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.
Identifies high affinity interaction spots over macromolecular systems by means of molecular dynamics simulations using solvent mixtures as solvation conditions. pyMDMix is a python module and a user interface that aims to ease the application of such technique. It allows an easy set up of several simulations for the same system under different conditions: solvent, temperature, restraining schemes, etc. Moreover, after simulations are done, many analysis tools will help to quality check and extract useful information from these simulations in a aqueous-organic environments.
Allows users to analyze and display trajectories from all kinds of molecular dynamics or Monte Carlo simulations. TRAVIS is an open source application with the aim of grouping several analyses in one program for evaluating simulations. This program can simulate a trajectory with wannier centers, compute IR or Raman spectra It requires a standard molecular dynamics (MD) trajectory for working.
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.
Increases the robustness reliability and reproducibility of molecular simulations. physical_validation consists of a two-fold approach allowing the test of physical validity. It can find subtle differences in the consistency of a programming code with Newton’s equations of motion caused by different cutoff schemes for Lennard-Jones interactions. This tool supports a number of simulation packages such as GROMACS, LAMMPS, HOOMD or GROMOS.
Performs statistical chain tracing by identifying connected alpha-carbon positions using a likelihood-based density target. Buccaneer is an application based on an automated technique for plotting protein chains in experimental electron density maps. It incorporates, in particular, the use of an oriented electron density probability target function to identify probable Cα positions. This method can also be used for low resolutions.
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.
Creates a standardized computational process. RUNER aims to enhance the reproducibility in molecular modeling of small molecules. This software serves as computational pipeline that manages the consistency of model definition across computational molecular modeling stages. It enables modifications and verified maintenance of atom force field parameters Its outputs contain the atom specific topology and force field parameters necessary for performing molecular modeling on the compound by Amber, CHARMM, and Xplor-NIH.
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).
Performs electronic structure modeling. Gaussian analyzes any real-world chemical problems of interest. It can be used for both stable species and compounds which are difficult or impossible to observe experimentally, whether due to their nature or their inherent fleeting nature. This tool allows users to verify that the predicted stationary points are in fact minima or transition structure.