Published in Acc Chem Res on February 01, 2006
Protein folding studied by single-molecule FRET. Curr Opin Struct Biol (2008) 4.33
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
Binding-induced folding of a natively unstructured transcription factor. PLoS Comput Biol (2008) 2.04
Functional residues serve a dominant role in mediating the cooperativity of the protein ensemble. Proc Natl Acad Sci U S A (2007) 1.22
On the importance of a funneled energy landscape for the assembly and regulation of multidomain Src tyrosine kinases. Proc Natl Acad Sci U S A (2007) 1.21
Capillarity theory for the fly-casting mechanism. Proc Natl Acad Sci U S A (2010) 1.11
Inorganic nanoparticles in cancer therapy. Pharm Res (2010) 1.11
Dynamics of the acetylcholinesterase tetramer. Biophys J (2007) 0.99
Prepaying the entropic cost for allosteric regulation in KIX. Proc Natl Acad Sci U S A (2014) 0.98
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
Heterogeneous Hydration of p53/MDM2 Complex. J Chem Theory Comput (2014) 0.88
The origin of nonmonotonic complex behavior and the effects of nonnative interactions on the diffusive properties of protein folding. Biophys J (2010) 0.85
Binding and folding of the small bacterial chaperone HdeA. J Phys Chem B (2013) 0.85
Arc-repressor dimerization on DNA: folding rate enhancement by colocalization. Biophys J (2009) 0.84
Dynamic conformational change regulates the protein-DNA recognition: an investigation on binding of a Y-family polymerase to its target DNA. PLoS Comput Biol (2014) 0.82
Protein folding in a reverse micelle environment: the role of confinement and dehydration. J Chem Phys (2011) 0.82
Bio-inspired hard-to-soft interface for implant integration to bone. Nanomedicine (2014) 0.80
Promiscuous and specific recognition among ephrins and Eph receptors. Biochim Biophys Acta (2014) 0.79
A model of protein association based on their hydrophobic and electric interactions. PLoS One (2014) 0.78
Changing the charge distribution of beta-helical-based nanostructures can provide the conditions for charge transfer. Biophys J (2007) 0.77
Capturing a Dynamic Chaperone-Substrate Interaction Using NMR-Informed Molecular Modeling. J Am Chem Soc (2016) 0.77
Characterization of the unfolded state of repeat proteins. HFSP J (2008) 0.75
Effects of Visible-Light Irradiation of Protoporphyrin IX on the Self-Assembly of Tubulin Heterodimers. Chemphyschem (2016) 0.75
Multivalent protein assembly using monovalent self-assembling building blocks. Int J Mol Sci (2013) 0.75
Vector description of electric and hydrophobic interactions in protein homodimers. Eur Biophys J (2015) 0.75
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
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
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
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
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
Ligand-induced global transitions in the catalytic domain of protein kinase A. Proc Natl Acad Sci U S A (2009) 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
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
Excited states of ribosome translocation revealed through integrative molecular modeling. Proc Natl Acad Sci U S A (2011) 1.04
The native energy landscape for interleukin-1beta. Modulation of the population ensemble through native-state topology. J Mol Biol (2005) 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
Jamming proteins with slipknots and their free energy landscape. Phys Rev Lett (2009) 1.00
Equilibrium and kinetic folding pathways of a TIM barrel with a funneled energy landscape. Biophys J (2005) 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
Extinction and resurrection in gene networks. Proc Natl Acad Sci U S A (2008) 0.96
Protein oligomerization through domain swapping: role of inter-molecular interactions and protein concentration. J Mol Biol (2005) 0.96
Mirror images as naturally competing conformations in protein folding. J Phys Chem B (2012) 0.94
Connecting energy landscapes with experimental rates for aminoacyl-tRNA accommodation in the ribosome. J Am Chem Soc (2010) 0.93
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
β-Bulge triggers route-switching on the functional landscape of interleukin-1β. Proc Natl Acad Sci U S A (2012) 0.93
Free energy landscape for the binding process of Huperzine A to acetylcholinesterase. Proc Natl Acad Sci U S A (2013) 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
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
Gatekeepers in the ribosomal protein s6: thermodynamics, kinetics, and folding pathways revealed by a minimalist protein model. J Mol Biol (2004) 0.89
Folding a protein in the computer: reality or hope? Structure (2005) 0.89
Equilibrium unfolding of the poly(glutamic acid)20 helix. Biopolymers (2007) 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
Topography of funneled landscapes determines the thermodynamics and kinetics of protein folding. Proc Natl Acad Sci U S A (2012) 0.86
Turning death into creative force during biofilm engineering. Proc Natl Acad Sci U S A (2012) 0.86
Knotting pathways in proteins. Biochem Soc Trans (2013) 0.86
A structural perspective on the dynamics of kinesin motors. Biophys J (2011) 0.86
The origin of nonmonotonic complex behavior and the effects of nonnative interactions on the diffusive properties of protein folding. Biophys J (2010) 0.85
A mechanobiochemical mechanism for monooriented chromosome oscillation in mitosis. Proc Natl Acad Sci U S A (2007) 0.84
Folding circular permutants of IL-1β: route selection driven by functional frustration. PLoS One (2012) 0.84
The unique cysteine knot regulates the pleotropic hormone leptin. PLoS One (2012) 0.84
A structural model of polyglutamine determined from a host-guest method combining experiments and landscape theory. Biophys J (2004) 0.84
The origin of minus-end directionality and mechanochemistry of Ncd motors. PLoS Comput Biol (2012) 0.83
The role of atomic level steric effects and attractive forces in protein folding. Proteins (2011) 0.83
An integrated mechanobiochemical feedback mechanism describes chromosome motility from prometaphase to anaphase in mitosis. Proc Natl Acad Sci U S A (2008) 0.82
Modeling the interplay between geometrical and energetic effects in protein folding. J Phys Chem B (2005) 0.82
Macromolecular assembly of polycystin-2 intracytosolic C-terminal domain. Proc Natl Acad Sci U S A (2011) 0.81
Substrate-specific reorganization of the conformational ensemble of CSK implicates novel modes of kinase function. PLoS Comput Biol (2012) 0.81
An analytical study of the interplay between geometrical and energetic effects in protein folding. J Chem Phys (2008) 0.80
Direct coupling analysis for protein contact prediction. Methods Mol Biol (2014) 0.80
Strand swapping regulates the iron-sulfur cluster in the diabetes drug target mitoNEET. Proc Natl Acad Sci U S A (2012) 0.79
The dominant folding route minimizes backbone distortion in SH3. PLoS Comput Biol (2012) 0.79