Published in Protein Sci on October 01, 1994
Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation. Proc Natl Acad Sci U S A (2000) 2.35
SAF-Box, a conserved protein domain that specifically recognizes scaffold attachment region DNA. Mol Cell Biol (2000) 1.84
ABSINTH: a new continuum solvation model for simulations of polypeptides in aqueous solutions. J Comput Chem (2009) 1.57
Covariation of residues in the homeodomain sequence family. Protein Sci (1995) 1.33
Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum. J Chem Phys (2007) 1.33
Structure of the even-skipped homeodomain complexed to AT-rich DNA: new perspectives on homeodomain specificity. EMBO J (1995) 1.33
The helix-turn-helix motif as an ultrafast independently folding domain: the pathway of folding of Engrailed homeodomain. Proc Natl Acad Sci U S A (2007) 1.23
Exploring the parameter space of the coarse-grained UNRES force field by random search: selecting a transferable medium-resolution force field. J Comput Chem (2009) 1.22
Prediction of amino acid sequence from structure. Protein Sci (2000) 1.19
Understanding ensemble protein folding at atomic detail. Proc Natl Acad Sci U S A (2006) 1.19
Insights into binding cooperativity of MATa1/MATalpha2 from the crystal structure of a MATa1 homeodomain-maltose binding protein chimera. Protein Sci (2003) 1.05
Mutations in HOXD13 underlie syndactyly type V and a novel brachydactyly-syndactyly syndrome. Am J Hum Genet (2007) 1.05
Different members of a simple three-helix bundle protein family have very different folding rate constants and fold by different mechanisms. J Mol Biol (2009) 1.00
Polarizable Atomic Multipole Solutes in a Generalized Kirkwood Continuum. J Chem Theory Comput (2007) 0.98
Refolding the engrailed homeodomain: structural basis for the accumulation of a folding intermediate. Biophys J (2010) 0.97
A one-dimensional reaction coordinate for identification of transition states from explicit solvent P(fold)-like calculations. Biophys J (2007) 0.97
An all-atom force field for tertiary structure prediction of helical proteins. Biophys J (2004) 0.93
A phage display selection of engrailed homeodomain mutants and the importance of residue Q50. Nucleic Acids Res (2004) 0.89
Intermediates in the protein folding process: a computational model. Int J Mol Sci (2011) 0.89
Comparison of multiple crystal structures with NMR data for engrailed homeodomain. J Biomol NMR (2008) 0.88
The N-terminus of the human RecQL4 helicase is a homeodomain-like DNA interaction motif. Nucleic Acids Res (2012) 0.87
Evaluating and optimizing computational protein design force fields using fixed composition-based negative design. Proc Natl Acad Sci U S A (2008) 0.86
Fast protein folding kinetics. Q Rev Biophys (2014) 0.86
The roles of entropy and kinetics in structure prediction. PLoS One (2009) 0.84
Karyopherins in nuclear transport of homeodomain proteins during development. Biochim Biophys Acta (2011) 0.83
Novel structural features in two ZHX homeodomains derived from a systematic study of single and multiple domains. BMC Struct Biol (2010) 0.81
Multimolecule test-tube simulations of protein unfolding and aggregation. Proc Natl Acad Sci U S A (2012) 0.81
Dioxane contributes to the altered conformation and oligomerization state of a designed engrailed homeodomain variant. Protein Sci (2005) 0.80
Investigation of homeodomain membrane translocation properties: insights from the structure determination of engrailed-2 homeodomain in aqueous and membrane-mimetic environments. Biophys J (2013) 0.80
Flexibility and Disorder in Gene Regulation: LacI/GalR and Hox Proteins. J Biol Chem (2015) 0.79
Computational design of co-assembling protein-DNA nanowires. Nature (2015) 0.79
Predicting the folding pathway of engrailed homeodomain with a probabilistic roadmap enhanced reaction-path algorithm. Biophys J (2007) 0.79
BCL::SAXS: GPU accelerated Debye method for computation of small angle X-ray scattering profiles. Proteins (2015) 0.79
Bayesian inference of protein structure from chemical shift data. PeerJ (2015) 0.78
