Published in Structure on October 01, 2006
Biophysical and computational studies of membrane penetration by the GRP1 pleckstrin homology domain. Structure (2011) 1.05
Absolute FKBP binding affinities obtained via nonequilibrium unbinding simulations. J Chem Phys (2009) 0.94
Computational design and experimental discovery of an antiestrogenic peptide derived from alpha-fetoprotein. J Am Chem Soc (2007) 0.79
Constant pH molecular dynamics (CpHMD) and molecular docking studies of CquiOBP1 pH-induced ligand releasing mechanism. J Mol Model (2012) 0.79
Operating mechanism and molecular dynamics of pheromone-binding protein ASP1 as influenced by pH. PLoS One (2014) 0.75
Extracting ligands from receptors by reversed targeted molecular dynamics. J Comput Aided Mol Des (2015) 0.75
Molecular anatomy of a trafficking organelle. Cell (2006) 11.47
Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution. Science (2008) 8.04
Anatomy and dynamics of a supramolecular membrane protein cluster. Science (2007) 3.75
Sphingosine-1-phosphate is a missing cofactor for the E3 ubiquitin ligase TRAF2. Nature (2010) 3.59
Structure of the CCR5 chemokine receptor-HIV entry inhibitor maraviroc complex. Science (2013) 3.17
Predicting protein-protein interactions based only on sequences information. Proc Natl Acad Sci U S A (2007) 3.06
Ligand docking and binding site analysis with PyMOL and Autodock/Vina. J Comput Aided Mol Des (2010) 2.67
Molecular mimicry regulates ABA signaling by SnRK2 kinases and PP2C phosphatases. Science (2011) 2.52
Thymine DNA glycosylase specifically recognizes 5-carboxylcytosine-modified DNA. Nat Chem Biol (2012) 2.45
Membrane protein sequestering by ionic protein-lipid interactions. Nature (2011) 2.40
PDTD: a web-accessible protein database for drug target identification. BMC Bioinformatics (2008) 2.35
TarFisDock: a web server for identifying drug targets with docking approach. Nucleic Acids Res (2006) 2.26
Effect of sodium chloride on a lipid bilayer. Biophys J (2003) 2.24
Structure and mechanism of the reversible photoswitch of a fluorescent protein. Proc Natl Acad Sci U S A (2005) 2.21
Sequential N- to C-terminal SNARE complex assembly drives priming and fusion of secretory vesicles. EMBO J (2006) 2.19
Mechanoenzymatics of titin kinase. Proc Natl Acad Sci U S A (2008) 2.17
Generalized correlation for biomolecular dynamics. Proteins (2006) 2.17
g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation. J Comput Chem (2010) 2.08
The 2009 pandemic H1N1 neuraminidase N1 lacks the 150-cavity in its active site. Nat Struct Mol Biol (2010) 1.98
Predicting free energy changes using structural ensembles. Nat Methods (2009) 1.93
Nanoseconds molecular dynamics simulation of primary mechanical energy transfer steps in F1-ATP synthase. Nat Struct Biol (2002) 1.92
Structural basis for molecular recognition at serotonin receptors. Science (2013) 1.86
The mechanism of proton exclusion in the aquaporin-1 water channel. J Mol Biol (2003) 1.80
Scrutinizing molecular mechanics force fields on the submicrosecond timescale with NMR data. Biophys J (2010) 1.75
Force spectroscopy of single biomolecules. Chemphyschem (2002) 1.73
Mechanically induced titin kinase activation studied by force-probe molecular dynamics simulations. Biophys J (2004) 1.70
Halogen bonding--a novel interaction for rational drug design? J Med Chem (2009) 1.68
Mechanism of selectivity in aquaporins and aquaglyceroporins. Proc Natl Acad Sci U S A (2008) 1.67
The dynamics and energetics of water permeation and proton exclusion in aquaporins. Curr Opin Struct Biol (2005) 1.65
Single-molecule FRET measures bends and kinks in DNA. Proc Natl Acad Sci U S A (2008) 1.58
