Published in J Phys Chem B on March 18, 2010
Tidal surge in the M2 proton channel, sensed by 2D IR spectroscopy. Proc Natl Acad Sci U S A (2011) 1.27
Spectroscopic studies of protein folding: linear and nonlinear methods. Protein Sci (2011) 1.10
Protein dynamics in cytochrome P450 molecular recognition and substrate specificity using 2D IR vibrational echo spectroscopy. J Am Chem Soc (2011) 1.04
Two-dimensional IR spectroscopy of protein dynamics using two vibrational labels: a site-specific genetically encoded unnatural amino acid and an active site ligand. J Phys Chem B (2011) 0.98
Site-specific infrared probes of proteins. Annu Rev Phys Chem (2015) 0.96
Direct assessment of the α-helix nucleation time. J Phys Chem B (2011) 0.95
Folding of a heterogeneous β-hairpin peptide from temperature-jump 2D IR spectroscopy. Proc Natl Acad Sci U S A (2013) 0.93
Three-dimensional structures by two-dimensional vibrational spectroscopy. Acc Chem Res (2012) 0.91
Monitoring the folding of Trp-cage peptide by two-dimensional infrared (2DIR) spectroscopy. J Phys Chem B (2013) 0.86
Utilizing Lifetimes to Suppress Random Coil Features in 2D IR Spectra of Peptides. J Phys Chem Lett (2011) 0.86
2D IR spectroscopy reveals the role of water in the binding of channel-blocking drugs to the influenza M2 channel. J Chem Phys (2014) 0.82
An alternative structural isoform in amyloid-like aggregates formed from thermally denatured human γD-crystallin. Protein Sci (2014) 0.78
Ultrafast Spectroscopy with Photocurrent Detection: Watching Excitonic Optoelectronic Systems at Work. J Phys Chem Lett (2016) 0.78
Kinetic Isotope Effect Provides Insight into the Vibrational Relaxation Mechanism of Aromatic Molecules: Application to Cyano-phenylalanine. J Phys Chem Lett (2016) 0.75
The protein folding network. J Mol Biol (2004) 2.63
Watching hydrogen-bond dynamics in a beta-turn by transient two-dimensional infrared spectroscopy. Nature (2006) 2.28
Evaluation of a fast implicit solvent model for molecular dynamics simulations. Proteins (2002) 2.27
The role of side-chain interactions in the early steps of aggregation: Molecular dynamics simulations of an amyloid-forming peptide from the yeast prion Sup35. Proc Natl Acad Sci U S A (2003) 2.14
The robustness of pollination networks to the loss of species and interactions: a quantitative approach incorporating pollinator behaviour. Ecol Lett (2010) 2.10
Wordom: a program for efficient analysis of molecular dynamics simulations. Bioinformatics (2007) 2.05
Predicting free energy changes using structural ensembles. Nat Methods (2009) 1.93
Prediction of aggregation rate and aggregation-prone segments in polypeptide sequences. Protein Sci (2005) 1.80
FACTS: Fast analytical continuum treatment of solvation. J Comput Chem (2008) 1.79
Local modularity measure for network clusterizations. Phys Rev E Stat Nonlin Soft Matter Phys (2005) 1.72
PARP1 ADP-ribosylates lysine residues of the core histone tails. Nucleic Acids Res (2010) 1.64
Interpreting the aggregation kinetics of amyloid peptides. J Mol Biol (2006) 1.58
Molecular dynamics simulations of protein folding from the transition state. Proc Natl Acad Sci U S A (2002) 1.51
The role of aromaticity, exposed surface, and dipole moment in determining protein aggregation rates. Protein Sci (2004) 1.50
New insights into the folding of a β-sheet miniprotein in a reduced space of collective hydrogen bond variables: application to a hydrodynamic analysis of the folding flow. J Phys Chem B (2013) 1.48
Macrodomain-containing proteins are new mono-ADP-ribosylhydrolases. Nat Struct Mol Biol (2013) 1.47
Quantum mechanical methods for drug design. Curr Top Med Chem (2010) 1.45
Phi-value analysis by molecular dynamics simulations of reversible folding. Proc Natl Acad Sci U S A (2005) 1.35
Designed armadillo repeat proteins as general peptide-binding scaffolds: consensus design and computational optimization of the hydrophobic core. J Mol Biol (2007) 1.33
Kinase selectivity potential for inhibitors targeting the ATP binding site: a network analysis. Bioinformatics (2009) 1.32
Wordom: a user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces. J Comput Chem (2010) 1.31
Picosecond conformational transition and equilibration of a cyclic peptide. Proc Natl Acad Sci U S A (2003) 1.31
Alpha-Helix folding in the presence of structural constraints. Proc Natl Acad Sci U S A (2008) 1.30
