Published in Protein Sci on August 01, 2002
Protein folding thermodynamics and dynamics: where physics, chemistry, and biology meet. Chem Rev (2006) 2.48
Folding lambda-repressor at its speed limit. Biophys J (2004) 2.44
Protein folding pathways from replica exchange simulations and a kinetic network model. Proc Natl Acad Sci U S A (2005) 1.72
The kinetics of conformational fluctuations in an unfolded protein measured by fluorescence methods. Proc Natl Acad Sci U S A (2005) 1.67
Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field. J Phys Chem A (2010) 1.19
Cooperativity in two-state protein folding kinetics. Protein Sci (2004) 1.14
Intermediates and the folding of proteins L and G. Protein Sci (2004) 1.13
Insights into the dynamics of HIV-1 protease: a kinetic network model constructed from atomistic simulations. J Am Chem Soc (2011) 1.02
Kinetic network study of the diversity and temperature dependence of Trp-Cage folding pathways: combining transition path theory with stochastic simulations. J Phys Chem B (2011) 0.98
Recovering kinetics from a simplified protein folding model using replica exchange simulations: a kinetic network and effective stochastic dynamics. J Phys Chem B (2009) 0.96
Kinetic analysis of ribosome-bound fluorescent proteins reveals an early, stable, cotranslational folding intermediate. J Biol Chem (2011) 0.93
Role of unfolded state heterogeneity and en-route ruggedness in protein folding kinetics. Protein Sci (2006) 0.92
Multiple folding pathways of the SH3 domain. Biophys J (2004) 0.91
Molecular crowders and cosolutes promote folding cooperativity of RNA under physiological ionic conditions. RNA (2014) 0.90
Sparsely populated folding intermediates of the Fyn SH3 domain: matching native-centric essential dynamics and experiment. Proc Natl Acad Sci U S A (2004) 0.90
What can one learn from experiments about the elusive transition state? Protein Sci (2004) 0.90
NMR relaxation in proteins with fast internal motions and slow conformational exchange: model-free framework and Markov state simulations. J Phys Chem B (2013) 0.87
An adaptive weighted ensemble procedure for efficient computation of free energies and first passage rates. J Chem Phys (2012) 0.87
Computational models of protein kinematics and dynamics: beyond simulation. Annu Rev Anal Chem (Palo Alto Calif) (2012) 0.84
A minimum-reaction-flux solution to master-equation models of protein folding. J Chem Phys (2008) 0.80
Markov dynamic models for long-timescale protein motion. Bioinformatics (2010) 0.80
Estimating first-passage time distributions from weighted ensemble simulations and non-Markovian analyses. Protein Sci (2015) 0.77
Network representation of conformational transitions between hidden intermediates of Rd-apocytochrome b562. J Chem Phys (2015) 0.77
Funnels, pathways, and the energy landscape of protein folding: a synthesis. Proteins (1995) 14.36
Spin glasses and the statistical mechanics of protein folding. Proc Natl Acad Sci U S A (1987) 11.69
From Levinthal to pathways to funnels. Nat Struct Biol (1997) 10.58
Hydrogen exchange and structural dynamics of proteins and nucleic acids. Q Rev Biophys (1983) 9.14
How does a protein fold? Nature (1994) 7.55
Protein folding intermediates: native-state hydrogen exchange. Science (1995) 5.91
"New view" of protein folding reconciled with the old through multiple unfolding simulations. Science (1997) 3.93
Exploring the energy landscape of a beta hairpin in explicit solvent. Proteins (2001) 3.88
Molecular dynamics simulations of unfolding and refolding of a beta-hairpin fragment of protein G. Proc Natl Acad Sci U S A (1999) 3.61
A statistical mechanical model for beta-hairpin kinetics. Proc Natl Acad Sci U S A (1998) 3.28
Protein folding kinetics: timescales, pathways and energy landscapes in terms of sequence-dependent properties. Fold Des (1997) 3.14
A theoretical search for folding/unfolding nuclei in three-dimensional protein structures. Proc Natl Acad Sci U S A (1999) 3.02
Investigating protein dynamics in collective coordinate space. Curr Opin Struct Biol (1999) 2.96
Cooperativity in protein-folding kinetics. Proc Natl Acad Sci U S A (1993) 2.87
Understanding protein folding via free-energy surfaces from theory and experiment. Trends Biochem Sci (2000) 2.73
Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: application to alpha-amylase inhibitor. Proteins (2000) 2.73
