Published in J Am Chem Soc on September 15, 2010
Enhanced and effective conformational sampling of protein molecular systems for their free energy landscapes. Biophys Rev (2012) 0.99
The underlying molecular and network level mechanisms in the evolution of robustness in gene regulatory networks. PLoS Comput Biol (2013) 0.83
Variation of free-energy landscape of the p53 C-terminal domain induced by acetylation: Enhanced conformational sampling. J Comput Chem (2016) 0.75
Exploration of the binding mode of α/β-type small acid soluble proteins (SASPs) with DNA. J Mol Model (2011) 0.75
Two different Swi5-containing protein complexes are involved in mating-type switching and recombination repair in fission yeast. Proc Natl Acad Sci U S A (2003) 1.78
Protein structural change upon ligand binding: linear response theory. Phys Rev Lett (2005) 1.53
Intrinsic nucleic acid-binding activity of Chp1 chromodomain is required for heterochromatic gene silencing. Mol Cell (2012) 1.42
Comparison between TRF2 and TRF1 of their telomeric DNA-bound structures and DNA-binding activities. Protein Sci (2005) 1.36
Structure of the small ubiquitin-like modifier (SUMO)-interacting motif of MBD1-containing chromatin-associated factor 1 bound to SUMO-3. J Biol Chem (2008) 1.23
Fission yeast Swi5/Sfr1 and Rhp55/Rhp57 differentially regulate Rhp51-dependent recombination outcomes. EMBO J (2007) 1.21
Structural insight into the TFIIE-TFIIH interaction: TFIIE and p53 share the binding region on TFIIH. EMBO J (2008) 1.17
A mass spectrometric approach to the study of DNA-binding proteins: interaction of human TRF2 with telomeric DNA. Biochemistry (2008) 1.17
Comparative simulations of aquaporin family: AQP1, AQPZ, AQP0 and GlpF. FEBS Lett (2005) 1.16
A free-energy landscape for coupled folding and binding of an intrinsically disordered protein in explicit solvent from detailed all-atom computations. J Am Chem Soc (2011) 1.15
Protonation of the acidic residues in the transmembrane cation-binding sites of the ca(2+) pump. J Am Chem Soc (2005) 1.11
Phylogeny of protein-folding trajectories reveals a unique pathway to native structure. Proc Natl Acad Sci U S A (2004) 1.10
Solution structure of the fibronectin type III domain from Bacillus circulans WL-12 chitinase A1. J Biol Chem (2001) 1.06
Water transport in aquaporins: osmotic permeability matrix analysis of molecular dynamics simulations. Biophys J (2007) 1.04
The neural repressor NRSF/REST binds the PAH1 domain of the Sin3 corepressor by using its distinct short hydrophobic helix. J Mol Biol (2005) 1.02
Structural polymorphism of chromodomains in Chd1. J Mol Biol (2006) 1.02
Molecular mechanism of ATP hydrolysis in F1-ATPase revealed by molecular simulations and single-molecule observations. J Am Chem Soc (2012) 1.02
A novel zinc finger structure in the large subunit of human general transcription factor TFIIE. J Biol Chem (2004) 0.97
Role of the DELSEED loop in torque transmission of F1-ATPase. Biophys J (2012) 0.97
Structure and functional characterization of Vibrio parahaemolyticus thermostable direct hemolysin. J Biol Chem (2010) 0.96
Generalized simulated tempering realized on expanded ensembles of non-Boltzmann weights. J Chem Phys (2004) 0.95
Minimum free energy path of ligand-induced transition in adenylate kinase. PLoS Comput Biol (2012) 0.95
Nonlinear temperature dependence of the crystal structure of lysozyme: correlation between coordinate shifts and thermal factors. Acta Crystallogr D Biol Crystallogr (2002) 0.95
PSCDB: a database for protein structural change upon ligand binding. Nucleic Acids Res (2011) 0.94
Classification and annotation of the relationship between protein structural change and ligand binding. J Mol Biol (2011) 0.94
Protein structural change upon ligand binding correlates with enzymatic reaction mechanism. J Mol Biol (2008) 0.93
Mechanistic insights into the activation of Rad51-mediated strand exchange from the structure of a recombination activator, the Swi5-Sfr1 complex. Structure (2012) 0.93
