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.
Performs multi-criteria drug design. Sybyl-X provides a complete drug and molecular design environment with comprehensive tools for molecular modelling. This suite includes small molecule and macromolecular modelling and simulation, cheminformatics, lead identification and lead optimization. It permits to identify leads using ligand-based or structure-based virtual screening, and chemical library design.
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 users to generate light, heat, or therapeutic radiation. LAMMPS is a classical molecular dynamics (MD) code that models ensembles of particles in a liquid, solid, or gaseous state. It can model atomic, polymeric, biological, solid-state, granular, coarse-grained, or macroscopic systems using a variety of interatomic potentials and boundary conditions.
An integrated drug discovery software. MOE is able to track design ideas and ligand modifications with property models, produce correlation plots to visualize Structure, Property, Activity Relationships and visualize hydrophobic and charged protein surface to study aggregation prone regions. It can also automatically align and superpose antibody structures using the MOE Project protocol, generate and search advanced antibody queries with the Project Search application and build full length Ig structures including bispecifics with the Antibody Homology Modeler.