Published in PLoS One on August 26, 2013
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Naïve Bayes for microRNA target predictions--machine learning for microRNA targets. Bioinformatics (2007) 1.60
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Constructing irregular surfaces to enclose macromolecular complexes for mesoscale modeling using the discrete surface charge optimization (DISCO) algorithm. J Comput Chem (2003) 1.20
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Tertiary motifs revealed in analyses of higher-order RNA junctions. J Mol Biol (2009) 1.10
Modeling studies of chromatin fiber structure as a function of DNA linker length. J Mol Biol (2010) 1.09
Correct and incorrect nucleotide incorporation pathways in DNA polymerase beta. Biochem Biophys Res Commun (2006) 1.09
A Hoogsteen base pair embedded in undistorted B-DNA. Nucleic Acids Res (2002) 1.08
Predicting candidate genomic sequences that correspond to synthetic functional RNA motifs. Nucleic Acids Res (2005) 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
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Substrate-induced DNA strand misalignment during catalytic cycling by DNA polymerase lambda. EMBO Rep (2008) 1.03
Learning from positive examples when the negative class is undetermined--microRNA gene identification. Algorithms Mol Biol (2008) 1.02
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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
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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
Modeling and detection of respiratory-related outbreak signatures. BMC Med Inform Decis Mak (2007) 0.98
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
Computational generation and screening of RNA motifs in large nucleotide sequence pools. Nucleic Acids Res (2010) 0.95
Sequential side-chain residue motions transform the binary into the ternary state of DNA polymerase lambda. Biophys J (2006) 0.95
A new program for optimizing periodic boundary models of solvated biomolecules (PBCAID). J Comput Chem (2001) 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
Recursive cluster elimination (RCE) for classification and feature selection from gene expression data. BMC Bioinformatics (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
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
RagPools: RNA-As-Graph-Pools--a web server for assisting the design of structured RNA pools for in vitro selection. Bioinformatics (2007) 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
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
Structural and electrostatic properties of ubiquitination and related pathways. Front Biosci (2007) 0.84
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
Candidate RNA structures for domain 3 of the foot-and-mouth-disease virus internal ribosome entry site. Nucleic Acids Res (2012) 0.83
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
Increasing cleavage specificity and activity of restriction endonuclease KpnI. Nucleic Acids Res (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
Insights into chromatin fibre structure by in vitro and in silico single-molecule stretching experiments. Biochem Soc Trans (2013) 0.81
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
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
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
Alteration of the CNS pathway to the hippocampus in a mouse model of Niemann-Pick, type C disease. J Chem Neuroanat (2011) 0.80
Sequence-dependent solution structure and motions of 13 TATA/TBP (TATA-box binding protein) complexes. Biopolymers (2003) 0.80
The effect of a G:T mispair on the dynamics of DNA. PLoS One (2013) 0.79
Mismatched base-pair simulations for ASFV Pol X/DNA complexes help interpret frequent G*G misincorporation. J Mol Biol (2008) 0.79
DNA pol λ's extraordinary ability to stabilize misaligned DNA. J Am Chem Soc (2010) 0.78
Effect of DNA superhelicity and bound proteins on mechanistic aspects of the Hin-mediated and Fis-enhanced inversion. Biophys J (2003) 0.78
Forced unraveling of chromatin fibers with nonuniform linker DNA lengths. J Phys Condens Matter (2015) 0.76
How DNA polymerase X preferentially accommodates incoming dATP opposite 8-oxoguanine on the template. Biophys J (2013) 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
Evaluation of data discretization methods to derive platform independent isoform expression signatures for multi-class tumor subtyping. BMC Genomics (2015) 0.75
Importance of Residual Water Permeability on the Excretion of Water during Water Diuresis in Rats. Electrolyte Blood Press (2010) 0.75