Structure and function of water channels. Curr Opin Struct Biol (2002) 1.55
A nonproton ligand sensor in the acid-sensing ion channel. Neuron (2010) 1.52
PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach. Nucleic Acids Res (2010) 1.50
Multistep binding of divalent cations to phospholipid bilayers: a molecular dynamics study. Angew Chem Int Ed Engl (2004) 1.50
Full correlation analysis of conformational protein dynamics. Proteins (2008) 1.47
Structural basis for the regulation of cysteine-protease activity by a new class of protease inhibitors in Plasmodium. Structure (2011) 1.46
Quaternary ammonium compounds as water channel blockers. Specificity, potency, and site of action. J Biol Chem (2006) 1.46
Kinetics, statistics, and energetics of lipid membrane electroporation studied by molecular dynamics simulations. Biophys J (2008) 1.43
Energy barriers and driving forces in tRNA translocation through the ribosome. Nat Struct Mol Biol (2013) 1.41
Crystal structure of a yeast aquaporin at 1.15 angstrom reveals a novel gating mechanism. PLoS Biol (2009) 1.41
Synaptotagmin-1 may be a distance regulator acting upstream of SNARE nucleation. Nat Struct Mol Biol (2011) 1.41
Interaction of urea with amino acids: implications for urea-induced protein denaturation. J Am Chem Soc (2007) 1.39
Phosphatidylinositol 4,5-bisphosphate clusters act as molecular beacons for vesicle recruitment. Nat Struct Mol Biol (2013) 1.38
Crystal structure of HAb18G/CD147: implications for immunoglobulin superfamily homophilic adhesion. J Biol Chem (2008) 1.38
Water permeation through gramicidin A: desformylation and the double helix: a molecular dynamics study. Biophys J (2002) 1.37
Protein thermostability calculations using alchemical free energy simulations. Biophys J (2010) 1.33
Self-consistent residual dipolar coupling based model-free analysis for the robust determination of nanosecond to microsecond protein dynamics. J Biomol NMR (2008) 1.33
Computational electrophysiology: the molecular dynamics of ion channel permeation and selectivity in atomistic detail. Biophys J (2011) 1.30
A yeast two-hybrid technology-based system for the discovery of PPARgamma agonist and antagonist. Anal Biochem (2004) 1.29
Membrane fusion. Curr Opin Cell Biol (2002) 1.29
Does CO2 permeate through aquaporin-1? Biophys J (2006) 1.28
Conformational transition of amyloid beta-peptide. Proc Natl Acad Sci U S A (2005) 1.28
Structure-based discovery of inhibitors of the YycG histidine kinase: new chemical leads to combat Staphylococcus epidermidis infections. BMC Microbiol (2006) 1.27
Detection of functional modes in protein dynamics. PLoS Comput Biol (2009) 1.27
How SNARE molecules mediate membrane fusion: recent insights from molecular simulations. Curr Opin Struct Biol (2012) 1.26
Mechanical properties of the icosahedral shell of southern bean mosaic virus: a molecular dynamics study. Biophys J (2009) 1.26
[6]-Gingerol suppresses colon cancer growth by targeting leukotriene A4 hydrolase. Cancer Res (2009) 1.26
Geometry-based sampling of conformational transitions in proteins. Structure (2007) 1.26
Peptide deformylase is a potential target for anti-Helicobacter pylori drugs: reverse docking, enzymatic assay, and X-ray crystallography validation. Protein Sci (2006) 1.25
Virtual screening on natural products for discovering active compounds and target information. Curr Med Chem (2003) 1.25
Caught in the act: visualization of SNARE-mediated fusion events in molecular detail. Chembiochem (2011) 1.25
Structural and functional analysis of laninamivir and its octanoate prodrug reveals group specific mechanisms for influenza NA inhibition. PLoS Pathog (2011) 1.25
