CHARMM

MaRDI QIDQ18091swMATHFDO

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

Cited in

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• Interconnection networks for parallel molecular dynamics simulation based on Hamiltonian cubic symmetric topology
• The application of the genetic algorithm to the minimization of potential energy functions
• Continuum solvation model: Computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation
• Masking resonance artifacts in force-splitting methods for biomolecular simulations by extrapolative Langevin dynamics
• NAMD2: Greater scalability for parallel molecular dynamics
• Molecular dynamics simulation of membranes and a transmembrane helix
• Comparative protein structure modeling in genomics
• Optimization methods for computing global minima of nonconvex potential energy functions
• IMD
• TNPACK
• Dielectric properties of proteins from simulations: Tools and techniques
• The waters of life
• AMBER
• PEPS
• NAMD
• TINKER
• Gromacs
• WebMO
• A study of the wetting characteristics of a nano-sized water droplet on heterogeneous striped surfaces
• A hydrophobicity study on wavy and orthogonal textured surfaces
• Stable carbon configurations
• A fast mollified impulse method for biomolecular atomistic simulations
• An implicit boundary integral method for computing electric potential of macromolecules in solvent
• Tuning interval branch-and-prune for protein structure determination
• Characterization of optimal carbon nanotubes under stretching and validation of the Cauchy-Born rule
• An optimization approach to the problem of protein structure prediction
• Fractal and complex network analyses of protein molecular dynamics
• APBS
• A fast recursive algorithm for molecular dynamics simulation
• LAMMPS
• Mathematical approaches to biomolecular structure and dynamics. Proceedings of the 1994 IMA summer program on molecular biology
• DESMOND
• PetFMM
• Goal-oriented adaptivity and multilevel preconditioning for the Poisson-Boltzmann equation
• Biomolecular electrostatics using a fast multipole BEM on up to 512 GPUs and a billion unknowns
• PNFFT
• Performance of protein-ligand docking with CDK4/6 inhibitors: a case study
• DOCK
• UHBD
• SDA
• GROMOS
• MIBPB
• BioShape
• GANM
• DYANA
• BetaSCP
• Perseus
• AFMPB
• LINCS
• FFTSVD
• Fastcap
• CometG
• Biomolecular topology: modelling and analysis
• RAPTOR
• Modern methods and software systems of molecular modeling and application of behavior algebra
• DL_POLY
• DL_POLY_3
• BioProspector
• NAMD2
• AutoDock
• PyMOL
• BetaSCP2
• Atom-specific persistent homology and its application to protein flexibility analysis
• The de Rham-Hodge analysis and modeling of biomolecules
• Reliable computer simulation methods for electrostatic biomolecular models based on the Poisson-Boltzmann equation
• CYLWAVE
• Energy-momentum conserving integration schemes for molecular dynamics
• FEtk
• QUESO
• Qmd-plot
• On preconditioning the treecode-accelerated boundary integral (TABI) Poisson-Boltzmann solver
• TK
• Molecular dynamics. With deterministic and stochastic numerical methods
• Global optimization of protein-peptide docking by a filling function method
• Mobile localized solutions for an electron in lattices with dispersive and non-dispersive phonons
• BioSPI
• Computer modeling of binding of diverse weak toxins to nicotinic acetylcholine receptors
• A new FFT-based algorithm to compute Born radii in the generalized Born theory of biomolecule solvation
• PHG
• PacthDock
• VADAR
• GANM: A protein-ligand docking approach based on genetic algorithm and normal modes
• Virtual model validation of complex multiscale systems: applications to nonlinear elastostatics
• Complex dynamics of a pyranose ring structure molecule attached to an atomic force micro\-scope
• SETTLE
• A hidden Markov model with molecular mechanics energy-scoring function for transmembrane helix prediction
• TexMol
• PDB2PQR
• X-PLOR
• Fitting timeseries by continuous-time Markov chains: a quadratic programming approach
• Modal reduction of mathematical models of biological molecules
• MMG3D
• Poisson-Nernst-Planck equations for simulating biomolecular diffusion-reaction processes. I: Finite element solutions
• TMSmesh
• OVITO
• A Cartesian FMM-accelerated Galerkin boundary integral Poisson-Boltzmann solver
• Jmol
• Petri nets formalism facilitates analysis of complex biomolecular structural data
• The geometry of \(C_{60}\): a rigorous approach via molecular mechanics
• An overview on protein structure determination by NMR: historical and future perspectives of the use of distance geometry methods

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