Published in J Phys Chem B on January 12, 2006
Distribution of amino acids in a lipid bilayer from computer simulations. Biophys J (2008) 2.53
Membrane assembly of simple helix homo-oligomers studied via molecular dynamics simulations. Biophys J (2006) 1.23
APBSmem: a graphical interface for electrostatic calculations at the membrane. PLoS One (2010) 1.12
Probing the periplasmic-open state of lactose permease in response to sugar binding and proton translocation. J Mol Biol (2010) 1.11
A fast and accurate computational approach to protein ionization. Protein Sci (2008) 1.07
Molecular dynamics simulations of a DMPC bilayer using nonadditive interaction models. Biophys J (2009) 1.06
Dynamic structure of retinylidene ligand of rhodopsin probed by molecular simulations. J Mol Biol (2007) 1.03
Design and application of implicit solvent models in biomolecular simulations. Curr Opin Struct Biol (2014) 0.88
Molecular recognition of CCR5 by an HIV-1 gp120 V3 loop. PLoS One (2014) 0.88
Anisotropic solvent model of the lipid bilayer. 1. Parameterization of long-range electrostatics and first solvation shell effects. J Chem Inf Model (2011) 0.85
Numerical Poisson-Boltzmann Model for Continuum Membrane Systems. Chem Phys Lett (2012) 0.84
Double bilayers and transmembrane gradients: a molecular dynamics study of a highly charged peptide. Biophys J (2008) 0.83
Three-dimensional stress field around a membrane protein: atomistic and coarse-grained simulation analysis of gramicidin A. Biophys J (2013) 0.82
Membrane protein native state discrimination by implicit membrane models. J Comput Chem (2012) 0.81
Inter-domain communication mechanisms in an ABC importer: a molecular dynamics study of the MalFGK2E complex. PLoS Comput Biol (2011) 0.81
Atomic-level description of protein-lipid interactions using an accelerated membrane model. Biochim Biophys Acta (2016) 0.81
Effect of flanking residues on the conformational sampling of the internal fusion peptide from Ebola virus. Proteins (2011) 0.79
Interactions between ionizable amino acid side chains at a lipid bilayer-water interface. J Phys Chem B (2011) 0.79
Charge equilibration force fields for lipid environments: applications to fully hydrated DPPC bilayers and DMPC-embedded gramicidin A. J Phys Chem B (2009) 0.78
Transferring the PRIMO Coarse-Grained Force Field to the Membrane Environment: Simulations of Membrane Proteins and Helix-Helix Association. J Chem Theory Comput (2014) 0.77
Structure-based prediction of drug distribution across the headgroup and core strata of a phospholipid bilayer using surrogate phases. Mol Pharm (2014) 0.75
Molecular dynamics simulation of hydrated DPPC monolayers using charge equilibration force fields. J Comput Chem (2011) 0.75
Recent advances in transferable coarse-grained modeling of proteins. Adv Protein Chem Struct Biol (2014) 0.75
Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J Comput Chem (2004) 17.97
Improved treatment of the protein backbone in empirical force fields. J Am Chem Soc (2004) 5.96
Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles. J Chem Theory Comput (2012) 5.57
New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations. J Comput Chem (2003) 3.81
An implicit membrane generalized born theory for the study of structure, stability, and interactions of membrane proteins. Biophys J (2003) 2.91
Solvation and hydration of proteins and nucleic acids: a theoretical view of simulation and experiment. Acc Chem Res (2002) 1.69
Highly accurate biomolecular electrostatics in continuum dielectric environments. J Comput Chem (2008) 1.66
A generalized Born formalism for heterogeneous dielectric environments: application to the implicit modeling of biological membranes. J Chem Phys (2005) 1.56
A distinct type of glycerol-3-phosphate acyltransferase with sn-2 preference and phosphatase activity producing 2-monoacylglycerol. Proc Natl Acad Sci U S A (2010) 1.55
Dynamic error correction and regulation of downstream bubble opening by human RNA polymerase II. Mol Cell (2005) 1.43
Evolution and physics in comparative protein structure modeling. Acc Chem Res (2002) 1.29
Physics-based protein structure refinement through multiple molecular dynamics trajectories and structure averaging. Proteins (2013) 1.20
The requirement for mechanical coupling between head and S2 domains in smooth muscle myosin ATPase regulation and its implications for dimeric motor function. J Mol Biol (2005) 1.17
Balancing an accurate representation of the molecular surface in generalized born formalisms with integrator stability in molecular dynamics simulations. J Comput Chem (2006) 1.16
Implicit solvent simulations of DNA and DNA-protein complexes: agreement with explicit solvent vs experiment. J Phys Chem B (2006) 1.16
Reduced native state stability in crowded cellular environment due to protein-protein interactions. J Am Chem Soc (2013) 1.13
Inclusion of many-body effects in the additive CHARMM protein CMAP potential results in enhanced cooperativity of α-helix and β-hairpin formation. Biophys J (2012) 1.12
NTP-driven translocation and regulation of downstream template opening by multi-subunit RNA polymerases. Biochem Cell Biol (2005) 1.11
