CHARMM
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Cited in
(only showing first 100 items - show all)- A fast recursive algorithm for molecular dynamics simulation
- Dielectric properties of proteins from simulations: Tools and techniques
- The waters of life
- 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
- 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
- An overview on protein structure determination by NMR: historical and future perspectives of the use of distance geometry methods
- A Random Batch Ewald Method for Particle Systems with Coulomb Interactions
- Metadynamics study of mutant human interferon-gamma forms
- A parallel Monte Carlo search algorithm for the conformational analysis of polypeptides
- 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
- 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
- Molecular nonlinear dynamics and protein thermal uncertainty quantification
- Mathematical approaches to biomolecular structure and dynamics. Proceedings of the 1994 IMA summer program on molecular biology
- Virtual model validation of complex multiscale systems: applications to nonlinear elastostatics
- A penalty function method for constrained molecular dynamics simulation
- 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
- Analytic evaluation of the gradient and Hessian of molecular potential energy functions
- Progress in developing Poisson-Boltzmann equation solvers
- On preconditioning the treecode-accelerated boundary integral (TABI) Poisson-Boltzmann solver
- An implicit boundary integral method for computing electric potential of macromolecules in solvent
- 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
- scientific article; zbMATH DE number 5049189 (Why is no real title available?)
- Masking resonance artifacts in force-splitting methods for biomolecular simulations by extrapolative Langevin dynamics
- scientific article; zbMATH DE number 956624 (Why is no real title available?)
- New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecular electrostatics
- 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
- 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
- Parameter estimation for partially observed hypoelliptic diffusions
- Molecular dynamics. With deterministic and stochastic numerical methods
- An optimization approach to the problem of protein structure prediction
- NAMD2: Greater scalability for parallel molecular dynamics
- Optimization methods for computing global minima of nonconvex potential energy functions
- Fluctuating charge force fields: recent developments and applications from small molecules to macromolecular biological systems
- Carbon-nanotube geometries as optimal configurations
- Reliable computer simulation methods for electrostatic biomolecular models based on the Poisson-Boltzmann equation
- Comparative protein structure modeling in genomics
- Molecular dynamics simulation of peeling a DNA molecule on substrate
- IMD
- TNPACK
- AMBER
- NAMD
- PEPS
- Gromacs
- TINKER
- WebMO
- APBS
- LAMMPS
- DESMOND
- PetFMM
- PNFFT
- DOCK
- GROMOS
- MIBPB
- SDA
- BioShape
- GANM
- DYANA
- UHBD
- BetaSCP
- AFMPB
- FFTSVD
- CometG
- Perseus
- Fastcap
- LINCS
- DL_POLY
- DL_POLY_3
- RAPTOR
- BioProspector
- AutoDock
- NAMD2
- BetaSCP2
- PyMOL
- CYLWAVE
- FEtk
- QUESO
- Qmd-plot
- BioSPI
- TK
- PHG
- PacthDock
- VADAR
- SETTLE
- PDB2PQR
- TexMol
- X-PLOR
- MMG3D
- OVITO
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