Binding polymorphism in the DNA bound state of the Pdx1 homeodomain. PLoS Comput Biol (2013) 0.78
A free-energy approach for all-atom protein simulation. Biophys J (2009) 0.77
Engineered lanthanide-binding metallohomeodomains: designing folded chimeras by modular turn substitution. Protein Sci (2006) 0.77
Two-state folding over a weak free-energy barrier. Biophys J (2003) 0.77
Promiscuous contacts and heightened dynamics increase thermostability in an engineered variant of the engrailed homeodomain. Protein Eng Des Sel (2012) 0.77
Structural guided scaffold phage display libraries as a source of bio-therapeutics. PLoS One (2013) 0.76
REMD and umbrella sampling simulations to probe the energy barrier of the folding pathways of engrailed homeodomain. J Mol Model (2014) 0.76
Traversing the folding pathway of proteins using temperature-aided cascade molecular dynamics with conformation-dependent charges. Eur Biophys J (2016) 0.76
Improvement of structure-based potentials for protein folding by native and nonnative hydrogen bonds. Biophys J (2011) 0.76
Deconvoluting Protein (Un)folding Structural Ensembles Using X-Ray Scattering, Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics Simulation. PLoS One (2015) 0.75
MOLS sampling and its applications in structural biophysics. Biophys Rev (2010) 0.75
Role of Backbone Dipole Interactions in the Formation of Secondary and Supersecondary Structures of Proteins. J Chem Theory Comput (2014) 0.75
Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction. J Chem Phys (2016) 0.75
Macromolecular Crystallography and Structural Biology Databases at NIST. J Res Natl Inst Stand Technol (2001) 0.75
Creating a Homeodomain with High Stability and DNA Binding Affinity by Sequence Averaging. J Am Chem Soc (2017) 0.75
The interpretation of protein structures: estimation of static accessibility. J Mol Biol (1971) 40.24
Crystallographic R factor refinement by molecular dynamics. Science (1987) 15.90
Coupling of local folding to site-specific binding of proteins to DNA. Science (1994) 9.49
Crystal structure of an engrailed homeodomain-DNA complex at 2.8 A resolution: a framework for understanding homeodomain-DNA interactions. Cell (1990) 7.99
The structure and function of the homeodomain. Biochim Biophys Acta (1989) 7.44
Aromatic-aromatic interaction: a mechanism of protein structure stabilization. Science (1985) 6.87
Crystal structure of a MAT alpha 2 homeodomain-operator complex suggests a general model for homeodomain-DNA interactions. Cell (1991) 5.14
The structure of the Antennapedia homeodomain determined by NMR spectroscopy in solution: comparison with prokaryotic repressors. Cell (1989) 4.13
Crystal structure of the Oct-1 POU domain bound to an octamer site: DNA recognition with tethered DNA-binding modules. Cell (1994) 3.98
Analysis of the relationship between side-chain conformation and secondary structure in globular proteins. J Mol Biol (1987) 3.63
DNA binding specificity of homeodomains. Biochemistry (1991) 3.17
Structure of the HMG box motif in the B-domain of HMG1. EMBO J (1993) 2.84
Helix stop signals in proteins and peptides: the capping box. Biochemistry (1993) 2.71
Nuclear magnetic resonance solution structure of the fushi tarazu homeodomain from Drosophila and comparison with the Antennapedia homeodomain. J Mol Biol (1994) 2.43
Determination of the nuclear magnetic resonance solution structure of an Antennapedia homeodomain-DNA complex. J Mol Biol (1993) 2.20
Electronic distributions within protein phenylalanine aromatic rings are reflected by the three-dimensional oxygen atom environments. Proc Natl Acad Sci U S A (1982) 1.47
Understanding the homeodomain. J Biol Chem (1993) 1.18
Crystallization and preliminary X-ray diffraction studies of the engrailed homeodomain and of an engrailed homeodomain/DNA complex. Biochem Biophys Res Commun (1990) 1.04
Protein-DNA recognition. Annu Rev Biochem (1984) 22.02
Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A. Science (1991) 15.97