Supramolecular organization and dual function of the IsiA chlorophyll-binding protein in cyanobacteria. Biochemistry (2004) 1.30
Membrane localization and flexibility of a lipidated ras peptide studied by molecular dynamics simulations. J Am Chem Soc (2004) 1.27
Photocycle of the flavin-binding photoreceptor AppA, a bacterial transcriptional antirepressor of photosynthesis genes. Biochemistry (2005) 1.26
The free energy landscape of small molecule unbinding. PLoS Comput Biol (2011) 1.25
The folding and dimerization of HIV-1 protease: evidence for a stable monomer from simulations. J Mol Biol (2004) 1.22
One-dimensional barrier-preserving free-energy projections of a beta-sheet miniprotein: new insights into the folding process. J Phys Chem B (2008) 1.21
Kinetic analysis of molecular dynamics simulations reveals changes in the denatured state and switch of folding pathways upon single-point mutation of a beta-sheet miniprotein. Proteins (2008) 1.20
Alpha-helix formation in a photoswitchable peptide tracked from picoseconds to microseconds by time-resolved IR spectroscopy. Proc Natl Acad Sci U S A (2005) 1.19
Weak temperature dependence of the free energy surface and folding pathways of structured peptides. Proteins (2002) 1.18
Analysis of the distributed computing approach applied to the folding of a small beta peptide. Proc Natl Acad Sci U S A (2003) 1.13
Efficient modularity optimization by multistep greedy algorithm and vertex mover refinement. Phys Rev E Stat Nonlin Soft Matter Phys (2008) 1.10
The chromodomain of LIKE HETEROCHROMATIN PROTEIN 1 is essential for H3K27me3 binding and function during Arabidopsis development. PLoS One (2009) 1.10
Protein ligand migration mapped by nonequilibrium 2D-IR exchange spectroscopy. Proc Natl Acad Sci U S A (2007) 1.07
Functional plasticity in the substrate binding site of beta-secretase. Structure (2005) 1.07
Complete phenotypic recovery of an Alzheimer's disease model by a quinone-tryptophan hybrid aggregation inhibitor. PLoS One (2010) 1.06
Efficient evaluation of binding free energy using continuum electrostatics solvation. J Med Chem (2004) 1.06
Pathways and intermediates of amyloid fibril formation. J Mol Biol (2007) 1.06
Discovery of cell-permeable non-peptide inhibitors of beta-secretase by high-throughput docking and continuum electrostatics calculations. J Med Chem (2005) 1.05
Phenylalanine assembly into toxic fibrils suggests amyloid etiology in phenylketonuria. Nat Chem Biol (2012) 1.05
Amyloid aggregation on lipid bilayers and its impact on membrane permeability. J Mol Biol (2008) 1.05
Double-resonance versus pulsed Fourier transform two-dimensional infrared spectroscopy: an experimental and theoretical comparison. J Chem Phys (2004) 1.04
A fluorescence quenching assay to discriminate between specific and nonspecific inhibitors of dengue virus protease. Anal Biochem (2009) 1.03
Structure-based optimization of potent and selective inhibitors of the tyrosine kinase erythropoietin producing human hepatocellular carcinoma receptor B4 (EphB4). J Med Chem (2009) 1.03
Estimation of protein folding probability from equilibrium simulations. J Chem Phys (2005) 1.02
Discovery of a non-peptidic inhibitor of west nile virus NS3 protease by high-throughput docking. PLoS Negl Trop Dis (2009) 1.01
Delineation of folding pathways of a β-sheet miniprotein. J Phys Chem B (2011) 1.01
Ser170 controls the conformational multiplicity of the loop 166-175 in prion proteins: implication for conversion and species barrier. FASEB J (2007) 1.01
Intramolecular disulfide bridges as a phototrigger to monitor the dynamics of small cyclic peptides. J Phys Chem B (2007) 1.01
Structure-based tailoring of compound libraries for high-throughput screening: discovery of novel EphB4 kinase inhibitors. Proteins (2008) 1.01
In silico discovery of beta-secretase inhibitors. J Am Chem Soc (2006) 1.01
Two-dimensional Raman-terahertz spectroscopy of water. Proc Natl Acad Sci U S A (2013) 1.00
Micelle-like architecture of the monomer ensemble of Alzheimer's amyloid-β peptide in aqueous solution and its implications for Aβ aggregation. J Mol Biol (2010) 1.00
The low-energy forms of photosystem I light-harvesting complexes: spectroscopic properties and pigment-pigment interaction characteristics. Biophys J (2007) 0.99
Epigenetic mechanisms regulate stage differentiation in the minimized protozoan Giardia lamblia. Mol Microbiol (2010) 0.99
