Published in Proteins on September 01, 2003
Accurate and efficient loop selections by the DFIRE-based all-atom statistical potential. Protein Sci (2004) 1.53
SuperLooper--a prediction server for the modeling of loops in globular and membrane proteins. Nucleic Acids Res (2009) 1.27
Membrane protein prediction methods. Methods (2007) 1.17
Modeling flexible loops in the dark-adapted and activated states of rhodopsin, a prototypical G-protein-coupled receptor. Biophys J (2005) 0.97
How a small change in retinal leads to G-protein activation: initial events suggested by molecular dynamics calculations. Proteins (2007) 0.86
Template-based protein structure modeling. Methods Mol Biol (2010) 0.86
Computational modeling of membrane proteins. Proteins (2014) 0.83
A combined MPI-CUDA parallel solution of linear and nonlinear Poisson-Boltzmann equation. Biomed Res Int (2014) 0.75
MDAnalysis: a toolkit for the analysis of molecular dynamics simulations. J Comput Chem (2011) 2.76
Interpretation of small angle X-ray measurements guided by molecular dynamics simulations of lipid bilayers. Chem Phys Lipids (2003) 1.62
Zipping and unzipping of adenylate kinase: atomistic insights into the ensemble of open<-->closed transitions. J Mol Biol (2009) 1.61
Theory of a systematic computational error in free energy differences. Phys Rev Lett (2002) 1.60
Atomistic simulations of biologically realistic transmembrane potential gradients. J Chem Phys (2004) 1.43
Insights into the molecular mechanism of membrane fusion from simulation: evidence for the association of splayed tails. Phys Rev Lett (2003) 1.40
Improving the efficiency and reliability of free energy perturbation calculations using overlap sampling methods. J Comput Chem (2004) 1.32
Reduced amino acid alphabet is sufficient to accurately recognize intrinsically disordered protein. FEBS Lett (2004) 1.25
Understanding the Hofmeister effect in interactions between chaotropic anions and lipid bilayers: molecular dynamics simulations. J Am Chem Soc (2003) 1.22
Folding is not required for bilayer insertion: replica exchange simulations of an alpha-helical peptide with an explicit lipid bilayer. Proteins (2005) 1.20
Interaction of protegrin-1 with lipid bilayers: membrane thinning effect. Biophys J (2006) 1.18
Changes in phosphatidylcholine headgroup tilt and water order induced by monovalent salts: molecular dynamics simulations. Biophys J (2004) 1.13
Rhodopsin exhibits a preference for solvation by polyunsaturated docosohexaenoic acid. J Am Chem Soc (2003) 1.13
Molecular dynamics simulation of dark-adapted rhodopsin in an explicit membrane bilayer: coupling between local retinal and larger scale conformational change. J Mol Biol (2003) 1.11
Insights into protein structure and function from disorder-complexity space. Proteins (2007) 0.93
How to lose a kink and gain a helix: pH independent conformational changes of the fusion domains from influenza hemagglutinin in heterogeneous lipid bilayers. Proteins (2008) 0.91
Multiple pathways in conformational transitions of the alanine dipeptide: an application of dynamic importance sampling. J Comput Chem (2006) 0.90
Picosecond protein dynamics: the origin of the time-dependent spectral shift in the fluorescence of the single Trp in the protein GB1. J Phys Chem B (2010) 0.90
How environment supports a state: molecular dynamics simulations of two states in bacteriorhodopsin suggest lipid and water compensation. Biophys J (2004) 0.88
Computing ensembles of transitions from stable states: Dynamic importance sampling. J Comput Chem (2011) 0.88
How a small change in retinal leads to G-protein activation: initial events suggested by molecular dynamics calculations. Proteins (2007) 0.86
Cooperative nature of gating transitions in K(+) channels as seen from dynamic importance sampling calculations. Proteins (2010) 0.85
Distinct phenotype of a Wilson disease mutation reveals a novel trafficking determinant in the copper transporter ATP7B. Proc Natl Acad Sci U S A (2014) 0.85
Double bilayers and transmembrane gradients: a molecular dynamics study of a highly charged peptide. Biophys J (2008) 0.83
Multiscale modeling of double-helical DNA and RNA: a unification through Lie groups. J Phys Chem B (2012) 0.83
Splaying of aliphatic tails plays a central role in barrier crossing during liposome fusion. J Phys Chem B (2010) 0.81
Examining the origins of the hydration force between lipid bilayers using all-atom simulations. J Membr Biol (2010) 0.80
From the gating charge response to pore domain movement: initial motions of Kv1.2 dynamics under physiological voltage changes. Mol Membr Biol (2009) 0.80
Coarse-grained simulations of transitions in the E2-to-E1 conformations for Ca ATPase (SERCA) show entropy-enthalpy compensation. J Mol Biol (2012) 0.80
Towards the prediction of order parameters from molecular dynamics simulations in proteins. J Chem Phys (2012) 0.79
Mesoscopic simulation of adsorption of peptides in a hydrophobic chromatography system. Anal Chem (2005) 0.78
Using overlap and funnel sampling to obtain accurate free energies from nonequilibrium work measurements. Phys Rev E Stat Nonlin Soft Matter Phys (2004) 0.78
Molecular dynamics simulations of transitions for ECD epidermal growth factor receptors show key differences between human and drosophila forms of the receptors. Proteins (2013) 0.78
Using non-Gaussian density functional fits to improve relative free energy calculations. J Chem Phys (2005) 0.78
The role of domain: domain interactions versus domain: water interactions in the coarse-grained simulations of the E1P to E2P transitions in Ca-ATPase (SERCA). Proteins (2012) 0.77
Computing ensembles of transitions with molecular dynamics simulations. Methods Mol Biol (2015) 0.76
Festschrift in the honor of Stephen H. White's 70th Birthday. J Membr Biol (2011) 0.75
Simulation and experiment of temperature and cosolvent effects in reversed phase chromatography of peptides. Biotechnol Prog (2005) 0.75
Stochastic dynamics and the dynamic phase transition in thin ferromagnetic films. Phys Rev E Stat Nonlin Soft Matter Phys (2004) 0.75