Fission yeast Swi5-Sfr1 protein complex, an activator of Rad51 recombinase, forms an extremely elongated dogleg-shaped structure. J Biol Chem (2011) 0.92
Simulation of charge effects on density maps obtained by high-resolution electron crystallography. J Electron Microsc (Tokyo) (2007) 0.92
Relationship between Ca2+-affinity and shielding of bulk water in the Ca2+-pump from molecular dynamics simulations. Proc Natl Acad Sci U S A (2010) 0.91
Intrinsic dynamics of restriction endonuclease EcoO109I studied by molecular dynamics simulations and X-ray scattering data analysis. Biophys J (2009) 0.91
A host small GTP-binding protein ARL8 plays crucial roles in tobamovirus RNA replication. PLoS Pathog (2011) 0.90
Disorder-to-order transition of an intrinsically disordered region of sortase revealed by multiscale enhanced sampling. J Am Chem Soc (2012) 0.90
Structural fluctuation and concerted motions in F(1)-ATPase: A molecular dynamics study. J Comput Chem (2010) 0.89
Water-mediated interactions between DNA and PhoB DNA-binding/transactivation domain: NMR-restrained molecular dynamics in explicit water environment. Proteins (2008) 0.89
Ligand mapping on protein surfaces by the 3D-RISM theory: toward computational fragment-based drug design. J Am Chem Soc (2009) 0.89
Function of homo- and hetero-oligomers of human nucleoplasmin/nucleophosmin family proteins NPM1, NPM2 and NPM3 during sperm chromatin remodeling. Nucleic Acids Res (2012) 0.88
A novel magnetic resonance-based method to measure gene expression in living cells. Nucleic Acids Res (2006) 0.86
Comparative molecular dynamics simulation study of crystal environment effect on protein structure. J Phys Chem B (2012) 0.86
Transcription regulation by feast/famine regulatory proteins, FFRPs, in archaea and eubacteria. Biol Pharm Bull (2008) 0.86
Rotation mechanism of F1-ATPase: crucial importance of the water entropy effect. J Am Chem Soc (2011) 0.86
Structural and biochemical analyses of the human PAD4 variant encoded by a functional haplotype gene. Acta Crystallogr D Biol Crystallogr (2011) 0.84
Extended string binding mode of the phosphorylated transactivation domain of tumor suppressor p53. J Am Chem Soc (2014) 0.84
Growth of carbon nanotubes via twisted graphene nanoribbons. Nat Commun (2013) 0.84
Top-down analysis of basic proteins by microchip capillary electrophoresis mass spectrometry. Rapid Commun Mass Spectrom (2006) 0.84
Mechanism of the conformational change of the F1-ATPase β subunit revealed by free energy simulations. J Am Chem Soc (2011) 0.84
Novel structural and functional mode of a knot essential for RNA binding activity of the Esa1 presumed chromodomain. J Mol Biol (2008) 0.83
Characterisation of an intrinsically disordered protein complex of Swi5-Sfr1 by ion mobility mass spectrometry and small-angle X-ray scattering. Analyst (2013) 0.83
Free-energy function for discriminating the native fold of a protein from misfolded decoys. Proteins (2011) 0.83
Structural changes in the cytoplasmic domain of phospholamban by phosphorylation at Ser16: a molecular dynamics study. Biochemistry (2006) 0.83
Investigation of molecular size of transcription factor TFIIE in solution. Proteins (2005) 0.82
NMR dynamics distinguish between hard and soft hydrophobic cores in the DNA-binding domain of PhoB and demonstrate different roles of the cores in binding to DNA. J Mol Biol (2007) 0.82
Telomeric repeats act as nucleosome-disfavouring sequences in vivo. Nucleic Acids Res (2013) 0.82
Molecular dynamics simulations of yeast F1-ATPase before and after 16° rotation of the γ subunit. J Phys Chem B (2013) 0.82
Crucial importance of the water-entropy effect in predicting hot spots in protein-protein complexes. Phys Chem Chem Phys (2011) 0.81
Functional rotation induced by alternating protonation states in the multidrug transporter AcrB: all-atom molecular dynamics simulations. Biochemistry (2013) 0.81
I-motif and quadruplex-based device that can control a protein release or bind and release small molecule to influence biological processes. Bioorg Med Chem (2006) 0.81