Mechanisms and kinetics of beta-hairpin formation. Proc Natl Acad Sci U S A (2000) 2.66
Protein folding intermediates and pathways studied by hydrogen exchange. Annu Rev Biophys Biomol Struct (2000) 2.57
Exploring the origins of topological frustration: design of a minimally frustrated model of fragment B of protein A. Proc Natl Acad Sci U S A (1999) 2.49
Structure of the transition state for folding of a protein derived from experiment and simulation. J Mol Biol (1996) 2.36
Pathways for protein folding: is a new view needed? Curr Opin Struct Biol (1998) 2.26
Deciphering the timescales and mechanisms of protein folding using minimal off-lattice models. Curr Opin Struct Biol (1999) 2.14
Protein folding mechanisms and the multidimensional folding funnel. Proteins (1998) 1.92
Transition states and the meaning of Phi-values in protein folding kinetics. Nat Struct Biol (2001) 1.75
Multiple protein folding nuclei and the transition state ensemble in two-state proteins. Proteins (2001) 1.61
Identifying the protein folding nucleus using molecular dynamics. J Mol Biol (2000) 1.60
Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus. Nat Struct Biol (2000) 1.56
Lattice models for proteins reveal multiple folding nuclei for nucleation-collapse mechanism. J Mol Biol (1998) 1.50
Staphylococcal protein A: unfolding pathways, unfolded states, and differences between the B and E domains. Proc Natl Acad Sci U S A (2000) 1.48
An amino acid code for protein folding. Proc Natl Acad Sci U S A (2001) 1.45
Kinetic evidence for incorrectly folded intermediate states in the refolding of denatured proteins. Nature (1971) 1.38
Folding pathway of a lattice model for proteins. Proc Natl Acad Sci U S A (1999) 1.31
A statistical mechanical model for hydrogen exchange in globular proteins. Protein Sci (1995) 1.28
Fast and slow tracks in lysozyme folding: insight into the role of domains in the folding process. J Mol Biol (1997) 1.27
Protein folding as a diffusional process. Biochemistry (1999) 1.10
The sequential unfolding of ribonuclease A: detection of a fast initial phase in the kinetics of unfolding. Proc Natl Acad Sci U S A (1971) 1.06
Thermal unfolding of an intermediate is associated with non-Arrhenius kinetics in the folding of hen lysozyme. J Mol Biol (2000) 0.91
The origin of the alpha-domain intermediate in the folding of hen lysozyme. J Mol Biol (1998) 0.88
Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics. J Chem Phys (2007) 4.52
Using quaternions to calculate RMSD. J Comput Chem (2004) 2.93
Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state. Proc Natl Acad Sci U S A (2005) 2.84
Global ribosome motions revealed with elastic network model. J Struct Biol (2004) 2.84
Binding of small-molecule ligands to proteins: "what you see" is not always "what you get". Structure (2009) 2.83
Coupling between catalytic site and collective dynamics: a requirement for mechanochemical activity of enzymes. Structure (2005) 2.75
Dynamics of large proteins through hierarchical levels of coarse-grained structures. J Comput Chem (2002) 2.60
ProDy: protein dynamics inferred from theory and experiments. Bioinformatics (2011) 2.55
Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulations. J Chem Theory Comput (2009) 2.53
Anisotropic network model: systematic evaluation and a new web interface. Bioinformatics (2006) 2.52
Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent. J Phys Chem B (2007) 2.31
Predicting absolute ligand binding free energies to a simple model site. J Mol Biol (2007) 2.19
The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding. Proc Natl Acad Sci U S A (2009) 2.12
On the use of orientational restraints and symmetry corrections in alchemical free energy calculations. J Chem Phys (2006) 2.10
High-efficiency bypass of DNA damage by human DNA polymerase Q. EMBO J (2004) 2.07
Assessment of protein structure refinement in CASP9. Proteins (2011) 2.06
A kinematic view of loop closure. J Comput Chem (2004) 2.03
Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site. J Mol Biol (2009) 1.90
Zebrafish chemical screening reveals an inhibitor of Dusp6 that expands cardiac cell lineages. Nat Chem Biol (2009) 1.88
How ions affect the structure of water. J Am Chem Soc (2002) 1.84
The Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change. J Chem Theory Comput (2007) 1.73
