Published in J Am Chem Soc on September 29, 2010
Biomolecular dynamics: order-disorder transitions and energy landscapes. Rep Prog Phys (2012) 1.12
Mechanisms of SecM-mediated stalling in the ribosome. Biophys J (2012) 1.11
Connecting the kinetics and energy landscape of tRNA translocation on the ribosome. PLoS Comput Biol (2013) 1.07
Excited states of ribosome translocation revealed through integrative molecular modeling. Proc Natl Acad Sci U S A (2011) 1.04
Computational studies of molecular machines: the ribosome. Curr Opin Struct Biol (2012) 0.96
Sizing up long non-coding RNAs: do lncRNAs have secondary and tertiary structure? Bioarchitecture (2012) 0.95
Simulating movement of tRNA through the ribosome during hybrid-state formation. J Chem Phys (2013) 0.87
Human immunoglobulin E flexes between acutely bent and extended conformations. Nat Struct Mol Biol (2014) 0.84
Capturing transition paths and transition states for conformational rearrangements in the ribosome. Biophys J (2014) 0.81
Biochemical aspects of bacterial strategies for handling the incomplete translation processes. Front Microbiol (2014) 0.80
A computational investigation on the connection between dynamics properties of ribosomal proteins and ribosome assembly. PLoS Comput Biol (2012) 0.80
Interplay of the bacterial ribosomal A-site, S12 protein mutations and paromomycin binding: a molecular dynamics study. PLoS One (2014) 0.78
Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT. Methods Enzymol (2015) 0.78
MINT: software to identify motifs and short-range interactions in trajectories of nucleic acids. Nucleic Acids Res (2015) 0.76
Tracking fluctuation hotspots on the yeast ribosome through the elongation cycle. Nucleic Acids Res (2017) 0.75
How EF-Tu can contribute to efficient proofreading of aa-tRNA by the ribosome. Nat Commun (2016) 0.75
Exploring the balance between folding and functional dynamics in proteins and RNA. Int J Mol Sci (2015) 0.75
The ribosome's energy landscape: Recent insights from computation. Biophys Rev (2015) 0.75
Kinetic proofreading: a new mechanism for reducing errors in biosynthetic processes requiring high specificity. Proc Natl Acad Sci U S A (1974) 9.17
Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy. Nature (2002) 6.92
The protein folding 'speed limit'. Curr Opin Struct Biol (2004) 6.19
Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy. Proc Natl Acad Sci U S A (2003) 3.64
Diffusion in a rough potential. Proc Natl Acad Sci U S A (1988) 3.62
Kinetic determinants of high-fidelity tRNA discrimination on the ribosome. Mol Cell (2004) 3.40
Fidelity of aminoacyl-tRNA selection on the ribosome: kinetic and structural mechanisms. Annu Rev Biochem (2001) 2.97
Simulating movement of tRNA into the ribosome during decoding. Proc Natl Acad Sci U S A (2005) 2.91
RNA and protein folding: common themes and variations. Biochemistry (2005) 2.47
Molecular dynamics simulations. Curr Opin Struct Biol (2002) 1.93
Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways. RNA (2010) 1.91
Translation at the single-molecule level. Annu Rev Biochem (2008) 1.87
The kinetics of ribosomal peptidyl transfer revisited. Mol Cell (2008) 1.70
Simulation of the pressure and temperature folding/unfolding equilibrium of a small RNA hairpin. J Am Chem Soc (2007) 1.61
Diffusion and electrophoretic mobility of single-stranded RNA from molecular dynamics simulations. Biophys J (2004) 1.49
Conformational sampling of aminoacyl-tRNA during selection on the bacterial ribosome. J Mol Biol (2010) 1.47
Configuration-dependent diffusion can shift the kinetic transition state and barrier height of protein folding. Proc Natl Acad Sci U S A (2007) 1.42
Molecular dynamics simulations of RNA: an in silico single molecule approach. Biopolymers (2007) 1.41
