Published in J Am Chem Soc on September 28, 2005
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Regulation of DNA repair fidelity by molecular checkpoints: "gates" in DNA polymerase beta's substrate selection. Biochemistry (2006) 1.40
How conformational dynamics of DNA polymerase select correct substrates: experiments and simulations. Structure (2012) 1.36
Exploring the role of large conformational changes in the fidelity of DNA polymerase beta. Proteins (2008) 1.29
Correct and incorrect nucleotide incorporation pathways in DNA polymerase beta. Biochem Biophys Res Commun (2006) 1.09
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Prechemistry versus preorganization in DNA replication fidelity. Proteins (2011) 1.02
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Sequential side-chain residue motions transform the binary into the ternary state of DNA polymerase lambda. Biophys J (2006) 0.95
Distinct energetics and closing pathways for DNA polymerase beta with 8-oxoG template and different incoming nucleotides. BMC Struct Biol (2007) 0.94
Differing conformational pathways before and after chemistry for insertion of dATP versus dCTP opposite 8-oxoG in DNA polymerase beta. Biophys J (2007) 0.93
Subtle but variable conformational rearrangements in the replication cycle of Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) may accommodate lesion bypass. Protein Sci (2005) 0.93
Perspective: pre-chemistry conformational changes in DNA polymerase mechanisms. Theor Chem Acc (2012) 0.87
In silico studies of the African swine fever virus DNA polymerase X support an induced-fit mechanism. Biophys J (2005) 0.86
Unfavorable electrostatic and steric interactions in DNA polymerase β E295K mutant interfere with the enzyme's pathway. J Am Chem Soc (2012) 0.84
Computational delineation of the catalytic step of a high-fidelity DNA polymerase. Protein Sci (2010) 0.83
Computational simulation strategies for analysis of multisubunit RNA polymerases. Chem Rev (2013) 0.82
"Gate-keeper" residues and active-site rearrangements in DNA polymerase μ help discriminate non-cognate nucleotides. PLoS Comput Biol (2013) 0.81
Fluorophore-quencher pair for monitoring protein motion. Biochem Biophys Res Commun (2009) 0.80
Relationship between conformational changes in pol lambda's active site upon binding incorrect nucleotides and mismatch incorporation rates. J Phys Chem B (2009) 0.80
Catalytic effects of mutations of distant protein residues in human DNA polymerase β: theory and experiment. Biochemistry (2012) 0.80
Mismatched base-pair simulations for ASFV Pol X/DNA complexes help interpret frequent G*G misincorporation. J Mol Biol (2008) 0.79
Computational delineation of tyrosyl-substrate recognition and catalytic landscapes by the epidermal growth factor receptor tyrosine kinase domain. Mol Biosyst (2014) 0.75
Insertion of oxidized nucleotide triggers rapid DNA polymerase opening. Nucleic Acids Res (2016) 0.75
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Kinetic mechanism of DNA polymerase I (Klenow). Biochemistry (1987) 3.93
An induced-fit kinetic mechanism for DNA replication fidelity: direct measurement by single-turnover kinetics. Biochemistry (1991) 3.86
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Computer simulation of the chemical catalysis of DNA polymerases: discriminating between alternative nucleotide insertion mechanisms for T7 DNA polymerase. J Am Chem Soc (2003) 1.58
Critical role of magnesium ions in DNA polymerase beta's closing and active site assembly. J Am Chem Soc (2004) 1.55
Polymerase beta simulations suggest that Arg258 rotation is a slow step rather than large subdomain motions per se. J Mol Biol (2002) 1.43
Dynamic characterization of a DNA repair enzyme: NMR studies of [methyl-13C]methionine-labeled DNA polymerase beta. Biochemistry (2004) 1.42
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Use of viscogens, dNTPalphaS, and rhodium(III) as probes in stopped-flow experiments to obtain new evidence for the mechanism of catalysis by DNA polymerase beta. Biochemistry (2005) 1.32
Structural insights into DNA polymerase beta fidelity: hold tight if you want it right. Chem Biol (1998) 1.28
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DNA polymerase beta: analysis of the contributions of tyrosine-271 and asparagine-279 to substrate specificity and fidelity of DNA replication by pre-steady-state kinetics. Biochem J (1997) 1.16
Inhibition of reverse transcription in vivo by elevated manganese ion concentration. Mol Cell (2002) 1.16
In silico evidence for DNA polymerase-beta's substrate-induced conformational change. Biophys J (2004) 1.14
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Highly organized but pliant active site of DNA polymerase beta: compensatory mechanisms in mutant enzymes revealed by dynamics simulations and energy analyses. Biophys J (2004) 1.07
Characterization of the active site of DNA polymerase beta by molecular dynamics and quantum chemical calculation. Proteins (2003) 1.07
