Published in Proteins on December 01, 2009
Genomics-aided structure prediction. Proc Natl Acad Sci U S A (2012) 1.63
High-resolution protein complexes from integrating genomic information with molecular simulation. Proc Natl Acad Sci U S A (2009) 1.57
Slipknotting upon native-like loop formation in a trefoil knot protein. Proc Natl Acad Sci U S A (2010) 1.15
Simulations of the alternating access mechanism of the sodium symporter Mhp1. Biophys J (2011) 1.15
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
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
Allostery in the ferredoxin protein motif does not involve a conformational switch. Proc Natl Acad Sci U S A (2011) 0.88
Dimeric interactions and complex formation using direct coevolutionary couplings. Sci Rep (2015) 0.86
Order and disorder control the functional rearrangement of influenza hemagglutinin. Proc Natl Acad Sci U S A (2014) 0.86
The unique cysteine knot regulates the pleotropic hormone leptin. PLoS One (2012) 0.84
Pierced Lasso Bundles are a new class of knot-like motifs. PLoS Comput Biol (2014) 0.83
The role of atomic level steric effects and attractive forces in protein folding. Proteins (2011) 0.83
Modeling Structural Flexibility of Proteins with Go-Models. J Chem Theory Comput (2012) 0.83
Differences between cotranscriptional and free riboswitch folding. Nucleic Acids Res (2013) 0.82
Constructing sequence-dependent protein models using coevolutionary information. Protein Sci (2015) 0.82
Macromolecular assembly of polycystin-2 intracytosolic C-terminal domain. Proc Natl Acad Sci U S A (2011) 0.81
SMOG 2: A Versatile Software Package for Generating Structure-Based Models. PLoS Comput Biol (2016) 0.81
Substrate-specific reorganization of the conformational ensemble of CSK implicates novel modes of kinase function. PLoS Comput Biol (2012) 0.81
A semi-analytical description of protein folding that incorporates detailed geometrical information. J Chem Phys (2011) 0.79
The dominant folding route minimizes backbone distortion in SH3. PLoS Comput Biol (2012) 0.79
Allosteric control in a metalloprotein dramatically alters function. Proc Natl Acad Sci U S A (2012) 0.79
Altered backbone and side-chain interactions result in route heterogeneity during the folding of interleukin-1β (IL-1β). Biophys J (2013) 0.79
Sampling of Protein Folding Transitions: Multicanonical Versus Replica Exchange Molecular Dynamics. J Chem Theory Comput (2013) 0.78
Chaperones rescue luciferase folding by separating its domains. J Biol Chem (2014) 0.77
Folding simulations of the A and B domains of protein G. J Phys Chem B (2012) 0.77
Theoretical Insights into the Biophysics of Protein Bi-stability and Evolutionary Switches. PLoS Comput Biol (2016) 0.75
Exploring the balance between folding and functional dynamics in proteins and RNA. Int J Mol Sci (2015) 0.75
Native structure-based modeling and simulation of biomolecular systems per mouse click. BMC Bioinformatics (2014) 0.75
Geometrical Frustration in Interleukin-33 Decouples the Dynamics of the Functional Element from the Folding Transition State Ensemble. PLoS One (2015) 0.75
Human Frataxin Folds Via an Intermediate State. Role of the C-Terminal Region. Sci Rep (2016) 0.75
Role of non-native electrostatic interactions in the coupled folding and binding of PUMA with Mcl-1. PLoS Comput Biol (2017) 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
Structural basis of histidine kinase autophosphorylation deduced by integrating genomics, molecular dynamics, and mutagenesis. Proc Natl Acad Sci U S A (2012) 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
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
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
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
Modulation of a pre-existing conformational equilibrium tunes adenylate kinase activity. J Am Chem Soc (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
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
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
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
Knotting pathways in proteins. Biochem Soc Trans (2013) 0.86
Turning death into creative force during biofilm engineering. Proc Natl Acad Sci U S A (2012) 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
A structural model of polyglutamine determined from a host-guest method combining experiments and landscape theory. Biophys J (2004) 0.84
The unique cysteine knot regulates the pleotropic hormone leptin. PLoS One (2012) 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