Cellular uptake of the tat protein from human immunodeficiency virus. Cell (1988) 10.19
Intrinsically disordered protein. J Mol Graph Model (2001) 8.54
Crystal structure of an engrailed homeodomain-DNA complex at 2.8 A resolution: a framework for understanding homeodomain-DNA interactions. Cell (1990) 7.99
How the lambda repressor and cro work. Cell (1980) 6.65
DNA recognition by Cys2His2 zinc finger proteins. Annu Rev Biophys Biomol Struct (2000) 6.61
The operator-binding domain of lambda repressor: structure and DNA recognition. Nature (1982) 6.03
Zinc finger phage: affinity selection of fingers with new DNA-binding specificities. Science (1994) 5.70
Crystal structure of a five-finger GLI-DNA complex: new perspectives on zinc fingers. Science (1993) 5.38
Zif268 protein-DNA complex refined at 1.6 A: a model system for understanding zinc finger-DNA interactions. Structure (1996) 5.30
Homology among DNA-binding proteins suggests use of a conserved super-secondary structure. Nature (1982) 5.21
Crystal structure of a MAT alpha 2 homeodomain-operator complex suggests a general model for homeodomain-DNA interactions. Cell (1991) 5.14
A general strategy for selecting high-affinity zinc finger proteins for diverse DNA target sites. Science (1997) 4.93
Structure of the lambda complex at 2.5 A resolution: details of the repressor-operator interactions. Science (1988) 4.67
Tat protein from human immunodeficiency virus forms a metal-linked dimer. Science (1988) 4.63
The DNA-binding domain of p53 contains the four conserved regions and the major mutation hot spots. Genes Dev (1993) 3.99
Crystal structure of the Oct-1 POU domain bound to an octamer site: DNA recognition with tethered DNA-binding modules. Cell (1994) 3.98
The lambda repressor contains two domains. Proc Natl Acad Sci U S A (1979) 3.68
Bacteriophage lambda repressor and cro protein: interactions with operator DNA. Methods Enzymol (1980) 3.52
Crystal structure of MyoD bHLH domain-DNA complex: perspectives on DNA recognition and implications for transcriptional activation. Cell (1994) 3.50
A bacterial two-hybrid selection system for studying protein-DNA and protein-protein interactions. Proc Natl Acad Sci U S A (2000) 3.35
Analysis of zinc fingers optimized via phage display: evaluating the utility of a recognition code. J Mol Biol (1999) 3.20
Refined 1.8 A crystal structure of the lambda repressor-operator complex. J Mol Biol (1992) 3.09
DNA recognition by beta-sheets in the Arc repressor-operator crystal structure. Nature (1994) 3.07
The N-terminal arms of lambda repressor wrap around the operator DNA. Nature (1982) 2.90
Regulatory functions of the lambda repressor reside in the amino-terminal domain. Nature (1979) 2.77
Structural basis of DNA recognition by the heterodimeric cell cycle transcription factor E2F-DP. Genes Dev (1999) 2.73
Two crystal structures of the B1 immunoglobulin-binding domain of streptococcal protein G and comparison with NMR. Biochemistry (1994) 2.67
Structure determination and refinement of human alpha class glutathione transferase A1-1, and a comparison with the Mu and Pi class enzymes. J Mol Biol (1993) 2.66
Crystal structure of a paired domain-DNA complex at 2.5 A resolution reveals structural basis for Pax developmental mutations. Cell (1995) 2.63
Beyond the "recognition code": structures of two Cys2His2 zinc finger/TATA box complexes. Structure (2001) 2.55
Crystal structure of the human Pax6 paired domain-DNA complex reveals specific roles for the linker region and carboxy-terminal subdomain in DNA binding. Genes Dev (1999) 2.54
Structure of phosphate-free ribonuclease A refined at 1.26 A. Biochemistry (1988) 2.53
Metal-dependent folding of a single zinc finger from transcription factor IIIA. Proc Natl Acad Sci U S A (1987) 2.53
Getting a handhold on DNA: design of poly-zinc finger proteins with femtomolar dissociation constants. Proc Natl Acad Sci U S A (1998) 2.51
The three-dimensional structure of a glutathione S-transferase from the mu gene class. Structural analysis of the binary complex of isoenzyme 3-3 and glutathione at 2.2-A resolution. Biochemistry (1992) 2.43