Side-chain recognition and gating in the ribosome exit tunnel. Proc Natl Acad Sci U S A (2008) 1.23
Stochastic gating and drug-ribosome interactions. J Mol Biol (2008) 1.16
Recognition of the regulatory nascent chain TnaC by the ribosome. Structure (2010) 1.01
Molecular dynamics simulations suggest that RNA three-way junctions can act as flexible RNA structural elements in the ribosome. Nucleic Acids Res (2010) 0.97
Molecular dynamics study of the ribosomal A-site. J Phys Chem B (2008) 0.96
Characterization of the cofactor-induced folding mechanism of a zinc-binding peptide using computationally designed mutants. J Mol Biol (2009) 0.85
Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Proc Natl Acad Sci U S A (2011) 4.08
Protein folding mediated by solvation: water expulsion and formation of the hydrophobic core occur after the structural collapse. Proc Natl Acad Sci U S A (2002) 3.78
Water mediation in protein folding and molecular recognition. Annu Rev Biophys Biomol Struct (2006) 3.32
Protein topology determines binding mechanism. Proc Natl Acad Sci U S A (2003) 3.16
Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites. Nature (2010) 2.85
Folding a protein in a computer: an atomic description of the folding/unfolding of protein A. Proc Natl Acad Sci U S A (2003) 2.80
Conformational transitions of adenylate kinase: switching by cracking. J Mol Biol (2006) 2.49
An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields. Proteins (2009) 2.44
Free state conformational sampling of the SAM-I riboswitch aptamer domain. Structure (2010) 2.02
A survey of flexible protein binding mechanisms and their transition states using native topology based energy landscapes. J Mol Biol (2005) 1.99
Quantifying the roughness on the free energy landscape: entropic bottlenecks and protein folding rates. J Am Chem Soc (2004) 1.99
SMOG@ctbp: simplified deployment of structure-based models in GROMACS. Nucleic Acids Res (2010) 1.95
Domain swapping is a consequence of minimal frustration. Proc Natl Acad Sci U S A (2004) 1.93
Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways. RNA (2010) 1.91
Absolute rate theories of epigenetic stability. Proc Natl Acad Sci U S A (2005) 1.89
Fly-casting in protein-DNA binding: frustration between protein folding and electrostatics facilitates target recognition. J Am Chem Soc (2007) 1.85
Topological frustration and the folding of interleukin-1 beta. J Mol Biol (2005) 1.77
Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: all-atom representation study of protein L. J Mol Biol (2003) 1.74
Deciding fate in adverse times: sporulation and competence in Bacillus subtilis. Proc Natl Acad Sci U S A (2009) 1.65
Genomics-aided structure prediction. Proc Natl Acad Sci U S A (2012) 1.63
MicroRNA-based regulation of epithelial-hybrid-mesenchymal fate determination. Proc Natl Acad Sci U S A (2013) 1.60
Structural architecture of the human long non-coding RNA, steroid receptor RNA activator. Nucleic Acids Res (2012) 1.58
Simple energy landscape model for the kinetics of functional transitions in proteins. J Phys Chem B (2005) 1.57
High-resolution protein complexes from integrating genomic information with molecular simulation. Proc Natl Acad Sci U S A (2009) 1.57
Mechanical control of the directional stepping dynamics of the kinesin motor. Proc Natl Acad Sci U S A (2007) 1.54
Molecular level stochastic model for competence cycles in Bacillus subtilis. Proc Natl Acad Sci U S A (2007) 1.54
Nonlocal helix formation is key to understanding S-adenosylmethionine-1 riboswitch function. Biophys J (2009) 1.51
Internal strain regulates the nucleotide binding site of the kinesin leading head. Proc Natl Acad Sci U S A (2007) 1.50
Understanding protein folding with energy landscape theory. Part I: Basic concepts. Q Rev Biophys (2002) 1.49
