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  • AMBER. Assisted Model Building with Energy Refinement.

  • AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.
  • CHARMm (Chemistry at HARvard Molecular Mechanics) is the academic version of the CHARMM simulation program available through Harvard. CHARMm uses empirical energy functions to describe the forces on atoms in molecules.
  • This ultimate chemistry & biology suite is designed to meet the needs of both chemists and biologists.
  • Desmond is a software package developed at D. E. Shaw research to perform high-speed molecular dynamics simulations of biological systems on conventional commodity clusters.
  • Discovery Studio® provides the most advanced software solutions for life science researchers available today.

  • DOCK addresses the problem of "docking" molecules to each other. In general, "docking" is the identification of the low-energy binding modes of a small molecule, or ligand, within the active site of a macromolecule, or receptor, whose structure is known.

  • GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

  • The structure determination of protein-protein complexes is a rather tedious and lengthy process, both by NMR and X-ray crystallography. Several methods based on docking to study protein complexes have been well developed over the past few years.

  • MS Modeling is Materials Studio's modeling and simulation product suite, and is designed for structural and computational researchers in chemicals and materials R&D who need to perform expert-level modeling and simulations tasks in an easy to learn yet powerful environment.

  • MOE
    The Molecular Operating Environment (MOE) is the next generation of chemical computing software. MOE is an integrated Applications Environment and Methodology Development Platform. MOE integrates visualization, simulation and application development in one package.
  • NAMD, recipient of a 2002 Gordon Bell Award, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.  Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms.

  • SAS

    SAS is a scalable, integrated software environment and a flexible and extensible programming language designed for data access, data manipulation, and data analysis. It offers data management and predictive analytic capabilities, data mining process, drug discovery solutions, and much more.

  • Schrödinger provides a complete suite of software solutions with the latest advances in pharmaceutical research and computational chemistry.
  • Pipeline Pilot, Accelrys' scientific informatics platform, was designed for scientists by scientists.
  • The SYBYL expert molecular modeling environment provides the fundamental components for understanding molecular structure and properties with special focus on the creation of new chemical entities.