Aberrant activity of the DNA repair enzyme AlkB. J Inorg Biochem (2004) 1.10
Protein crowding affects hydration structure and dynamics. J Am Chem Soc (2012) 1.08
Conformational coupling, bridge helix dynamics and active site dehydration in catalysis by RNA polymerase. Biochim Biophys Acta (2010) 1.06
Conformational sampling of peptides in cellular environments. Biophys J (2007) 1.04
Conformational sampling of peptides in the presence of protein crowders from AA/CG-multiscale simulations. J Phys Chem B (2012) 1.01
Accurate prediction of protonation state as a prerequisite for reliable MM-PB(GB)SA binding free energy calculations of HIV-1 protease inhibitors. J Comput Chem (2008) 1.00
Deciphering the mismatch recognition cycle in MutS and MSH2-MSH6 using normal-mode analysis. Biophys J (2009) 1.00
Protein Structure Refinement through Structure Selection and Averaging from Molecular Dynamics Ensembles. J Chem Theory Comput (2012) 1.00
PRIMO/PRIMONA: a coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy. Proteins (2010) 0.99
Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions. J Comput Chem (2008) 0.96
Energetic and structural details of the trigger-loop closing transition in RNA polymerase II. Biophys J (2013) 0.95
Synthetic curcuminoids modulate the arachidonic acid metabolism of human platelet 12-lipoxygenase and reduce sprout formation of human endothelial cells. Mol Cancer Ther (2006) 0.95
Purification and characterization of the FeII- and alpha-ketoglutarate-dependent xanthine hydroxylase from Aspergillus nidulans. Biochemistry (2007) 0.93
Conformational sampling of influenza fusion peptide in membrane bilayers as a function of termini and protonation states. J Phys Chem B (2010) 0.93
A correlation-based method for the enhancement of scoring functions on funnel-shaped energy landscapes. Proteins (2006) 0.93
PRIMO: A Transferable Coarse-grained Force Field for Proteins. J Chem Theory Comput (2013) 0.91
Dynamic Heterogeneous Dielectric Generalized Born (DHDGB): An implicit membrane model with a dynamically varying bilayer thickness. J Chem Theory Comput (2013) 0.90
The unorthodox SNAP50 zinc finger domain contributes to cooperative promoter recognition by human SNAPC. J Biol Chem (2006) 0.90
Conformational change in MSH2-MSH6 upon binding DNA coupled to ATPase activity. Biophys J (2009) 0.89
Effect of membrane thickness on conformational sampling of phospholamban from computer simulations. Biophys J (2010) 0.89
DNA bending propensity in the presence of base mismatches: implications for DNA repair. J Phys Chem B (2013) 0.88
Sampling of near-native protein conformations during protein structure refinement using a coarse-grained model, normal modes, and molecular dynamics simulations. Proteins (2008) 0.87
Base-flipping mechanism in postmismatch recognition by MutS. Biophys J (2011) 0.86
Evidence that the Bacillus subtilis SpoIIGA protein is a novel type of signal-transducing aspartic protease. J Biol Chem (2008) 0.86
Role of conformational sampling of Ser16 and Thr17-phosphorylated phospholamban in interactions with SERCA. Biochim Biophys Acta (2012) 0.83
Scoring confidence index: statistical evaluation of ligand binding mode predictions. J Comput Aided Mol Des (2009) 0.83
Computational simulation strategies for analysis of multisubunit RNA polymerases. Chem Rev (2013) 0.82
Structural basis for the enantiospecificities of R- and S-specific phenoxypropionate/alpha-ketoglutarate dioxygenases. Protein Sci (2006) 0.80
Effect of flanking residues on the conformational sampling of the internal fusion peptide from Ebola virus. Proteins (2011) 0.79
Molecular mechanism by which palmitate inhibits PKR autophosphorylation. Biochemistry (2011) 0.79
Density-biased sampling: a robust computational method for studying pore formation in membranes. J Chem Theory Comput (2015) 0.78
Conformational preferences of DNA in reduced dielectric environments. J Phys Chem B (2014) 0.77
Molecular dynamics trajectory compression with a coarse-grained model. IEEE/ACM Trans Comput Biol Bioinform (2011) 0.76
Substrate specificity of SpoIIGA, a signal-transducing aspartic protease in Bacilli. J Biochem (2011) 0.76
Intrinsic Base-Pair Rearrangement in the Hairpin Ribozyme Directs RNA Conformational Sampling and Tertiary Interface Formation. J Phys Chem B (2016) 0.76
Interionic hydration structures of NaCl in aqueous solution: a combined study of quantum mechanical cluster calculations and QM/EFP-MD simulations. J Phys Chem B (2012) 0.75
Interactions of amino acid side-chain analogs within membrane environments. J Phys Chem B (2015) 0.75
Binding site multiplicity with fatty acid ligands: implications for the regulation of PKR kinase autophosphorylation with palmitate. Proteins (2014) 0.75
Solvent electronic polarization effects on Na(+)-Na(+) and Cl(-)-Cl(-) pair associations in aqueous solution. J Phys Chem B (2013) 0.75
Crowding in Cellular Environments at an Atomistic Level from Computer Simulations. J Phys Chem B (2017) 0.75
Thermodynamics of Macromolecular Association in Heterogeneous Crowding Environments: Theoretical and Simulation Studies with a Simplified Model. J Phys Chem B (2016) 0.75