Folding and unfolding of a photoswitchable peptide from picoseconds to microseconds. Proc Natl Acad Sci U S A (2007) 0.99
Structure of the higher plant light harvesting complex I: in vivo characterization and structural interdependence of the Lhca proteins. Biochemistry (2005) 0.99
Active phase stabilization in Fourier-transform two-dimensional infrared spectroscopy. Opt Lett (2005) 0.97
Automatic and efficient decomposition of two-dimensional structures of small molecules for fragment-based high-throughput docking. J Med Chem (2006) 0.95
High-throughput virtual screening using quantum mechanical probes: discovery of selective kinase inhibitors. ChemMedChem (2010) 0.95
9,10-Anthraquinone hinders beta-aggregation: how does a small molecule interfere with Abeta-peptide amyloid fibrillation? Protein Sci (2009) 0.94
Spontaneous formation of detergent micelles around the outer membrane protein OmpX. Biophys J (2005) 0.94
Fragment-based de novo ligand design by multiobjective evolutionary optimization. J Chem Inf Model (2008) 0.94
Fast protein folding on downhill energy landscape. Protein Sci (2003) 0.94
Organism complexity anti-correlates with proteomic beta-aggregation propensity. Protein Sci (2005) 0.94
Characterization and further stabilization of designed ankyrin repeat proteins by combining molecular dynamics simulations and experiments. J Mol Biol (2007) 0.94
Labeling vibrations by light: ultrafast transient 2D-IR spectroscopy tracks vibrational modes during photoinduced charge transfer. J Am Chem Soc (2004) 0.94
Polarization portraits of single multichromophoric systems: visualizing conformation and energy transfer. Small (2009) 0.93
Energy transport in peptide helices. Proc Natl Acad Sci U S A (2007) 0.93
Coherent multidimensional optical spectroscopy. Acc Chem Res (2009) 0.92
Origin of the 701-nm fluorescence emission of the Lhca2 subunit of higher plant photosystem I. J Biol Chem (2004) 0.92
Flaviviral protease inhibitors identified by fragment-based library docking into a structure generated by molecular dynamics. J Med Chem (2009) 0.91
Fluorescence properties of the chromophore-binding domain of bacteriophytochrome from Deinococcus radiodurans. J Phys Chem B (2013) 0.91
Amyloid fibril polymorphism is under kinetic control. J Am Chem Soc (2010) 0.91
Disordered binding of small molecules to Aβ(12-28). J Biol Chem (2011) 0.90
Is quantum mechanics necessary for predicting binding free energy? J Med Chem (2008) 0.90
Kinetic response of a photoperturbed allosteric protein. Proc Natl Acad Sci U S A (2013) 0.89
Biological and biomedical applications of two-dimensional vibrational spectroscopy: proteomics, imaging, and structural analysis. Acc Chem Res (2009) 0.89
Automated docking of highly flexible ligands by genetic algorithms: a critical assessment. J Comput Chem (2004) 0.89
Equilibrium distribution from distributed computing (simulations of protein folding). J Phys Chem B (2011) 0.89
A gain-of-function mutation of Arabidopsis cryptochrome1 promotes flowering. Plant Physiol (2010) 0.88
Calculation of protein ionization equilibria with conformational sampling: pK(a) of a model leucine zipper, GCN4 and barnase. Proteins (2002) 0.88
Protein identification and quantification by two-dimensional infrared spectroscopy: implications for an all-optical proteomic platform. Proc Natl Acad Sci U S A (2008) 0.88
Optical fingerprinting of peptides using two-dimensional infrared spectroscopy: proof of principle. Anal Biochem (2007) 0.88
Totally laparoscopic versus open gastrectomy for gastric cancer: a matched cohort study. J Laparoendosc Adv Surg Tech A (2012) 0.88
Discovery of kinase inhibitors by high-throughput docking and scoring based on a transferable linear interaction energy model. J Med Chem (2008) 0.87
Change of the unbinding mechanism upon a mutation: a molecular dynamics study of an antibody-hapten complex. Protein Sci (2005) 0.87
Purely absorptive three-dimensional infrared spectroscopy. J Chem Phys (2009) 0.87
Three-dimensional infrared spectroscopy of isotope-substituted liquid water reveals heterogeneous dynamics. J Phys Chem B (2011) 0.87
An efficient homogeneous intermolecular rhenium-based photocatalytic system for the production of H2. Inorg Chem (2009) 0.86
Library screening by fragment-based docking. J Mol Recognit (2010) 0.86
Ligand binding studied by 2D IR spectroscopy using the azidohomoalanine label. J Phys Chem B (2012) 0.86