Published in J Mol Biol on February 21, 2003
Protein folding thermodynamics and dynamics: where physics, chemistry, and biology meet. Chem Rev (2006) 2.48
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
SMOG@ctbp: simplified deployment of structure-based models in GROMACS. Nucleic Acids Res (2010) 1.95
The effects of nonnative interactions on protein folding rates: theory and simulation. Protein Sci (2004) 1.82
Insights from coarse-grained Gō models for protein folding and dynamics. Int J Mol Sci (2009) 1.52
Coarse-grained sequences for protein folding and design. Proc Natl Acad Sci U S A (2003) 1.35
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
Balancing energy and entropy: a minimalist model for the characterization of protein folding landscapes. Proc Natl Acad Sci U S A (2005) 1.20
Macromolecular crowding modulates folding mechanism of alpha/beta protein apoflavodoxin. Biophys J (2009) 1.16
Slipknotting upon native-like loop formation in a trefoil knot protein. Proc Natl Acad Sci U S A (2010) 1.15
Biomolecular dynamics: order-disorder transitions and energy landscapes. Rep Prog Phys (2012) 1.12
Characterization of the folding landscape of monomeric lactose repressor: quantitative comparison of theory and experiment. Proc Natl Acad Sci U S A (2005) 1.12
Capillarity theory for the fly-casting mechanism. Proc Natl Acad Sci U S A (2010) 1.11
Mechanical resistance of proteins explained using simple molecular models. Biophys J (2005) 1.10
The shadow map: a general contact definition for capturing the dynamics of biomolecular folding and function. J Phys Chem B (2012) 1.10
Rerouting the folding pathway of the Notch ankyrin domain by reshaping the energy landscape. J Am Chem Soc (2008) 1.08
On the precision of experimentally determined protein folding rates and phi-values. Protein Sci (2006) 1.06
Thermodynamics of alpha- and beta-structure formation in proteins. Biophys J (2003) 1.00
Variations in the fast folding rates of the lambda-repressor: a hybrid molecular dynamics study. Biophys J (2004) 0.99
Quantitative criteria for native energetic heterogeneity influences in the prediction of protein folding kinetics. Proc Natl Acad Sci U S A (2008) 0.99
Dynamics of lysozyme structure network: probing the process of unfolding. Biophys J (2007) 0.97
Exploring the energy landscapes of protein folding simulations with Bayesian computation. Biophys J (2012) 0.97
Similarity and difference in the unfolding of thermophilic and mesophilic cold shock proteins studied by molecular dynamics simulations. Biophys J (2006) 0.91
What have we learned from the studies of two-state folders, and what are the unanswered questions about two-state protein folding? Phys Biol (2009) 0.91
De novo prediction of protein folding pathways and structure using the principle of sequential stabilization. Proc Natl Acad Sci U S A (2012) 0.91
Cooperativity, connectivity, and folding pathways of multidomain proteins. Proc Natl Acad Sci U S A (2008) 0.91
Multiple folding pathways of the SH3 domain. Biophys J (2004) 0.91
The folding transition state of protein L is extensive with nonnative interactions (and not small and polarized). J Mol Biol (2012) 0.90
Guanylate kinase, induced fit, and the allosteric spring probe. Biophys J (2006) 0.90
Conformational dependence of a protein kinase phosphate transfer reaction. Proc Natl Acad Sci U S A (2005) 0.88
Assembly of the five-way junction in the ribosomal small subunit using hybrid MD-Gō simulations. J Phys Chem B (2012) 0.86
Comparison of sequence-based and structure-based energy functions for the reversible folding of a peptide. Biophys J (2005) 0.85
Unfolding of globular proteins: monte carlo dynamics of a realistic reduced model. Biophys J (2003) 0.83
Identifying critical residues in protein folding: Insights from phi-value and P(fold) analysis. J Chem Phys (2008) 0.83
A critical assessment of the topomer search model of protein folding using a continuum explicit-chain model with extensive conformational sampling. Protein Sci (2005) 0.81
Knotted proteins: A tangled tale of Structural Biology. Comput Struct Biotechnol J (2015) 0.81
Even with nonnative interactions, the updated folding transition states of the homologs Proteins G & L are extensive and similar. Proc Natl Acad Sci U S A (2015) 0.80
Reversible thermal denaturation of a 60-kDa genetically engineered beta-sheet polypeptide. Biophys J (2006) 0.79
The dominant folding route minimizes backbone distortion in SH3. PLoS Comput Biol (2012) 0.79
A semi-analytical description of protein folding that incorporates detailed geometrical information. J Chem Phys (2011) 0.79
Modulation of folding energy landscape by charge-charge interactions: linking experiments with computational modeling. Proc Natl Acad Sci U S A (2015) 0.79