A Stevedore's protein knot. PLoS Comput Biol (2010) 1.43
Symmetry and frustration in protein energy landscapes: a near degeneracy resolves the Rop dimer-folding mystery. Proc Natl Acad Sci U S A (2005) 1.42
Understanding stochastic simulations of the smallest genetic networks. J Chem Phys (2007) 1.37
Understanding protein folding with energy landscape theory. Part II: Quantitative aspects. Q Rev Biophys (2002) 1.35
Interprotein electron transfer from cytochrome c2 to photosynthetic reaction center: tunneling across an aqueous interface. Proc Natl Acad Sci U S A (2005) 1.35
Extracting function from a beta-trefoil folding motif. Proc Natl Acad Sci U S A (2008) 1.34
Facile transfer of [2Fe-2S] clusters from the diabetes drug target mitoNEET to an apo-acceptor protein. Proc Natl Acad Sci U S A (2011) 1.31
Mechanisms of protein assembly: lessons from minimalist models. Acc Chem Res (2006) 1.30
Robustness and generalization of structure-based models for protein folding and function. Proteins (2009) 1.29
Conformational transitions in adenylate kinase. Allosteric communication reduces misligation. J Biol Chem (2007) 1.27
Ligand-induced global transitions in the catalytic domain of protein kinase A. Proc Natl Acad Sci U S A (2009) 1.25
Multiple routes lead to the native state in the energy landscape of the beta-trefoil family. Proc Natl Acad Sci U S A (2006) 1.25
Backtracking on the folding landscape of the beta-trefoil protein interleukin-1beta? Proc Natl Acad Sci U S A (2008) 1.22
Mutations as trapdoors to two competing native conformations of the Rop-dimer. Proc Natl Acad Sci U S A (2007) 1.20
The dual-basin landscape in GFP folding. Proc Natl Acad Sci U S A (2008) 1.16
Slipknotting upon native-like loop formation in a trefoil knot protein. Proc Natl Acad Sci U S A (2010) 1.15
Transition state and encounter complex for fast association of cytochrome c2 with bacterial reaction center. Proc Natl Acad Sci U S A (2004) 1.15
NAF-1 and mitoNEET are central to human breast cancer proliferation by maintaining mitochondrial homeostasis and promoting tumor growth. Proc Natl Acad Sci U S A (2013) 1.14
Coevolutionary signals across protein lineages help capture multiple protein conformations. Proc Natl Acad Sci U S A (2013) 1.14
A driving and coupling "Pac-Man" mechanism for chromosome poleward translocation in anaphase A. Proc Natl Acad Sci U S A (2006) 1.13
Biomolecular dynamics: order-disorder transitions and energy landscapes. Rep Prog Phys (2012) 1.12
The shadow map: a general contact definition for capturing the dynamics of biomolecular folding and function. J Phys Chem B (2012) 1.10
Folding time predictions from all-atom replica exchange simulations. J Mol Biol (2007) 1.09
Connecting the kinetics and energy landscape of tRNA translocation on the ribosome. PLoS Comput Biol (2013) 1.07
Direct single-molecule observation of a protein living in two opposed native structures. Proc Natl Acad Sci U S A (2009) 1.07
Effective stochastic dynamics on a protein folding energy landscape. J Chem Phys (2006) 1.05
Continuum electrostatic model for the binding of cytochrome c2 to the photosynthetic reaction center from Rhodobacter sphaeroides. Biochemistry (2003) 1.04
The native energy landscape for interleukin-1beta. Modulation of the population ensemble through native-state topology. J Mol Biol (2005) 1.04
Excited states of ribosome translocation revealed through integrative molecular modeling. Proc Natl Acad Sci U S A (2011) 1.04
Structure of infectious prions: stabilization by domain swapping. FASEB J (2005) 1.03
Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information. Proc Natl Acad Sci U S A (2014) 1.03
Overcoming residual frustration in domain-swapping: the roles of disulfide bonds in dimerization and aggregation. Phys Biol (2005) 1.02
