CHARMM
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Modeling and computation of heterogeneous implicit solvent and its applications for biomolecules ⋮ Modeling and computation of heterogeneous implicit solvent and its applications for biomolecules ⋮ Unnamed Item ⋮ Atomistic-based continuum constitutive relation for microtubules: elastic modulus prediction ⋮ Computer modeling of binding of diverse weak toxins to nicotinic acetylcholine receptors ⋮ Unnamed Item ⋮ A new FFT-based algorithm to compute Born radii in the generalized Born theory of biomolecule solvation ⋮ The General Utility Lattice Program (<scp>GULP</scp>) ⋮ Poisson-Nernst-Planck equations for simulating biomolecular diffusion-reaction processes. I: Finite element solutions ⋮ A study of the wetting characteristics of a nano-sized water droplet on heterogeneous striped surfaces ⋮ A topological approach for protein classification ⋮ A hydrophobicity study on wavy and orthogonal textured surfaces ⋮ Decoding transcriptional regulatory interactions ⋮ A new Poisson-Nernst-Planck model with ion-water interactions for charge transport in ion channels ⋮ New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecular electrostatics ⋮ A Bayesian framework for adaptive selection, calibration, and validation of coarse-grained models of atomistic systems ⋮ Unnamed Item ⋮ 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 ⋮ A program for performing exact quantum dynamics calculations using cylindrical polar coordinates: a nanotube application ⋮ Analytic evaluation of the gradient and Hessian of molecular potential energy functions ⋮ Dielectric properties of proteins from simulations: Tools and techniques ⋮ Determination of protein structure and dynamics combining immune algorithms and pattern search methods ⋮ Stable carbon configurations ⋮ Molecular dynamics simulation of peeling a DNA molecule on substrate ⋮ Atom-specific persistent homology and its application to protein flexibility analysis ⋮ The waters of life ⋮ Goal-oriented adaptivity and multilevel preconditioning for the Poisson-Boltzmann equation ⋮ DelEnsembleElec: Computing Ensemble-Averaged Electrostatics Using DelPhi ⋮ DelPhi Web Server: A Comprehensive Online Suite for Electrostatic Calculations of Biological Macromolecules and Their Complexes ⋮ A fast mollified impulse method for biomolecular atomistic simulations ⋮ Computational and theoretical modeling of intermediate filament networks: structure, mechanics and disease ⋮ Molecular nonlinear dynamics and protein thermal uncertainty quantification ⋮ Multiscale molecular dynamics using the matched interface and boundary method ⋮ The de Rham-Hodge analysis and modeling of biomolecules ⋮ Computational Physics ⋮ A Cartesian FMM-accelerated Galerkin boundary integral Poisson-Boltzmann solver ⋮ Biomolecular electrostatics using a fast multipole BEM on up to 512 GPUs and a billion unknowns ⋮ Carbon-Nanotube Geometries as Optimal Configurations ⋮ Membrane protein stability analyses by means of protein energy profiles in case of nephrogenic diabetes insipidus ⋮ Analyzing effects of naturally occurring missense mutations ⋮ An implicit boundary integral method for computing electric potential of macromolecules in solvent ⋮ Reliable computer simulation methods for electrostatic biomolecular models based on the Poisson-Boltzmann equation ⋮ GANM: A protein-ligand docking approach based on genetic algorithm and normal modes ⋮ A computational framework for transverse compression of microtubules based on a higher-order Cauchy-Born rule ⋮ Virtual model validation of complex multiscale systems: applications to nonlinear elastostatics ⋮ 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 ⋮ Complex dynamics of a pyranose ring structure molecule attached to an atomic force micro\-scope ⋮ Parameter Estimation for Partially Observed Hypoelliptic Diffusions ⋮ Performance of protein-ligand docking with CDK4/6 inhibitors: a case study ⋮ Bone Remodelling in BioShape ⋮ Energy-momentum conserving integration schemes for molecular dynamics ⋮ PetFMM-A dynamically load-balancing parallel fast multipole library ⋮ DL_POLY_2 adaptations for solvation studies ⋮ A Linear Scaling in Accuracy Numerical Method for Computing the Electrostatic Forces in the $N$-Body Dielectric Spheres Problem ⋮ Tuning interval branch-and-prune for protein structure determination ⋮ Characterization of optimal carbon nanotubes under stretching and validation of the Cauchy-Born rule ⋮ Metadynamics study of mutant human interferon-gamma forms ⋮ Convergence analysis of truncated incomplete Hessian Newton minimization method and application in biomolecular potential energy minimization ⋮ The application of the genetic algorithm to the minimization of potential energy functions ⋮ An optimization approach to the problem of protein structure prediction ⋮ Fast analysis of molecular dynamics trajectories with graphics processing units -- radial distribution function histogramming ⋮ A parallel Monte Carlo search algorithm for the conformational analysis of polypeptides ⋮ A hidden Markov model with molecular mechanics energy-scoring function for transmembrane helix prediction ⋮ A new class of hybrid global optimization algorithms for peptide structure prediction: integrated hybrids ⋮ Unnamed Item ⋮ Fractal and complex network analyses of protein molecular dynamics ⋮ Finite Element Modeling of Biomolecular Systems in Ionic Solution ⋮ Fitting timeseries by continuous-time Markov chains: a quadratic programming approach ⋮ Efficient implementation of the many-body reactive bond order (REBO) potential on GPU ⋮ Comparison of the Ewald and Wolf methods for modeling electrostatic interactions in nanowires ⋮ Fast Molecular Solvation Energetics and Forces Computation ⋮ Petri nets formalism facilitates analysis of complex biomolecular structural data ⋮ Discriminate protein decoys from native by using a scoring function based on ubiquitous phi and psi angles computed for all atom ⋮ A fast recursive algorithm for molecular dynamics simulation ⋮ Large-scale molecular dynamics simulation of DNA: implementation and validation of the AMBER98 force field in LAMMPS ⋮ Mathematical approaches to biomolecular structure and dynamics. Proceedings of the 1994 IMA summer program on molecular biology ⋮ The Geometry of $C_{60}$: A Rigorous Approach via Molecular Mechanics ⋮ On preconditioning the treecode-accelerated boundary integral (TABI) Poisson-Boltzmann solver ⋮ Interconnection networks for parallel molecular dynamics simulation based on Hamiltonian cubic symmetric topology ⋮ Fluctuating charge force fields: recent developments and applications from small molecules to macromolecular biological systems ⋮ An Overview on Protein Structure Determination by NMR: Historical and Future Perspectives of the use of Distance Geometry Methods ⋮ Continuum solvation model: Computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation ⋮ Modal reduction of mathematical models of biological molecules ⋮ A Random Batch Ewald Method for Particle Systems with Coulomb Interactions ⋮ Molecular dynamics. With deterministic and stochastic numerical methods ⋮ 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 ⋮ Biomolecular topology: modelling and analysis ⋮ Global optimization of protein-peptide docking by a filling function method ⋮ Progress in developing Poisson-Boltzmann equation solvers ⋮ A Stochastic Solver of the Generalized Born Model ⋮ Analysis of fast boundary-integral approximations for modeling electrostatic contributions of molecular binding ⋮ Modern methods and software systems of molecular modeling and application of behavior algebra ⋮ Unnamed Item ⋮ Optimization methods for computing global minima of nonconvex potential energy functions ⋮ Molecular dynamics simulations of tubulin structure and calculations of electrostatic properties of microtubules ⋮ BetaSCP2: A Program for the Optimal Prediction of Side-Chains in Proteins ⋮ Mobile localized solutions for an electron in lattices with dispersive and non-dispersive phonons
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