Protein folding by zipping and assembly. Proc Natl Acad Sci U S A (2007) 1.72
Signal propagation in proteins and relation to equilibrium fluctuations. PLoS Comput Biol (2007) 1.67
Nonuniversal power law scaling in the probability distribution of scientific citations. Proc Natl Acad Sci U S A (2010) 1.66
Insights into equilibrium dynamics of proteins from comparison of NMR and X-ray data with computational predictions. Structure (2007) 1.66
Markov propagation of allosteric effects in biomolecular systems: application to GroEL-GroES. Mol Syst Biol (2006) 1.66
iGNM: a database of protein functional motions based on Gaussian Network Model. Bioinformatics (2005) 1.65
Elastic network models for understanding biomolecular machinery: from enzymes to supramolecular assemblies. Phys Biol (2005) 1.64
Relating molecular flexibility to function: a case study of tubulin. Biophys J (2002) 1.62
Time-resolved mechanism of extracellular gate opening and substrate binding in a glutamate transporter. J Biol Chem (2008) 1.61
oGNM: online computation of structural dynamics using the Gaussian Network Model. Nucleic Acids Res (2006) 1.60
Escherichia coli adenylate kinase dynamics: comparison of elastic network model modes with mode-coupling (15)N-NMR relaxation data. Proteins (2004) 1.55
The interface of protein structure, protein biophysics, and molecular evolution. Protein Sci (2012) 1.54
Assessment of the protein-structure refinement category in CASP8. Proteins (2009) 1.53
Allosteric transitions of supramolecular systems explored by network models: application to chaperonin GroEL. PLoS Comput Biol (2009) 1.50
Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics. Bioinformatics (2009) 1.50
Identification of core amino acids stabilizing rhodopsin. Proc Natl Acad Sci U S A (2004) 1.48
Treating entropy and conformational changes in implicit solvent simulations of small molecules. J Phys Chem B (2008) 1.47
Charge asymmetries in hydration of polar solutes. J Phys Chem B (2008) 1.45
Common mechanism of pore opening shared by five different potassium channels. Biophys J (2006) 1.40
Structural and spectroscopic studies of peptoid oligomers with alpha-chiral aliphatic side chains. J Am Chem Soc (2003) 1.39
Maturation dynamics of bacteriophage HK97 capsid. Structure (2005) 1.38
A test on peptide stability of AMBER force fields with implicit solvation. J Phys Chem B (2008) 1.38
Ion pairing in molecular simulations of aqueous alkali halide solutions. J Phys Chem B (2009) 1.35
Surfaces affect ion pairing. J Phys Chem B (2005) 1.29
Conformational changes in HIV-1 reverse transcriptase induced by nonnucleoside reverse transcriptase inhibitor binding. Curr HIV Res (2004) 1.26
Coupling between global dynamics and signal transduction pathways: a mechanism of allostery for chaperonin GroEL. Mol Biosyst (2008) 1.24
Inhibitor binding alters the directions of domain motions in HIV-1 reverse transcriptase. Proteins (2002) 1.23
Predictions of hydration free energies from all-atom molecular dynamics simulations. J Phys Chem B (2009) 1.23
Inflammatory modulation of hepatocyte apoptosis by nitric oxide: in vivo, in vitro, and in silico studies. Curr Mol Med (2004) 1.21
Folding rates and low-entropy-loss routes of two-state proteins. J Mol Biol (2003) 1.21
Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models. Bioinformatics (2007) 1.20
Modeling aqueous solvation with semi-explicit assembly. Proc Natl Acad Sci U S A (2011) 1.20
Biomimetic nanostructures: creating a high-affinity zinc-binding site in a folded nonbiological polymer. J Am Chem Soc (2008) 1.19
Mechanism of signal propagation upon retinal isomerization: insights from molecular dynamics simulations of rhodopsin restrained by normal modes. Biophys J (2008) 1.18
Druggability Assessment of Allosteric Proteins by Dynamics Simulations in the Presence of Probe Molecules. J Chem Theory Comput (2012) 1.18
Folding a nonbiological polymer into a compact multihelical structure. J Am Chem Soc (2005) 1.18
Functional motions of influenza virus hemagglutinin: a structure-based analytical approach. Biophys J (2002) 1.17
Teaching the principles of statistical dynamics. Am J Phys (2006) 1.17
The ultimate speed limit to protein folding is conformational searching. J Am Chem Soc (2007) 1.15
Large collective motions regulate the functional properties of glutamate transporter trimers. Proc Natl Acad Sci U S A (2011) 1.15