Evaluation of protein-DNA binding affinity by electrospray ionization mass spectrometry. J Am Soc Mass Spectrom (2005) 0.81
Ring and zipper formation is the key to understanding the structural variety in all-beta proteins. FEBS Lett (2003) 0.81
Effects of ionic strength on SAXS data for proteins revealed by molecular dynamics simulations. J Chem Phys (2011) 0.81
Comparative simulations of the ground state and the M-intermediate state of the sensory rhodopsin II-transducer complex with a HAMP domain model. Biochemistry (2012) 0.80
Scalable free energy calculation of proteins via multiscale essential sampling. J Chem Phys (2010) 0.80
Alteration of oligomeric state and domain architecture is essential for functional transformation between transferase and hydrolase with the same scaffold. Protein Sci (2009) 0.80
Linear response theory in dihedral angle space for protein structural change upon ligand binding. J Comput Chem (2009) 0.80
Nickel binding to NikA: an additional binding site reconciles spectroscopy, calorimetry and crystallography. Acta Crystallogr D Biol Crystallogr (2007) 0.80
Functionality mapping on internal surfaces of multidrug transporter AcrB based on molecular theory of solvation: implications for drug efflux pathway. J Phys Chem B (2011) 0.79
Deimination stabilizes histone H2A/H2B dimers as revealed by electrospray ionization mass spectrometry. J Mass Spectrom (2010) 0.79
Interaction of acetone with single wall carbon nanotubes at cryogenic temperatures: a combined temperature programmed desorption and theoretical study. Langmuir (2008) 0.78
Expression, purification and crystallization of Swi5 and the Swi5-Sfr1 complex from fission yeast. Acta Crystallogr Sect F Struct Biol Cryst Commun (2010) 0.78
Conclusive evidence of the reconstituted hexasome proven by native mass spectrometry. Biochemistry (2013) 0.78
Multiscale enhanced path sampling based on the Onsager-Machlup action: application to a model polymer. J Chem Phys (2013) 0.78
Unfolding pathways of goat alpha-lactalbumin as revealed in multiple alignment of molecular dynamics trajectories. J Mol Biol (2007) 0.78
Structural and functional analysis of the intrinsic inhibitor subunit epsilon of F1-ATPase from photosynthetic organisms. Biochem J (2009) 0.78
Gas-phase structure of the histone multimers characterized by ion mobility mass spectrometry and molecular dynamics simulation. Anal Chem (2013) 0.78
Mass spectrometric approach for characterizing the disordered tail regions of the histone H2A/H2B dimer. Anal Chem (2015) 0.78
Atomically detailed description of the unfolding of alpha-lactalbumin by the combined use of experiments and simulations. J Mol Biol (2005) 0.78
Homology-modelled structure of the βB2B3-crystallin heterodimer studied by ion mobility and radical probe MS. FEBS J (2011) 0.78
The crystal structure of the tryptophan synthase beta subunit from the hyperthermophile Pyrococcus furiosus. Investigation of stabilization factors. Eur J Biochem (2004) 0.78
Determination of multicanonical weight based on a stochastic model of sampling dynamics. Phys Rev E Stat Nonlin Soft Matter Phys (2003) 0.78
Probabilistic description of protein alignments for sequences and structures. Proteins (2004) 0.78
Conformational change of Sos-derived proline-rich peptide upon binding Grb2 N-terminal SH3 domain probed by NMR. Sci Rep (2013) 0.77
Characterization of experimentally determined native-structure models of a protein using energetic and entropic components of free-energy function. J Phys Chem B (2012) 0.77
A native disulfide stabilizes non-native helical structures in partially folded states of equine β-lactoglobulin. Biochemistry (2011) 0.77
Structural insights into the asymmetric effects of zinc-ligand cysteine mutations in the novel zinc ribbon domain of human TFIIEalpha for transcription. J Biochem (2005) 0.77
Probabilistic alignment detects remote homology in a pair of protein sequences without homologous sequence information. Proteins (2007) 0.77