CHARMM

swMATH5953MaRDI QIDQ18091FDOQ18091

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Official website: http://www.charmm.org/

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
• An overview on protein structure determination by NMR: historical and future perspectives of the use of distance geometry methods
• 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
• Virtual model validation of complex multiscale systems: applications to nonlinear elastostatics
• 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
• Comparison of the Ewald and Wolf methods for modeling electrostatic interactions in nanowires
• 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
• New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecular electrostatics
• Parameter estimation for partially observed hypoelliptic diffusions
• Molecular dynamics. With deterministic and stochastic numerical methods
• Fluctuating charge force fields: recent developments and applications from small molecules to macromolecular biological systems
• Carbon-nanotube geometries as optimal configurations
• NAMD2: Greater scalability for parallel molecular dynamics
• Optimization methods for computing global minima of nonconvex potential energy functions
• Molecular dynamics simulation of peeling a DNA molecule on substrate
• A topological approach for protein classification
• IMD
• TNPACK
• AMBER
• A computational framework for transverse compression of microtubules based on a higher-order Cauchy-Born rule
• DOCK
• Goal-oriented adaptivity and multilevel preconditioning for the Poisson-Boltzmann equation
• AFMPB
• FFTSVD
• CometG
• LINCS
• RAPTOR
• BioProspector
• NAMD2
• SETTLE
• PDB2PQR
• TexMol
• mCSM
• PoPMuSiC
• ARIA
• HOOMD-blue
• MLAPM
• MMM2D
• OpenMM
• CHARMM-GUI
• Apbsmem
• SCWRL4
• RASPA
• PatchDock
• A new class of hybrid global optimization algorithms for peptide structure prediction: integrated hybrids
• Atomistic-based continuum constitutive relation for microtubules: elastic modulus prediction
• JPred
• MLMOD
• QTFier
• 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
• Discriminate protein decoys from native by using a scoring function based on ubiquitous phi and psi angles computed for all atom
• Modeling and computation of heterogeneous implicit solvent and its applications for biomolecules
• 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
• PetFMM -- a dynamically load-balancing parallel fast multipole library
• The General Utility Lattice Program (<scp>GULP</scp>)
• BetaSCP2: a program for the optimal prediction of side-chains in proteins
• DelPhi web server: A comprehensive online suite for electrostatic calculations of biological macromolecules and their complexes
• Tuning interval branch-and-prune for protein structure determination
• DelEnsembleElec: computing ensemble-averaged electrostatics using DelPhi
• Poisson-Nernst-Planck equations for simulating biomolecular diffusion-reaction processes. I: Finite element solutions
• Fast molecular solvation energetics and forces computation
• 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
• A Random Batch Ewald Method for Particle Systems with Coulomb Interactions
• A parallel Monte Carlo search algorithm for the conformational analysis of polypeptides
• 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
• GANM: A protein-ligand docking approach based on genetic algorithm and normal modes
• 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
• A penalty function method for constrained molecular dynamics simulation
• Title not available (Why is that?)
• On preconditioning the treecode-accelerated boundary integral (TABI) Poisson-Boltzmann solver
• An implicit boundary integral method for computing electric potential of macromolecules in solvent
• Title not available (Why is that?)
• Characterization of optimal carbon nanotubes under stretching and validation of the Cauchy-Born rule
• Efficient implementation of the many-body reactive bond order (REBO) potential on GPU

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