Hydrophobic aided replica exchange: an efficient algorithm for protein folding in explicit solvent.

PubWeight™: 1.20‹?› | Rank: Top 10%

🔗 View Article (PMC 3057047)

Published in J Phys Chem B on September 28, 2006

Authors

Pu Liu1, Xuhui Huang, Ruhong Zhou, B J Berne

Author Affiliations

1: Department of Chemistry, Columbia University, New York, New York 10027, USA.

Articles citing this

Rapid equilibrium sampling initiated from nonequilibrium data. Proc Natl Acad Sci U S A (2009) 1.54

Computational techniques for efficient conformational sampling of proteins. Curr Opin Struct Biol (2008) 1.54

Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering. J Chem Theory Comput (2015) 1.47

Recent theoretical and computational advances for modeling protein-ligand binding affinities. Adv Protein Chem Struct Biol (2011) 1.15

Simple continuous and discrete models for simulating replica exchange simulations of protein folding. J Phys Chem B (2008) 1.01

TIGER2: an improved algorithm for temperature intervals with global exchange of replicas. J Chem Phys (2009) 0.96

Generalized replica exchange method. J Chem Phys (2010) 0.93

Roles of boundary conditions in DNA simulations: analysis of ion distributions with the finite-difference Poisson-Boltzmann method. Biophys J (2009) 0.93

Replica exchange with nonequilibrium switches. Proc Natl Acad Sci U S A (2009) 0.92

The temperature intervals with global exchange of replicas empirical accelerated sampling method: parameter sensitivity and extension to a complex molecular system. J Comput Chem (2010) 0.88

Replica exchange statistical temperature Monte Carlo. J Chem Phys (2009) 0.86

Protein folding in a reverse micelle environment: the role of confinement and dehydration. J Chem Phys (2011) 0.82

Replica exchanging self-guided Langevin dynamics for efficient and accurate conformational sampling. J Chem Phys (2012) 0.82

Optimal replica exchange method combined with Tsallis weight sampling. J Chem Phys (2009) 0.79

Computational design and experimental discovery of an antiestrogenic peptide derived from alpha-fetoprotein. J Am Chem Soc (2007) 0.79

In silico chaperonin-like cycle helps folding of proteins for structure prediction. Biophys J (2008) 0.75

Bio-mimicking of proline-rich motif applied to carbon nanotube reveals unexpected subtleties underlying nanoparticle functionalization. Sci Rep (2014) 0.75

Folding and Stabilization of Native-Sequence-Reversed Proteins. Sci Rep (2016) 0.75

Using a reduced dimensionality model to compute the thermodynamic properties of finite polypeptide aggregates. J Biol Phys (2012) 0.75

Articles cited by this

Toward high-resolution de novo structure prediction for small proteins. Science (2005) 9.18

Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science (1998) 8.46

Folding dynamics and mechanism of beta-hairpin formation. Nature (1997) 7.30

Absolute comparison of simulated and experimental protein-folding dynamics. Nature (2002) 5.68

The free energy landscape for beta hairpin folding in explicit water. Proc Natl Acad Sci U S A (2001) 4.39

A short linear peptide that folds into a native stable beta-hairpin in aqueous solution. Nat Struct Biol (1994) 4.17

Can a continuum solvent model reproduce the free energy landscape of a beta -hairpin folding in water? Proc Natl Acad Sci U S A (2002) 3.41

A statistical mechanical model for beta-hairpin kinetics. Proc Natl Acad Sci U S A (1998) 3.28

Hydrophobic collapse in multidomain protein folding. Science (2004) 2.94

Observation of a dewetting transition in the collapse of the melittin tetramer. Nature (2005) 2.93

Replica exchange with solute tempering: a method for sampling biological systems in explicit water. Proc Natl Acad Sci U S A (2005) 2.88

Dewetting-induced collapse of hydrophobic particles. Proc Natl Acad Sci U S A (2003) 2.42

Folding of protein G B1 domain studied by the conformational characterization of fragments comprising its secondary structure elements. Eur J Biochem (1995) 2.15

Exploring the kinetic requirements for enhancement of protein folding rates in the GroEL cavity. J Mol Biol (1999) 1.85

Free energy surfaces of beta-hairpin and alpha-helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model. Proteins (2004) 1.67

Efficient sampling of protein structures by model hopping. Phys Rev Lett (2005) 1.43

Nanopore-protein interactions dramatically alter stability and yield of the native state in restricted spaces. J Mol Biol (2006) 1.22

Mimicking the action of folding chaperones in molecular dynamics simulations: Application to the refinement of homology-based protein structures. Protein Sci (2004) 0.93

Articles by these authors

The free energy landscape for beta hairpin folding in explicit water. Proc Natl Acad Sci U S A (2001) 4.39

Comprehensive interrogation of natural TALE DNA-binding modules and transcriptional repressor domains. Nat Commun (2012) 3.60

Hydrophobic collapse in multidomain protein folding. Science (2004) 2.94

Observation of a dewetting transition in the collapse of the melittin tetramer. Nature (2005) 2.93

