Published in J Comput Chem on January 15, 2008
MIBPB: a software package for electrostatic analysis. J Comput Chem (2010) 1.77
Differential geometry based solvation model I: Eulerian formulation. J Comput Phys (2010) 1.74
DelPhi: a comprehensive suite for DelPhi software and associated resources. BMC Biophys (2012) 1.64
PBEQ-Solver for online visualization of electrostatic potential of biomolecules. Nucleic Acids Res (2008) 1.61
Multiscale molecular dynamics using the matched interface and boundary method. J Comput Phys (2011) 1.39
Differential geometry based multiscale models. Bull Math Biol (2010) 1.38
Progress in the prediction of pKa values in proteins. Proteins (2011) 1.36
Differential geometry based solvation model II: Lagrangian formulation. J Math Biol (2011) 1.27
APBSmem: a graphical interface for electrostatic calculations at the membrane. PLoS One (2010) 1.12
Achieving Energy Conservation in Poisson-Boltzmann Molecular Dynamics: Accuracy and Precision with Finite-Difference Algorithms. Chem Phys Lett (2009) 1.09
AQUASOL: An efficient solver for the dipolar Poisson-Boltzmann-Langevin equation. J Chem Phys (2010) 1.03
Biomolecular surface construction by PDE transform. Int J Numer Method Biomed Eng (2011) 0.98
Variational multiscale models for charge transport. SIAM Rev Soc Ind Appl Math (2012) 0.95
Differential geometry based solvation model. III. Quantum formulation. J Chem Phys (2011) 0.95
Poisson-Nernst-Planck Equations for Simulating Biomolecular Diffusion-Reaction Processes I: Finite Element Solutions. J Comput Phys (2010) 0.95
Multidimensional persistence in biomolecular data. J Comput Chem (2015) 0.93
Computational methods for optical molecular imaging. Commun Numer Methods Eng (2009) 0.93
Predicting ion binding properties for RNA tertiary structures. Biophys J (2010) 0.93
Rapid calculation of protein pKa values using Rosetta. Biophys J (2012) 0.90
Importance of diffuse metal ion binding to RNA. Met Ions Life Sci (2011) 0.88
Discretization of the induced-charge boundary integral equation. Phys Rev E Stat Nonlin Soft Matter Phys (2009) 0.87
Progress in developing Poisson-Boltzmann equation solvers. Mol Based Math Biol (2013) 0.84
MIB Galerkin method for elliptic interface problems. J Comput Appl Math (2014) 0.83
Membrane Protein Properties Revealed through Data-Rich Electrostatics Calculations. Structure (2015) 0.82
A Galerkin formulation of the MIB method for three dimensional elliptic interface problems. Comput Math Appl (2014) 0.81
A Nonlinear Elasticity Model of Macromolecular Conformational Change Induced by Electrostatic Forces. J Math Anal Appl (2008) 0.81
Fast Analytical Methods for Macroscopic Electrostatic Models in Biomolecular Simulations. SIAM Rev Soc Ind Appl Math (2011) 0.81
Quantum Dynamics in Continuum for Proton Transport I: Basic Formulation. Commun Comput Phys (2012) 0.81
Exploring accurate Poisson-Boltzmann methods for biomolecular simulations. Comput Theor Chem (2013) 0.79
Exploring a charge-central strategy in the solution of Poisson's equation for biomolecular applications. Phys Chem Chem Phys (2012) 0.79
ADAPTIVE FINITE ELEMENT MODELING TECHNIQUES FOR THE POISSON-BOLTZMANN EQUATION. Commun Comput Phys (2012) 0.77
Modeling the electrostatic potential of asymmetric lipopolysaccharide membranes: the MEMPOT algorithm implemented in DelPhi. J Comput Chem (2014) 0.77
A multiscale model for virus capsid dynamics. Int J Biomed Imaging (2010) 0.77
Analysis of fast boundary-integral approximations for modeling electrostatic contributions of molecular binding. Mol Based Math Biol (2013) 0.75
Second order Method for Solving 3D Elasticity Equations with Complex Interfaces. J Comput Phys (2015) 0.75
Matched Interface and Boundary Method for Elasticity Interface Problems. J Comput Appl Math (2015) 0.75
Parameter optimization in differential geometry based solvation models. J Chem Phys (2015) 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
Local spectral time-domain method for electromagnetic wave propagation. Opt Lett (2003) 1.85