Basis for recognition of cisplatin-modified DNA by high-mobility-group proteins. Nature (1999) 2.35
Structure of the operator-binding domain of bacteriophage lambda repressor: implications for DNA recognition and gene regulation. Cold Spring Harb Symp Quant Biol (1983) 2.15
Structure-based design of transcription factors. Science (1995) 1.93
Three-dimensional structure of Schistosoma japonicum glutathione S-transferase fused with a six-amino acid conserved neutralizing epitope of gp41 from HIV. Protein Sci (1994) 1.91
High-resolution structures of variant Zif268-DNA complexes: implications for understanding zinc finger-DNA recognition. Structure (1998) 1.86
Thousands of proteins likely to have long disordered regions. Pac Symp Biocomput (1998) 1.79
Engrailed homeodomain-DNA complex at 2.2 A resolution: a detailed view of the interface and comparison with other engrailed structures. J Mol Biol (1998) 1.74
Structure of the L-arabinose-binding protein from Escherichia coli at 2.4 A resolution. J Mol Biol (1981) 1.72
Rearrangement of side-chains in a Zif268 mutant highlights the complexities of zinc finger-DNA recognition. J Mol Biol (2001) 1.71
Three-dimensional structure, catalytic properties, and evolution of a sigma class glutathione transferase from squid, a progenitor of the lens S-crystallins of cephalopods. Biochemistry (1995) 1.66
Oct-1 POU domain-DNA interactions: cooperative binding of isolated subdomains and effects of covalent linkage. Genes Dev (1996) 1.65
Distinctive DNA conformation with enlarged major groove is found in Zn-finger-DNA and other protein-DNA complexes. Proc Natl Acad Sci U S A (1994) 1.61
Structure of form III crystals of bovine pancreatic trypsin inhibitor. J Mol Biol (1987) 1.58
The DNA binding arm of lambda repressor: critical contacts from a flexible region. Science (1991) 1.58
Comparison of X-ray and NMR structures for the Antennapedia homeodomain-DNA complex. Nat Struct Biol (1998) 1.57
A metal-mediated hydride shift mechanism for xylose isomerase based on the 1.6 A Streptomyces rubiginosus structures with xylitol and D-xylose. Proteins (1991) 1.55
Contribution of tyrosine 6 to the catalytic mechanism of isoenzyme 3-3 of glutathione S-transferase. J Biol Chem (1992) 1.54
Biological function made crystal clear - annotation of hypothetical proteins via structural genomics. Curr Opin Biotechnol (2000) 1.52
Comparison of the structures of cro and lambda repressor proteins from bacteriophage lambda. J Mol Biol (1983) 1.48
Structure and control of pyridoxal phosphate dependent allosteric threonine deaminase. Structure (1998) 1.47
Fingering too many proteins. Cell (1988) 1.47
Binding studies with mutants of Zif268. Contribution of individual side chains to binding affinity and specificity in the Zif268 zinc finger-DNA complex. J Biol Chem (1999) 1.42
The engineering of binding affinity at metal ion binding sites for the stabilization of proteins: subtilisin as a test case. Biochemistry (1988) 1.37
An engineered intersubunit disulfide enhances the stability and DNA binding of the N-terminal domain of lambda repressor. Biochemistry (1986) 1.37
Dimerization of the tat protein from human immunodeficiency virus: a cysteine-rich peptide mimics the normal metal-linked dimer interface. Proc Natl Acad Sci U S A (1988) 1.37
Design of TATA box-binding protein/zinc finger fusions for targeted regulation of gene expression. Proc Natl Acad Sci U S A (1997) 1.31
Engrailed (Gln50-->Lys) homeodomain-DNA complex at 1.9 A resolution: structural basis for enhanced affinity and altered specificity. Structure (1997) 1.31
Heteronuclear NMR and crystallographic studies of wild-type and H187Q Escherichia coli uracil DNA glycosylase: electrophilic catalysis of uracil expulsion by a neutral histidine 187. Biochemistry (1999) 1.30
Transcriptional repression by zinc finger peptides. Exploring the potential for applications in gene therapy. J Biol Chem (1997) 1.30
