CHARMM

swMATH5953MaRDI QIDQ18091FDOQ18091

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Cited In (only showing first 100 items - show all)

• A fast recursive algorithm for molecular dynamics simulation
• Computational and theoretical modeling of intermediate filament networks: structure, mechanics and disease
• Convergence analysis of truncated incomplete Hessian Newton minimization method and application in biomolecular potential energy minimization
• A parallel Monte Carlo search algorithm for the conformational analysis of polypeptides
• Metadynamics study of mutant human interferon-gamma forms
• Fractal and complex network analyses of protein molecular dynamics
• Fast analysis of molecular dynamics trajectories with graphics processing units -- radial distribution function histogramming
• Determination of protein structure and dynamics combining immune algorithms and pattern search methods
• Molecular nonlinear dynamics and protein thermal uncertainty quantification
• The de Rham-Hodge analysis and modeling of biomolecules
• Fitting timeseries by continuous-time Markov chains: a quadratic programming approach
• Mathematical approaches to biomolecular structure and dynamics. Proceedings of the 1994 IMA summer program on molecular biology
• BetaSCP2: A Program for the Optimal Prediction of Side-Chains in Proteins
• Virtual model validation of complex multiscale systems: applications to nonlinear elastostatics
• PetFMM-A dynamically load-balancing parallel fast multipole library
• Analyzing effects of naturally occurring missense mutations
• Membrane protein stability analyses by means of protein energy profiles in case of nephrogenic diabetes insipidus
• Molecular dynamics simulation of membranes and a transmembrane helix
• Molecular dynamics simulations of tubulin structure and calculations of electrostatic properties of microtubules
• Progress in developing Poisson-Boltzmann equation solvers
• Analytic evaluation of the gradient and Hessian of molecular potential energy functions
• Title not available (Why is that?)
• Comparison of the Ewald and Wolf methods for modeling electrostatic interactions in nanowires
• Fast Molecular Solvation Energetics and Forces Computation
• The application of the genetic algorithm to the minimization of potential energy functions
• Masking resonance artifacts in force-splitting methods for biomolecular simulations by extrapolative Langevin dynamics
• An Overview on Protein Structure Determination by NMR: Historical and Future Perspectives of the use of Distance Geometry Methods
• New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecular electrostatics
• Efficient implementation of the many-body reactive bond order (REBO) potential on GPU
• Molecular dynamics. With deterministic and stochastic numerical methods
• An optimization approach to the problem of protein structure prediction
• Fluctuating charge force fields: recent developments and applications from small molecules to macromolecular biological systems
• NAMD2: Greater scalability for parallel molecular dynamics
• Optimization methods for computing global minima of nonconvex potential energy functions
• DelPhi Web Server: A Comprehensive Online Suite for Electrostatic Calculations of Biological Macromolecules and Their Complexes
• Reliable computer simulation methods for electrostatic biomolecular models based on the Poisson-Boltzmann equation
• DelEnsembleElec: Computing Ensemble-Averaged Electrostatics Using DelPhi
• Molecular dynamics simulation of peeling a DNA molecule on substrate
• A hydrophobicity study on wavy and orthogonal textured surfaces
• Stable carbon configurations
• A topological approach for protein classification
• A computational framework for transverse compression of microtubules based on a higher-order Cauchy-Born rule
• Goal-oriented adaptivity and multilevel preconditioning for the Poisson-Boltzmann equation
• Interconnection networks for parallel molecular dynamics simulation based on Hamiltonian cubic symmetric topology
• Complex dynamics of a pyranose ring structure molecule attached to an atomic force micro\-scope
• A new class of hybrid global optimization algorithms for peptide structure prediction: integrated hybrids
• Atomistic-based continuum constitutive relation for microtubules: elastic modulus prediction
• A program for performing exact quantum dynamics calculations using cylindrical polar coordinates: a nanotube application
• A new Poisson-Nernst-Planck model with ion-water interactions for charge transport in ion channels
• A Bayesian framework for adaptive selection, calibration, and validation of coarse-grained models of atomistic systems
• Decoding transcriptional regulatory interactions
• Multiscale molecular dynamics using the matched interface and boundary method
• Continuum solvation model: Computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation
• Global optimization of protein-peptide docking by a filling function method
• Discriminate protein decoys from native by using a scoring function based on ubiquitous phi and psi angles computed for all atom
• Parameter Estimation for Partially Observed Hypoelliptic Diffusions
• Modeling and computation of heterogeneous implicit solvent and its applications for biomolecules
• The geometry of \(C_{60}\): a rigorous approach via molecular mechanics
• Biomolecular electrostatics using a fast multipole BEM on up to 512 GPUs and a billion unknowns
• Protein structure optimization by side-chain positioning via beta-complex
• Coarse grained normal mode analysis vs. refined Gaussian network model for protein residue-level structural fluctuations
• Modal reduction of mathematical models of biological molecules
• Hydrophobic and ionic-interactions in bulk and confined water with implications for collapse and folding of proteins
• A new boundary integral equation for molecular electrostatics with charges over whole space
• Energy-momentum conserving integration schemes for molecular dynamics
• The General Utility Lattice Program (<scp>GULP</scp>)
• Tuning interval branch-and-prune for protein structure determination
• Carbon-Nanotube Geometries as Optimal Configurations
• Poisson-Nernst-Planck equations for simulating biomolecular diffusion-reaction processes. I: Finite element solutions
• Dielectric properties of proteins from simulations: Tools and techniques
• The waters of life
• Computer modeling of binding of diverse weak toxins to nicotinic acetylcholine receptors
• Modern methods and software systems of molecular modeling and application of behavior algebra
• Computational Physics
• A Random Batch Ewald Method for Particle Systems with Coulomb Interactions
• A Linear Scaling in Accuracy Numerical Method for Computing the Electrostatic Forces in the $N$-Body Dielectric Spheres Problem
• GANM: A protein-ligand docking approach based on genetic algorithm and normal modes
• On preconditioning the treecode-accelerated boundary integral (TABI) Poisson-Boltzmann solver
• An implicit boundary integral method for computing electric potential of macromolecules in solvent
• Finite Element Modeling of Biomolecular Systems in Ionic Solution
• Title not available (Why is that?)
• Characterization of optimal carbon nanotubes under stretching and validation of the Cauchy-Born rule
• Bone Remodelling in BioShape
• Mobile localized solutions for an electron in lattices with dispersive and non-dispersive phonons
• A study of the wetting characteristics of a nano-sized water droplet on heterogeneous striped surfaces
• Title not available (Why is that?)
• Comparative protein structure modeling in genomics
• Petri nets formalism facilitates analysis of complex biomolecular structural data
• Modeling and computation of heterogeneous implicit solvent and its applications for biomolecules
• Large-scale molecular dynamics simulation of DNA: implementation and validation of the AMBER98 force field in LAMMPS
• A new FFT-based algorithm to compute Born radii in the generalized Born theory of biomolecule solvation
• A fast mollified impulse method for biomolecular atomistic simulations
• A hidden Markov model with molecular mechanics energy-scoring function for transmembrane helix prediction
• Atom-specific persistent homology and its application to protein flexibility analysis
• A Cartesian FMM-accelerated Galerkin boundary integral Poisson-Boltzmann solver
• Title not available (Why is that?)
• DL_POLY_2 adaptations for solvation studies
• A stochastic solver of the generalized Born model
• Analysis of fast boundary-integral approximations for modeling electrostatic contributions of molecular binding
• The solution of the boundary-value problems for the simulation of transition of protein confor\-mation

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