Conformational transition pathway of polymerase beta/DNA upon binding correct incoming substrate. J Phys Chem B (2005) 1.01
A new program for optimizing periodic boundary models of solvated biomolecules (PBCAID). J Comput Chem (2001) 0.95
Biomolecular free energy profiles by a shooting/umbrella sampling protocol, "BOLAS". J Chem Phys (2004) 0.92
Orchestration of cooperative events in DNA synthesis and repair mechanism unraveled by transition path sampling of DNA polymerase beta's closing. Proc Natl Acad Sci U S A (2004) 1.76
Exploring the repertoire of RNA secondary motifs using graph theory; implications for RNA design. Nucleic Acids Res (2003) 1.63
RAG: RNA-As-Graphs database--concepts, analysis, and features. Bioinformatics (2004) 1.63
Role of histone tails in chromatin folding revealed by a mesoscopic oligonucleosome model. Proc Natl Acad Sci U S A (2006) 1.59
Critical role of magnesium ions in DNA polymerase beta's closing and active site assembly. J Am Chem Soc (2004) 1.55
Electrostatic mechanism of nucleosomal array folding revealed by computer simulation. Proc Natl Acad Sci U S A (2005) 1.54
Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions. Proc Natl Acad Sci U S A (2009) 1.53
Polymerase beta simulations suggest that Arg258 rotation is a slow step rather than large subdomain motions per se. J Mol Biol (2002) 1.43
Computational approaches to 3D modeling of RNA. J Phys Condens Matter (2010) 1.42
Regulation of DNA repair fidelity by molecular checkpoints: "gates" in DNA polymerase beta's substrate selection. Biochemistry (2006) 1.40
A tale of tails: how histone tails mediate chromatin compaction in different salt and linker histone environments. J Phys Chem A (2009) 1.39
Analysis of four-way junctions in RNA structures. J Mol Biol (2009) 1.37
Flexible histone tails in a new mesoscopic oligonucleosome model. Biophys J (2006) 1.35
In vitro RNA random pools are not structurally diverse: a computational analysis. RNA (2005) 1.32
Computational approaches to RNA structure prediction, analysis, and design. Curr Opin Struct Biol (2011) 1.28
RAG: RNA-As-Graphs web resource. BMC Bioinformatics (2004) 1.28
Candidates for novel RNA topologies. J Mol Biol (2004) 1.23
Annotation of tertiary interactions in RNA structures reveals variations and correlations. RNA (2008) 1.21
Constructing irregular surfaces to enclose macromolecular complexes for mesoscale modeling using the discrete surface charge optimization (DISCO) algorithm. J Comput Chem (2003) 1.20
Predicting helical topologies in RNA junctions as tree graphs. PLoS One (2013) 1.20
Mismatch-induced conformational distortions in polymerase beta support an induced-fit mechanism for fidelity. Biochemistry (2005) 1.16
In silico evidence for DNA polymerase-beta's substrate-induced conformational change. Biophys J (2004) 1.14
Local deformations revealed by dynamics simulations of DNA polymerase Beta with DNA mismatches at the primer terminus. J Mol Biol (2002) 1.14
Tertiary motifs revealed in analyses of higher-order RNA junctions. J Mol Biol (2009) 1.10
Correct and incorrect nucleotide incorporation pathways in DNA polymerase beta. Biochem Biophys Res Commun (2006) 1.09
Modeling studies of chromatin fiber structure as a function of DNA linker length. J Mol Biol (2010) 1.09
Predicting candidate genomic sequences that correspond to synthetic functional RNA motifs. Nucleic Acids Res (2005) 1.08
A Hoogsteen base pair embedded in undistorted B-DNA. Nucleic Acids Res (2002) 1.08
Highly organized but pliant active site of DNA polymerase beta: compensatory mechanisms in mutant enzymes revealed by dynamics simulations and energy analyses. Biophys J (2004) 1.07
Inherent speedup limitations in multiple time step/particle mesh Ewald algorithms. J Comput Chem (2003) 1.05
RAG: an update to the RNA-As-Graphs resource. BMC Bioinformatics (2011) 1.05
Substrate-induced DNA strand misalignment during catalytic cycling by DNA polymerase lambda. EMBO Rep (2008) 1.03
DNA polymerase beta catalysis: are different mechanisms possible? J Am Chem Soc (2007) 1.02
Analysis of protein sequence/structure similarity relationships. Biophys J (2002) 1.01
Conformational transition pathway of polymerase beta/DNA upon binding correct incoming substrate. J Phys Chem B (2005) 1.01
A computational proposal for designing structured RNA pools for in vitro selection of RNAs. RNA (2007) 1.00
Predicting coaxial helical stacking in RNA junctions. Nucleic Acids Res (2011) 0.99
Crucial role of dynamic linker histone binding and divalent ions for DNA accessibility and gene regulation revealed by mesoscale modeling of oligonucleosomes. Nucleic Acids Res (2012) 0.99
Quantum mechanics/molecular mechanics investigation of the chemical reaction in Dpo4 reveals water-dependent pathways and requirements for active site reorganization. J Am Chem Soc (2008) 0.95
A new program for optimizing periodic boundary models of solvated biomolecules (PBCAID). J Comput Chem (2001) 0.95