Replica exchange with solute tempering: a method for sampling biological systems in explicit water. Proc Natl Acad Sci U S A (2005) 2.88

Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution. Science (2009) 2.68

Binding of blood proteins to carbon nanotubes reduces cytotoxicity. Proc Natl Acad Sci U S A (2011) 2.66

Using generalized ensemble simulations and Markov state models to identify conformational states. Methods (2009) 2.60

Development of a polarizable force field for proteins via ab initio quantum chemistry: first generation model and gas phase tests. J Comput Chem (2002) 2.59

Dewetting-induced collapse of hydrophobic particles. Proc Natl Acad Sci U S A (2003) 2.42

Dewetting and hydrophobic interaction in physical and biological systems. Annu Rev Phys Chem (2009) 2.22

Probing the chemistry of thioredoxin catalysis with force. Nature (2007) 2.17

Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding. Proc Natl Acad Sci U S A (2008) 2.03

Destructive extraction of phospholipids from Escherichia coli membranes by graphene nanosheets. Nat Nanotechnol (2013) 1.51

Interpretation of the light scattering from long rods. J Mol Biol (1974) 1.50

Role of water in mediating the assembly of Alzheimer amyloid-beta Abeta16-22 protofilaments. J Am Chem Soc (2008) 1.42

Structural insight into RNA hairpin folding intermediates. J Am Chem Soc (2008) 1.39

X-ray structure and mechanism of RNA polymerase II stalled at an antineoplastic monofunctional platinum-DNA adduct. Proc Natl Acad Sci U S A (2010) 1.39

Inelastic light scattering by large structured particles. Biophys J (1974) 1.35

Replica exchange with solute scaling: a more efficient version of replica exchange with solute tempering (REST2). J Phys Chem B (2011) 1.35

A role for both conformational selection and induced fit in ligand binding by the LAO protein. PLoS Comput Biol (2011) 1.35

Ligand binding to protein-binding pockets with wet and dry regions. Proc Natl Acad Sci U S A (2011) 1.30

Single homopolypeptide chains collapse into mechanically rigid conformations. Proc Natl Acad Sci U S A (2009) 1.25

The predicted structure of the headpiece of the Huntingtin protein and its implications on Huntingtin aggregation. J Mol Biol (2009) 1.24

Nanoscale dewetting transition in protein complex folding. J Phys Chem B (2007) 1.22

Effect of ions on the hydrophobic interaction between two plates. J Am Chem Soc (2007) 1.21

Aggregation of γ-crystallins associated with human cataracts via domain swapping at the C-terminal β-strands. Proc Natl Acad Sci U S A (2011) 1.21

Dynamics of pyrophosphate ion release and its coupled trigger loop motion from closed to open state in RNA polymerase II. J Am Chem Soc (2012) 1.20

Electrostatic gating of a nanometer water channel. Proc Natl Acad Sci U S A (2007) 1.19

Plugging into proteins: poisoning protein function by a hydrophobic nanoparticle. ACS Nano (2010) 1.17

A computationally inexpensive modification of the point dipole electrostatic polarization model for molecular simulations. J Comput Chem (2003) 1.16

Interplay between hydrodynamics and the free energy surface in the assembly of nanoscale hydrophobes. J Phys Chem B (2011) 1.15

Initiation complex structure and promoter proofreading. Science (2011) 1.13

On achieving high accuracy and reliability in the calculation of relative protein-ligand binding affinities. Proc Natl Acad Sci U S A (2012) 1.12

Serial replica exchange. J Phys Chem B (2007) 1.11

Temperature dependence of dimerization and dewetting of large-scale hydrophobes: a molecular dynamics study. J Phys Chem B (2008) 1.11

Topological methods for exploring low-density states in biomolecular folding pathways. J Chem Phys (2009) 1.10

Urea's action on hydrophobic interactions. J Am Chem Soc (2009) 1.09

Number fluctuation spectroscopy of motile microorganisms. Biophys J (1975) 1.09

Dewetting transitions in protein cavities. Proteins (2010) 1.08

Network models for molecular kinetics and their initial applications to human health. Cell Res (2010) 1.06

Thermal denaturing of mutant lysozyme with both the OPLSAA and the CHARMM force fields. J Am Chem Soc (2006) 1.06

Drying and hydrophobic collapse of paraffin plates. J Phys Chem B (2005) 1.06

beta-Strand interactions at the domain interface critical for the stability of human lens gammaD-crystallin. Protein Sci (2010) 1.03

Hydrogen-bond dynamics in the air-water interface. J Phys Chem B (2005) 1.03

Molecular mechanism of pancreatic tumor metastasis inhibition by Gd@C82(OH)22 and its implication for de novo design of nanomedicine. Proc Natl Acad Sci U S A (2012) 1.03

Replica exchange with solute tempering: efficiency in large scale systems. J Phys Chem B (2007) 1.03

A displaced-solvent functional analysis of model hydrophobic enclosures. J Chem Theory Comput (2010) 1.02

Free-energy simulations reveal that both hydrophobic and polar interactions are important for influenza hemagglutinin antibody binding. Biophys J (2012) 1.02

