of AIDS: a comparative study of two populations from Mexico and the United States. J Acquir Immune Defic Syndr Hum Retrovirol (1995) 0.80
Patterns of auditory abnormality in multiple sclerosis. Audiology (1986) 0.79
Structure and function of the proteins encoded by the myb gene family. Curr Top Microbiol Immunol (1996) 0.79