Sequential side-chain residue motions transform the binary into the ternary state of DNA polymerase lambda. Biophys J (2006) 0.95
Computational generation and screening of RNA motifs in large nucleotide sequence pools. Nucleic Acids Res (2010) 0.95
Distinct energetics and closing pathways for DNA polymerase beta with 8-oxoG template and different incoming nucleotides. BMC Struct Biol (2007) 0.94
Modular RNA architecture revealed by computational analysis of existing pseudoknots and ribosomal RNAs. Nucleic Acids Res (2005) 0.94
Differing conformational pathways before and after chemistry for insertion of dATP versus dCTP opposite 8-oxoG in DNA polymerase beta. Biophys J (2007) 0.93
Analysis of riboswitch structure and function by an energy landscape framework. J Mol Biol (2009) 0.93
Subtle but variable conformational rearrangements in the replication cycle of Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) may accommodate lesion bypass. Protein Sci (2005) 0.93
Biomolecular free energy profiles by a shooting/umbrella sampling protocol, "BOLAS". J Chem Phys (2004) 0.92
Dynamic energy landscapes of riboswitches help interpret conformational rearrangements and function. PLoS Comput Biol (2012) 0.92
Graph-based sampling for approximating global helical topologies of RNA. Proc Natl Acad Sci U S A (2014) 0.91
Modeling DNA polymerase μ motions: subtle transitions before chemistry. Biophys J (2010) 0.89
A quantum mechanical investigation of possible mechanisms for the nucleotidyl transfer reaction catalyzed by DNA polymerase beta. J Phys Chem B (2007) 0.89
RagPools: RNA-As-Graph-Pools--a web server for assisting the design of structured RNA pools for in vitro selection. Bioinformatics (2007) 0.89
The effect of linker histone's nucleosome binding affinity on chromatin unfolding mechanisms. Biophys J (2011) 0.89
Unbiased rotational moves for rigid-body dynamics. Biophys J (2003) 0.88
In silico studies of the African swine fever virus DNA polymerase X support an induced-fit mechanism. Biophys J (2005) 0.86
A computational screen for C/D box snoRNAs in the human genomic region associated with Prader-Willi and Angelman syndromes. J Biomed Sci (2008) 0.86
Structural motifs in ribosomal RNAs: implications for RNA design and genomics. Biopolymers (2004) 0.85
Unfavorable electrostatic and steric interactions in DNA polymerase β E295K mutant interfere with the enzyme's pathway. J Am Chem Soc (2012) 0.84
Efficient global biopolymer sampling with end-transfer configurational bias Monte Carlo. J Chem Phys (2007) 0.84
Stereochemistry and position-dependent effects of carcinogens on TATA/TBP binding. Biophys J (2005) 0.83
Chromatin ionic atmosphere analyzed by a mesoscale electrostatic approach. Biophys J (2010) 0.83
Candidate RNA structures for domain 3 of the foot-and-mouth-disease virus internal ribosome entry site. Nucleic Acids Res (2012) 0.83
Deformations of promoter DNA bound to carcinogens help interpret effects on TATA-element structure and activity. Philos Trans A Math Phys Eng Sci (2004) 0.81
Insights into chromatin fibre structure by in vitro and in silico single-molecule stretching experiments. Biochem Soc Trans (2013) 0.81
"Gate-keeper" residues and active-site rearrangements in DNA polymerase μ help discriminate non-cognate nucleotides. PLoS Comput Biol (2013) 0.81
Simulations of DNA pol lambda R517 mutants indicate 517's crucial role in ternary complex stability and suggest DNA slippage origin. J Am Chem Soc (2008) 0.80
Sequence-dependent solution structure and motions of 13 TATA/TBP (TATA-box binding protein) complexes. Biopolymers (2003) 0.80
Relationship between conformational changes in pol lambda's active site upon binding incorrect nucleotides and mismatch incorporation rates. J Phys Chem B (2009) 0.80
Optimal and variant metal-ion routes in DNA polymerase β's conformational pathways. J Am Chem Soc (2014) 0.80
Mismatched base-pair simulations for ASFV Pol X/DNA complexes help interpret frequent G*G misincorporation. J Mol Biol (2008) 0.79
Effect of DNA superhelicity and bound proteins on mechanistic aspects of the Hin-mediated and Fis-enhanced inversion. Biophys J (2003) 0.78
DNA pol λ's extraordinary ability to stabilize misaligned DNA. J Am Chem Soc (2010) 0.78
How DNA polymerase X preferentially accommodates incoming dATP opposite 8-oxoguanine on the template. Biophys J (2013) 0.76
Forced unraveling of chromatin fibers with nonuniform linker DNA lengths. J Phys Condens Matter (2015) 0.76
Estimating the fraction of non-coding RNAs in mammalian transcriptomes. Bioinform Biol Insights (2008) 0.75
A new toolkit for modeling RNA from a pseudo-torsional space: commentary on "discrete RNA libraries from pseudo-torsional space" by Humphris-Narayanan and Pyle (J. Mol. Biol. March 2012). J Mol Biol (2012) 0.75
Dependence of the Linker Histone and Chromatin Condensation on the Nucleosome Environment. J Phys Chem B (2017) 0.75
Computational strategies to address chromatin structure problems. Phys Biol (2016) 0.75