Published in J Chem Phys on March 01, 2004
Classical electrostatics for biomolecular simulations. Chem Rev (2013) 1.00
Towards an accurate representation of electrostatics in classical force fields: efficient implementation of multipolar interactions in biomolecular simulations. J Chem Phys (2004) 2.32
Differential transactivation by the p53 transcription factor is highly dependent on p53 level and promoter target sequence. Mol Cell Biol (2002) 1.83
Calculation of protein-ligand binding free energy by using a polarizable potential. Proc Natl Acad Sci U S A (2008) 1.75
NMDA receptor activation by HIV-Tat protein is clade dependent. J Neurosci (2008) 1.74
Simulation of Ca2+ and Mg2+ solvation using polarizable atomic multipole potential. J Phys Chem B (2006) 1.73
Towards a force field based on density fitting. J Chem Phys (2006) 1.70
Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure. J Chem Phys (2006) 1.69
Anisotropic, Polarizable Molecular Mechanics Studies of Inter- and Intramolecular Interactions and Ligand-Macromolecule Complexes. A Bottom-Up Strategy. J Chem Theory Comput (2007) 1.58
Intermolecular electrostatic energies using density fitting. J Chem Phys (2005) 1.42
Generalization of the Gaussian electrostatic model: extension to arbitrary angular momentum, distributed multipoles, and speedup with reciprocal space methods. J Chem Phys (2006) 1.34
Molecular dynamics simulations of the d(CCAACGTTGG)(2) decamer in crystal environment: comparison of atomic point-charge, extra-point, and polarizable force fields. J Chem Phys (2004) 1.33
Microscope-based techniques to study cell adhesion and migration. Nat Cell Biol (2002) 1.18
Differential roles for STIM1 and STIM2 in store-operated calcium entry in rat neurons. PLoS One (2011) 1.17
Staggered Mesh Ewald: An extension of the Smooth Particle-Mesh Ewald method adding great versatility. J Chem Theory Comput (2009) 1.16
Adaptively biased molecular dynamics for free energy calculations. J Chem Phys (2008) 1.07
Crystal structure of beta 1,3-glucuronyltransferase I in complex with active donor substrate UDP-GlcUA. J Biol Chem (2002) 1.05
Glucosaminylglycan biosynthesis: what we can learn from the X-ray crystal structures of glycosyltransferases GlcAT1 and EXTL2. Biochem Biophys Res Commun (2003) 1.05
Conformations and free energy landscapes of polyproline peptides. Proc Natl Acad Sci U S A (2009) 1.03
Gaussian Multipole Model (GMM). J Chem Theory Comput (2010) 1.02
Molecular dynamics simulations of DNA with polarizable force fields: convergence of an ideal B-DNA structure to the crystallographic structure. J Phys Chem B (2006) 1.01
Identification of a specific motif of the DSS1 protein required for proteasome interaction and p53 protein degradation. J Mol Biol (2008) 0.98
Reaction mechanism of the epsilon subunit of E. coli DNA polymerase III: insights into active site metal coordination and catalytically significant residues. J Am Chem Soc (2009) 0.95
Reaction path ensemble of the B-Z-DNA transition: a comprehensive atomistic study. Nucleic Acids Res (2012) 0.95
The free energy landscape of small peptides as obtained from metadynamics with umbrella sampling corrections. J Chem Phys (2006) 0.93
Surface solvation for an ion in a water cluster. J Chem Phys (2005) 0.92
Numerical fitting of molecular properties to Hermite Gaussians. J Phys Chem A (2007) 0.91
Quantum mechanics/molecular mechanics electrostatic embedding with continuous and discrete functions. J Phys Chem B (2006) 0.90
A statistical analysis of the PPII propensity of amino acid guests in proline-rich peptides. Biophys J (2011) 0.90
A classical molecular dynamics investigation of the free energy and structure of short polyproline conformers. J Chem Phys (2010) 0.89
Presenilin-dependent expression of STIM proteins and dysregulation of capacitative Ca2+ entry in familial Alzheimer's disease. Biochim Biophys Acta (2008) 0.89
Ab initio investigations of lithium diffusion in carbon nanotube systems. Phys Rev Lett (2002) 0.88
Predicted solution structure of zymogen human coagulation FVII. J Comput Chem (2002) 0.86
PPII propensity of multiple-guest amino acids in a proline-rich environment. J Phys Chem B (2011) 0.85
Mapping the dimer interface in the C-terminal domains of the yeast MLH1-PMS1 heterodimer. Biochemistry (2006) 0.83
S/G-1: an ab initio force-field blending frozen Hermite Gaussian densities and distributed multipoles. Proof of concept and first applications to metal cations. J Phys Chem A (2014) 0.82
Dynamical scaling exponents for polymer translocation through a nanopore. Phys Rev E Stat Nonlin Soft Matter Phys (2008) 0.81
Are long-range structural correlations behind the aggregration phenomena of polyglutamine diseases? PLoS Comput Biol (2012) 0.81
The α-sheet: a missing-in-action secondary structure? Proteins (2011) 0.80
Deprotonation of solvated formic acid: Car-Parrinello and metadynamics simulations. J Phys Chem B (2006) 0.80
P2Y1 nucleotide receptor silencing and its effect on glioma C6 calcium signaling. Acta Biochim Pol (2012) 0.77
P2Y(1) and P2Y(12) receptor cross-talk in calcium signalling: Evidence from nonstarved and long-term serum-deprived glioma C6 cells. Purinergic Signal (2007) 0.77
Structural determination of large molecules through the reassembly of optimized fragments. J Mol Graph Model (2008) 0.77
Structural characterization of the conformational change in calbindin-D28k upon calcium binding using differential surface modification analyzed by mass spectrometry. Biochemistry (2009) 0.77
DNAtraffic--a new database for systems biology of DNA dynamics during the cell life. Nucleic Acids Res (2011) 0.77
Self-assembled patterns and strain-induced instabilities for modulated systems. Phys Rev E Stat Nonlin Soft Matter Phys (2005) 0.76
Defective calcium release during in vitro fertilization of maturing oocytes of LT/Sv mice. Int J Dev Biol (2008) 0.76
Recipes for free energy calculations in biomolecular systems. Methods Mol Biol (2013) 0.76
Picosecond melting of peptide nanotubes using an infrared laser: a nonequilibrium simulation study. Phys Chem Chem Phys (2015) 0.75
Quantum simulations of the structure and binding of glycopeptide antibiotic aglycons to cell wall analogues. J Phys Chem B (2005) 0.75
Regulation of subcellular localization of muscle FBPase in cardiomyocytes. The decisive role of calcium ions. Acta Biochim Pol (2010) 0.75
First principles investigation of vancomycin and teicoplanin binding to bacterial cell wall termini. J Am Chem Soc (2004) 0.75
New and exotic self-organized patterns for modulated nanoscale systems. Nano Lett (2005) 0.75
Three-dimensional solution structure of Tropidechis carinatus venom extract trocarin: a structural homologue of Xa and prothrombin activator. J Mol Model (2002) 0.75