Dynamics detection software tools | Protein structure data analysis
Protein dynamics has been described to be the time-dependent changes in the structure of a protein, which includes equilibrium fluctuations governing biological function. The internal deformations of protein structures have been used successfully to describe components of these time-dependent fluctuations.
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.
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.
Enables molecular dynamics simulations of biomolecular systems. NAMD has been designed to permit continuous software development in view of ever-changing technologies, to utilize parallel computers of any size effectively via message driven computation, to run well on platforms from laptops and desktops to parallel computers with thousands of processors. The most essential feature is Tool Command Language scripting capability, which has been used to implement, e.g., replica exchange dynamics, adaptive biasing forces, and advanced phase space sampling protocols.
Supplies a platform able to visualize, model and analyze molecular structures. Discovery Studio® Visualizer can handle macromolecules, small molecules, sequences, X-ray reflection data, scripts, and more. It includes a wide range of features such as ligand-based, structure-based and macromolecular design, and functionalities for sharing information between users and visualizing the results through Microsoft Office or web pages.
Provides numerous programs that work together to setup, perform, and analyze molecular dynamics (MD) simulations. AMBER is a biomolecular simulation package which also contains software designed to parameterize more complex molecules and fragments not currently present in the force field libraries. The suite can be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models.
Allows macromolecular constrains of all bonds. P-LINCS is a standard constraint algorithm which is only used for water molecules. It provides an efficient solver for the matrix equation, a velocity correction that prevents rotational lengthening and a length correction that improves accuracy and stability. It is used for application to a leap-frog or Verlet-type algorithm for molecular dynamics.
Allows the modeling of ring structures, with an application to cholesterol. MARTINI is a program designed for performing biomolecular simulations. The key feature of its model is its systematic parametrization based on thermodynamic data, especially experimental partitioning data.