Treatment of geometric singularities in implicit solvent models. J Chem Phys (2007) 1.85
Differential geometry based solvation model I: Eulerian formulation. J Comput Phys (2010) 1.74
Solvation and hydration of proteins and nucleic acids: a theoretical view of simulation and experiment. Acc Chem Res (2002) 1.69
Minimal molecular surfaces and their applications. J Comput Chem (2008) 1.57
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
Multiscale molecular dynamics using the matched interface and boundary method. J Comput Phys (2011) 1.39
Evolution and physics in comparative protein structure modeling. Acc Chem Res (2002) 1.29
Differential geometry based solvation model II: Lagrangian formulation. J Math Biol (2011) 1.27
Matched interface and boundary (MIB) for the implementation of boundary conditions in high-order central finite differences. Int J Numer Methods Eng (2009) 1.22
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
Molecular dynamics simulations of large integral membrane proteins with an implicit membrane model. J Phys Chem B (2006) 1.07
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
Variational approach for nonpolar solvation analysis. J Chem Phys (2012) 0.97
Evolution-operator-based single-step method for image processing. Int J Biomed Imaging (2006) 0.96
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
A correlation-based method for the enhancement of scoring functions on funnel-shaped energy landscapes. Proteins (2006) 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
Purification and characterization of the FeII- and alpha-ketoglutarate-dependent xanthine hydroxylase from Aspergillus nidulans. Biochemistry (2007) 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
Evidence that the Bacillus subtilis SpoIIGA protein is a novel type of signal-transducing aspartic protease. J Biol Chem (2008) 0.86
Base-flipping mechanism in postmismatch recognition by MutS. Biophys J (2011) 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
Molecular mechanism by which palmitate inhibits PKR autophosphorylation. Biochemistry (2011) 0.79
Effect of flanking residues on the conformational sampling of the internal fusion peptide from Ebola virus. Proteins (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
Substrate specificity of SpoIIGA, a signal-transducing aspartic protease in Bacilli. J Biochem (2011) 0.76
Molecular dynamics trajectory compression with a coarse-grained model. IEEE/ACM Trans Comput Biol Bioinform (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
Binding site multiplicity with fatty acid ligands: implications for the regulation of PKR kinase autophosphorylation with palmitate. Proteins (2014) 0.75
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
Phase synchronization between two essentially different chaotic systems. Phys Rev E Stat Nonlin Soft Matter Phys (2005) 0.75
Complete synchronization and generalized synchronization of one-way coupled time-delay systems. Phys Rev E Stat Nonlin Soft Matter Phys (2003) 0.75
Controllability of flow turbulence. Phys Rev E Stat Nonlin Soft Matter Phys (2004) 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
Lagrange wavelets for signal processing. IEEE Trans Image Process (2001) 0.75
Controlling wake turbulence. Phys Rev Lett (2002) 0.75
Bistable chaos without symmetry in generalized synchronization. Phys Rev E Stat Nonlin Soft Matter Phys (2005) 0.75
Crowding in Cellular Environments at an Atomistic Level from Computer Simulations. J Phys Chem B (2017) 0.75
Solvent electronic polarization effects on Na(+)-Na(+) and Cl(-)-Cl(-) pair associations in aqueous solution. J Phys Chem B (2013) 0.75
Integrating the Kuramoto-Sivashinsky equation in polar coordinates: application of the distributed approximating functional approach. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics (1999) 0.75
Transition from intermittency to periodicity in lag synchronization in coupled Rössler oscillators. Phys Rev E Stat Nonlin Soft Matter Phys (2002) 0.75