Discovery of novel Myc-Max heterodimer disruptors with a three-dimensional pharmacophore model. J Med Chem (2009) 1.14
Cooperativity in two-state protein folding kinetics. Protein Sci (2004) 1.14
Sequence evolution correlates with structural dynamics. Mol Biol Evol (2012) 1.14
Theory for the three-dimensional Mercedes-Benz model of water. J Chem Phys (2009) 1.12
The flexibility in the proline ring couples to the protein backbone. Protein Sci (2005) 1.12
Maximum Caliber: a variational approach applied to two-state dynamics. J Chem Phys (2008) 1.11
Computing protein stabilities from their chain lengths. Proc Natl Acad Sci U S A (2009) 1.10
Analysis of correlated mutations in HIV-1 protease using spectral clustering. Bioinformatics (2008) 1.10
Pre-existing soft modes of motion uniquely defined by native contact topology facilitate ligand binding to proteins. Protein Sci (2011) 1.09
Molecular simulations elucidate the substrate translocation pathway in a glutamate transporter. Proc Natl Acad Sci U S A (2009) 1.09
Oil/water transfer is partly driven by molecular shape, not just size. J Am Chem Soc (2010) 1.09
Role of Hsp70 ATPase domain intrinsic dynamics and sequence evolution in enabling its functional interactions with NEFs. PLoS Comput Biol (2010) 1.07
Coupled global and local changes direct substrate translocation by neurotransmitter-sodium symporter ortholog LeuT. Biophys J (2013) 1.07
Blind prediction of charged ligand binding affinities in a model binding site. J Mol Biol (2013) 1.05
Dynamics and allosteric potential of the AMPA receptor N-terminal domain. EMBO J (2011) 1.05
Folding very short peptides using molecular dynamics. PLoS Comput Biol (2006) 1.04
Fast protein folding kinetics. Proc Natl Acad Sci U S A (2003) 1.04
Folding kinetics of two-state proteins: effect of circularization, permutation, and crosslinks. J Mol Biol (2003) 1.04
Computational generation inhibitor-bound conformers of p38 MAP kinase and comparison with experiments. Pac Symp Biocomput (2011) 1.02
Tenascin cytotactin epidermal growth factor-like repeat binds epidermal growth factor receptor with low affinity. J Cell Physiol (2007) 1.02
An introduction to simulation and visualization of biological systems at multiple scales: a summer training program for interdisciplinary research. Biotechnol Prog (2006) 1.02
The sodium/galactose symporter crystal structure is a dynamic, not so occluded state. Mol Biosyst (2010) 1.01
Exploring zipping and assembly as a protein folding principle. Proteins (2007) 1.01
On the conservation of the slow conformational dynamics within the amino acid kinase family: NAGK the paradigm. PLoS Comput Biol (2010) 1.01
Frequent mutation of receptor protein tyrosine phosphatases provides a mechanism for STAT3 hyperactivation in head and neck cancer. Proc Natl Acad Sci U S A (2014) 1.01
The origin and extent of coarse-grained regularities in protein internal packing. Proteins (2003) 1.00
Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: an accurate correction scheme for electrostatic finite-size effects. J Chem Phys (2013) 1.00
Blind test of physics-based prediction of protein structures. Biophys J (2009) 0.99
Toward a molecular understanding of the anisotropic response of proteins to external forces: insights from elastic network models. Biophys J (2008) 0.99
Computing the transition state populations in simple protein models. Biopolymers (2003) 0.99
Incorporation of chemoselective functionalities into peptoids via solid-phase submonomer synthesis. Bioconjug Chem (2004) 0.98
Predicting peptide structures in native proteins from physical simulations of fragments. PLoS Comput Biol (2009) 0.98
Mining frequent patterns in protein structures: a study of protease families. Bioinformatics (2004) 0.98
Predicting drug-target interactions using probabilistic matrix factorization. J Chem Inf Model (2013) 0.98
A maximum entropy framework for nonexponential distributions. Proc Natl Acad Sci U S A (2013) 0.97
Transition-states in protein folding kinetics: the structural interpretation of Phi values. J Mol Biol (2006) 0.96
Global transitions of proteins explored by a multiscale hybrid methodology: application to adenylate kinase. Biophys J (2013) 0.96
Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae. BMC Bioinformatics (2006) 0.96