Speeding up parallel GROMACS on high-latency networks. J Comput Chem (2007) 1.23
Detecting protein-induced folding of the U4 snRNA kink-turn by single-molecule multiparameter FRET measurements. RNA (2005) 1.23
Simulation of fluorescence anisotropy experiments: probing protein dynamics. Biophys J (2005) 1.21
Differential peptide dynamics is linked to major histocompatibility complex polymorphism. J Biol Chem (2004) 1.19
Collective Langevin dynamics of conformational motions in proteins. J Chem Phys (2006) 1.18
Protein cysteine phosphorylation of SarA/MgrA family transcriptional regulators mediates bacterial virulence and antibiotic resistance. Proc Natl Acad Sci U S A (2012) 1.18
Inherent dynamics of the acid-sensing ion channel 1 correlates with the gating mechanism. PLoS Biol (2009) 1.17
Enterovirus 71 and coxsackievirus A16 3C proteases: binding to rupintrivir and their substrates and anti-hand, foot, and mouth disease virus drug design. J Virol (2011) 1.16
Structural heterogeneity and quantitative FRET efficiency distributions of polyprolines through a hybrid atomistic simulation and Monte Carlo approach. PLoS One (2011) 1.16
Aqueous urea solutions: structure, energetics, and urea aggregation. J Phys Chem B (2007) 1.16
Cinanserin is an inhibitor of the 3C-like proteinase of severe acute respiratory syndrome coronavirus and strongly reduces virus replication in vitro. J Virol (2005) 1.15
Acyl chain order parameter profiles in phospholipid bilayers: computation from molecular dynamics simulations and comparison with 2H NMR experiments. Eur Biophys J (2007) 1.14
Functional dynamics in the voltage-dependent anion channel. Proc Natl Acad Sci U S A (2010) 1.13
Mechanism of hyaluronan degradation by Streptococcus pneumoniae hyaluronate lyase. Structures of complexes with the substrate. J Biol Chem (2002) 1.13
Normal modes and essential dynamics. Methods Mol Biol (2008) 1.12
Can principal components yield a dimension reduced description of protein dynamics on long time scales? J Phys Chem B (2006) 1.12
Quorum-sensing agr mediates bacterial oxidation response via an intramolecular disulfide redox switch in the response regulator AgrA. Proc Natl Acad Sci U S A (2012) 1.11
Structural basis for catalytic and inhibitory mechanisms of beta-hydroxyacyl-acyl carrier protein dehydratase (FabZ). J Biol Chem (2007) 1.11
Quantitative structural analysis of importin-β flexibility: paradigm for solenoid protein structures. Structure (2010) 1.11
Arctigenin effectively ameliorates memory impairment in Alzheimer's disease model mice targeting both β-amyloid production and clearance. J Neurosci (2013) 1.10
pH-dependent conformational flexibility of the SARS-CoV main proteinase (M(pro)) dimer: molecular dynamics simulations and multiple X-ray structure analyses. J Mol Biol (2005) 1.09
Vacuolar protein sorting: two different functional states of the AAA-ATPase Vps4p. J Mol Biol (2008) 1.09
Constant pH Molecular Dynamics in Explicit Solvent with λ-Dynamics. J Chem Theory Comput (2011) 1.09
Mechanical properties of single motor molecules studied by three-dimensional thermal force probing in optical tweezers. Chemphyschem (2004) 1.09
Structural and functional characterization of Falcipain-2, a hemoglobinase from the malarial parasite Plasmodium falciparum. J Biol Chem (2006) 1.09
Short-range order and collective dynamics of DMPC bilayers: a comparison between molecular dynamics simulations, X-ray, and neutron scattering experiments. Biophys J (2007) 1.07
Conformational dynamics of the nicotinic acetylcholine receptor channel: a 35-ns molecular dynamics simulation study. J Am Chem Soc (2005) 1.07
Kinetics of conformational sampling in ubiquitin. Angew Chem Int Ed Engl (2011) 1.07