Identification of protein folds: matching hydrophobicity patterns of sequence sets with solvent accessibility patterns of known structures. Proteins (1990) 1.29
Lambda repressor: a model system for understanding protein-DNA interactions and protein stability. Adv Protein Chem (1990) 1.29
A genetic switch in a bacterial virus. Sci Am (1982) 1.28
Crystal structure of Escherichia coli uracil DNA glycosylase and its complexes with uracil and glycerol: structure and glycosylase mechanism revisited. Proteins (1999) 1.25
Functional implications of interleukin-1 beta based on the three-dimensional structure. Proteins (1992) 1.22
Stressing-out DNA? The contribution of serine-phosphodiester interactions in catalysis by uracil DNA glycosylase. Biochemistry (2000) 1.22
Dimerization of the operator binding domain of phage lambda repressor. Biochemistry (1987) 1.19
Snapshots along the reaction coordinate of an SNAr reaction catalyzed by glutathione transferase. Biochemistry (1993) 1.18
Tyrosine 115 participates both in chemical and physical steps of the catalytic mechanism of a glutathione S-transferase. J Biol Chem (1993) 1.18
Heparin binding by fibronectin module III-13 involves six discontinuous basic residues brought together to form a cationic cradle. J Biol Chem (1995) 1.17
Phage display methods for selecting zinc finger proteins with novel DNA-binding specificities. Methods Enzymol (1996) 1.16
Crystal structure of an OCA-B peptide bound to an Oct-1 POU domain/octamer DNA complex: specific recognition of a protein-DNA interface. Genes Dev (1999) 1.15
Systematic variation in DNA length yields highly ordered repressor-operator cocrystals. Science (1985) 1.15
Proteases of enhanced stability: characterization of a thermostable variant of subtilisin. Proteins (1986) 1.14
Structure and function of the xenobiotic substrate-binding site and location of a potential non-substrate-binding site in a class pi glutathione S-transferase. Biochemistry (1997) 1.12
Computer-aided model-building strategies for protein design. Biochemistry (1986) 1.12
Crystal structure of dephospho-coenzyme A kinase from Haemophilus influenzae. J Struct Biol (2001) 1.10
Crystal structure and amino acid sequence of Wolinella succinogenes L-asparaginase. Eur J Biochem (1996) 1.07
Structure-based design of a dimeric zinc finger protein. Biochemistry (1998) 1.07
Crystallization and preliminary X-ray diffraction studies of the engrailed homeodomain and of an engrailed homeodomain/DNA complex. Biochem Biophys Res Commun (1990) 1.04
Calcium-independent subtilisin by design. Proteins (1993) 1.01
Combining experimental information from crystal and solution studies: joint X-ray and NMR refinement. Science (1992) 1.00
Exploring the role of glutamine 50 in the homeodomain-DNA interface: crystal structure of engrailed (Gln50 --> ala) complex at 2.0 A. Biochemistry (2000) 1.00
Directed evolution of a subtilisin with calcium-independent stability. Biotechnology (N Y) (1995) 0.99
Crystal structure of a cyclic AMP-independent mutant of catabolite gene activator protein. J Biol Chem (1987) 0.99
Deposition of macromolecular data. Acta Crystallogr D Biol Crystallogr (1996) 0.96
L-Arabinose-binding protein-sugar complex at 2.4 A resolution. Stereochemistry and evidence for a structural change. J Biol Chem (1981) 0.95
Engineering the independent folding of the subtilisin BPN' prodomain: analysis of two-state folding versus protein stability. Biochemistry (1997) 0.95
The 2.8-A resolution structure of the L-arabinose-binding protein from Escherichia coli. Polypeptide chain folding, domain similarity, and probable location of sugar-binding site. J Biol Chem (1977) 0.93
First-sphere and second-sphere electrostatic effects in the active site of a class mu gluthathione transferase. Biochemistry (1996) 0.93
X-ray structure of a ribonuclease A-uridine vanadate complex at 1.3 A resolution. Acta Crystallogr D Biol Crystallogr (1997) 0.93
Crystal structure of two covalent nucleoside derivatives of ribonuclease A. Biochemistry (1990) 0.92