Performs molecular dynamics simulations and energy minimization. GROMACS provides a rich set of calculation types, preparation and analysis tools. It also distributes computational work across ensembles of simulations, multiple program paths and domains within simulations, multiple cores working on each domain, exploiting instruction-level parallelism across those cores handles wide classes of biomolecules, such as proteins, nucleic acids and lipids, and comes with all commonly used force fields for these molecules built-in.
Provides an approach for the generation of ligand images filling protein pockets based on deep neural networks. LigVoxel produces predictions that are responsive to the number of atoms selected as input. These predictions significantly overlap with ligand features of previously unseen ligands, and they can be used to select poses and conformers close to the native ligand orientation and geometry.
A molecular dynamics and modeling framework for the determination of the structure and dynamics of proteins and nucleic acids. Almost aims to provide support for a wide range of different structure determination protocols that make use of experimental observables as conformational restraints. To achieve its objectives, Almost has been designed with a flexible architecture, consisting of three application layers : (i) core data structures for the computational representation of molecules, (ii) core algorithms required for an efficient calculation of energies and interaction forces, (iii) methods and algorithms for the structural analysis and assessment of structures and trajectories.
Allows simulations of arbitrary mixtures of both rigid and flexible molecules. MDynaMix is a general purpose molecular dynamics simulation package that employs a double time step algorithm for fast and slow modes, an Ewald method for electrostatic interactions, and a constant temperature constant-pressure algorithm. The software was used in simulations of very different molecular systems.
Allows molecular simulation. CHARMM is a program that focuses on molecules of biological interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. The software offers a set of energy functions and several sampling methods. It has applications for many-particle systems, as well as for inorganic materials, with applications in materials design.
Constructs an atomic solvent environment model for a given atomic macromolecule model (solute). Solvate generates irregularly-shaped solvent volumes specifically adapted to the shape of the solute. The software performs the following steps: (i) reading in solute, (ii) creation of minimal convex volume, (iii) computation of an approximate density function, (iv) adjustment of boundary distance from solute, (v) creation of solvent volume, (vi) performing of distance approximation statistics, (vii) placing and grouping water molecules, and (viii) placing Hydrogens (and optionally ions).
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