CHARMM
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Software:18091
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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