Proteins at work: a combined small angle X-RAY scattering and theoretical determination of the multiple structures involved on the protein kinase functional landscape. J Biol Chem (2010) 1.02
Probing the kinetics of single molecule protein folding. Biophys J (2004) 1.01
Water and proteins: a love-hate relationship. Proc Natl Acad Sci U S A (2004) 1.01
Equilibrium and kinetic folding pathways of a TIM barrel with a funneled energy landscape. Biophys J (2005) 1.00
Jamming proteins with slipknots and their free energy landscape. Phys Rev Lett (2009) 1.00
Magnesium fluctuations modulate RNA dynamics in the SAM-I riboswitch. J Am Chem Soc (2012) 0.98
Integrated strategy reveals the protein interface between cancer targets Bcl-2 and NAF-1. Proc Natl Acad Sci U S A (2014) 0.98
Rise of the RNA machines: exploring the structure of long non-coding RNAs. J Mol Biol (2013) 0.98
Tertiary contacts control switching of the SAM-I riboswitch. Nucleic Acids Res (2010) 0.97
Functional role of the sarcin-ricin loop of the 23S rRNA in the elongation cycle of protein synthesis. J Mol Biol (2012) 0.96
Protein oligomerization through domain swapping: role of inter-molecular interactions and protein concentration. J Mol Biol (2005) 0.96
Extinction and resurrection in gene networks. Proc Natl Acad Sci U S A (2008) 0.96
Sizing up long non-coding RNAs: do lncRNAs have secondary and tertiary structure? Bioarchitecture (2012) 0.95
Mirror images as naturally competing conformations in protein folding. J Phys Chem B (2012) 0.94
The expression platform and the aptamer: cooperativity between Mg2+ and ligand in the SAM-I riboswitch. Nucleic Acids Res (2012) 0.94
The folding energy landscape of the dimerization domain of Escherichia coli Trp repressor: a joint experimental and theoretical investigation. J Mol Biol (2006) 0.93
Free energy landscape for the binding process of Huperzine A to acetylcholinesterase. Proc Natl Acad Sci U S A (2013) 0.93
β-Bulge triggers route-switching on the functional landscape of interleukin-1β. Proc Natl Acad Sci U S A (2012) 0.93
Geometrical features of the protein folding mechanism are a robust property of the energy landscape: a detailed investigation of several reduced models. J Phys Chem B (2008) 0.93
Key intermolecular interactions in the E. coli 70S ribosome revealed by coarse-grained analysis. J Am Chem Soc (2011) 0.91
From protein folding to protein function and biomolecular binding by energy landscape theory. Curr Opin Pharmacol (2010) 0.91
Interdomain communication revealed in the diabetes drug target mitoNEET. Proc Natl Acad Sci U S A (2011) 0.91
Equilibrium unfolding of the poly(glutamic acid)20 helix. Biopolymers (2007) 0.89
Folding a protein in the computer: reality or hope? Structure (2005) 0.89
Gatekeepers in the ribosomal protein s6: thermodynamics, kinetics, and folding pathways revealed by a minimalist protein model. J Mol Biol (2004) 0.89
Kinesin's backsteps under mechanical load. Phys Chem Chem Phys (2009) 0.89
Allostery in the ferredoxin protein motif does not involve a conformational switch. Proc Natl Acad Sci U S A (2011) 0.88
From structure to function: the convergence of structure based models and co-evolutionary information. Phys Chem Chem Phys (2014) 0.88
Hysteresis as a Marker for Complex, Overlapping Landscapes in Proteins. J Phys Chem Lett (2012) 0.88
Simulating movement of tRNA through the ribosome during hybrid-state formation. J Chem Phys (2013) 0.87
Topography of funneled landscapes determines the thermodynamics and kinetics of protein folding. Proc Natl Acad Sci U S A (2012) 0.86
Knotting pathways in proteins. Biochem Soc Trans (2013) 0.86
Consensus among flexible fitting approaches improves the interpretation of cryo-EM data. J Struct Biol (2011) 0.86