Effects of disulfide bonds on folding behavior and mechanism of the beta-sheet protein tendamistat. Biophys J (2005) 0.78
Two-state folding over a weak free-energy barrier. Biophys J (2003) 0.77
Folding simulations of the A and B domains of protein G. J Phys Chem B (2012) 0.77
Quantifying Nonnative Interactions in the Protein-Folding Free-Energy Landscape. Biophys J (2016) 0.76
Union of geometric constraint-based simulations with molecular dynamics for protein structure prediction. Biophys J (2010) 0.76
Polymer uncrossing and knotting in protein folding, and their role in minimal folding pathways. PLoS One (2013) 0.75
Evidence for the principle of minimal frustration in the evolution of protein folding landscapes. Proc Natl Acad Sci U S A (2017) 0.75
Characterization of the unfolded state of repeat proteins. HFSP J (2008) 0.75
Implication of the cause of differences in 3D structures of proteins with high sequence identity based on analyses of amino acid sequences and 3D structures. BMC Res Notes (2014) 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
Simulation of the folding equilibrium of alpha-helical peptides: a comparison of the generalized Born approximation with explicit solvent. Proc Natl Acad Sci U S A (2003) 2.31
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
Peptide folding simulations. Curr Opin Struct Biol (2003) 1.71
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
Reversible temperature and pressure denaturation of a protein fragment: a replica exchange molecular dynamics simulation study. Phys Rev Lett (2004) 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
Computing the stability diagram of the Trp-cage miniprotein. Proc Natl Acad Sci U S A (2008) 1.45
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
Atomic-level description of amyloid beta-dimer formation. J Am Chem Soc (2006) 1.41
Atomic simulations of protein folding, using the replica exchange algorithm. Methods Enzymol (2004) 1.40
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
Replica exchange simulation of reversible folding/unfolding of the Trp-cage miniprotein in explicit solvent: on the structure and possible role of internal water. J Struct Biol (2006) 1.29
High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations. Proc Natl Acad Sci U S A (2013) 1.29
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
Molecular dynamics study of water penetration in staphylococcal nuclease. Proteins (2005) 1.25
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
Helix-coil transition of alanine peptides in water: force field dependence on the folded and unfolded structures. Proteins (2005) 1.23
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
Equilibrium study of protein denaturation by urea. J Am Chem Soc (2010) 1.17
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
Aβ monomers transiently sample oligomer and fibril-like configurations: ensemble characterization using a combined MD/NMR approach. J Mol Biol (2013) 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
Nature of structural inhomogeneities on folding a helix and their influence on spectral measurements. Proc Natl Acad Sci U S A (2004) 1.10
Role of backbone hydration and salt-bridge formation in stability of alpha-helix in solution. Biophys J (2003) 1.10
Folding time predictions from all-atom replica exchange simulations. J Mol Biol (2007) 1.09
Role of flexibility and polarity as determinants of the hydration of internal cavities and pockets in proteins. Biophys J (2007) 1.08
Free energy of translocating an arginine-rich cell-penetrating peptide across a lipid bilayer suggests pore formation. Biophys J (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
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
Cosolvent effects on protein stability. Annu Rev Phys Chem (2013) 1.04
Backbone and side-chain contributions in protein denaturation by urea. Biophys J (2011) 1.03
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
Local structure formation in simulations of two small proteins. J Struct Biol (2006) 0.98
Water penetration in the low and high pressure native states of ubiquitin. Proteins (2008) 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
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
Mirror images as naturally competing conformations in protein folding. J Phys Chem B (2012) 0.94
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
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
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
Equilibrium unfolding of the poly(glutamic acid)20 helix. Biopolymers (2007) 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