Fully differentiable coarse-grained and all-atom knowledge-based potentials for RNA structure evaluation. RNA (2011) 1.01

Dissecting entropic coiling and poor solvent effects in protein collapse. J Am Chem Soc (2008) 1.01

Catalytic tempering: A method for sampling rough energy landscapes by Monte Carlo. Proc Natl Acad Sci U S A (2000) 1.01

Structure and dynamics of the solvation of bovine pancreatic trypsin inhibitor in explicit water: a comparative study of the effects of solvent and protein polarizability. J Phys Chem B (2005) 1.00

Aggregation and dispersion of small hydrophobic particles in aqueous electrolyte solutions. J Phys Chem B (2006) 1.00

Dynamics of water confined in the interdomain region of a multidomain protein. J Phys Chem B (2006) 0.97

Molecular dynamics simulations of Ago silencing complexes reveal a large repertoire of admissible 'seed-less' targets. Sci Rep (2012) 0.97

Hydration and dewetting near fluorinated superhydrophobic plates. J Am Chem Soc (2006) 0.97

Free energy simulations reveal a double mutant avian H5N1 virus hemagglutinin with altered receptor binding specificity. J Comput Chem (2009) 0.97

Dynamics of an intrinsically disordered protein reveal metastable conformations that potentially seed aggregation. J Am Chem Soc (2013) 0.96

Elasticity, structure, and relaxation of extended proteins under force. Proc Natl Acad Sci U S A (2013) 0.94

How hydrophobic drying forces impact the kinetics of molecular recognition. Proc Natl Acad Sci U S A (2013) 0.94

Are hydrodynamic interactions important in the kinetics of hydrophobic collapse? J Phys Chem B (2012) 0.94

Polarizable molecules in the vibrational spectroscopy of water. Proc Natl Acad Sci U S A (2005) 0.93

Water's role in the force-induced unfolding of ubiquitin. Proc Natl Acad Sci U S A (2010) 0.93

Hydrophobic interactions in model enclosures from small to large length scales: non-additivity in explicit and implicit solvent models. Faraday Discuss (2010) 0.93

Chaotic motifs in gene regulatory networks. PLoS One (2012) 0.93

Thermal and structural stability of adsorbed proteins. Biophys J (2010) 0.92

Is Poisson-Boltzmann theory insufficient for protein folding simulations? J Chem Phys (2006) 0.92

Thermodynamic properties of liquid water: an application of a nonparametric approach to computing the entropy of a neat fluid. J Chem Theory Comput (2009) 0.91

How force unfolding differs from chemical denaturation. Proc Natl Acad Sci U S A (2014) 0.91

Simulating the T-jump-triggered unfolding dynamics of trpzip2 peptide and its time-resolved IR and two-dimensional IR signals using the Markov state model approach. J Phys Chem B (2011) 0.91

Interactions between proteins and carbon-based nanoparticles: exploring the origin of nanotoxicity at the molecular level. Small (2012) 0.90

Hydration and dewetting near graphite-CH(3) and graphite-COOH plates. J Phys Chem B (2005) 0.90

Scanning tunneling microscopy images of alkane derivatives on graphite: role of electronic effects. Nano Lett (2008) 0.90

Amino acid analogues bind to carbon nanotube via π-π interactions: comparison of molecular mechanical and quantum mechanical calculations. J Chem Phys (2012) 0.90

Using a mutual information-based site transition network to map the genetic evolution of influenza A/H3N2 virus. Bioinformatics (2009) 0.90

A two-state model for the dynamics of the pyrophosphate ion release in bacterial RNA polymerase. PLoS Comput Biol (2013) 0.90

The folding transition state of protein L is extensive with nonnative interactions (and not small and polarized). J Mol Biol (2012) 0.90

Non-destructive inhibition of metallofullerenol Gd@C(82)(OH)(22) on WW domain: implication on signal transduction pathway. Sci Rep (2012) 0.89

Water-mediated signal multiplication with Y-shaped carbon nanotubes. Proc Natl Acad Sci U S A (2009) 0.89

Urea-induced drying of carbon nanotubes suggests existence of a dry globule-like transient state during chemical denaturation of proteins. J Phys Chem B (2010) 0.89

Single mutation effects on conformational change and membrane deformation of influenza hemagglutinin fusion peptides. J Phys Chem B (2010) 0.89

Probing the self-assembly mechanism of diphenylalanine-based peptide nanovesicles and nanotubes. ACS Nano (2012) 0.88

Monitoring and inhibition of insulin fibrillation by a small organic fluorogen with aggregation-induced emission characteristics. J Am Chem Soc (2012) 0.86

Unraveling quantum mechanical effects in water using isotopic fractionation. Proc Natl Acad Sci U S A (2012) 0.86

A tetraphenylethylene core-based 3D structure small molecular acceptor enabling efficient non-fullerene organic solar cells. Adv Mater (2014) 0.86

Multiscale modeling of macromolecular biosystems. Brief Bioinform (2012) 0.84

Characterization of heterogeneous solutions using laser light scattering: study of the tubulin system. Biochemistry (1977) 0.84