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  • ADF

    The molecular ADF program can be applied to gas phase molecules, solvated molecules, and molecules in protein environments. It can treat all elements of the periodic table, and contains state-of-the-art relativistic methods (ZORA and spin-orbit coupling) to treat heavy nuclei.

  • AMBER. Assisted Model Building with Energy Refinement.

  • A suite of programs that analyze the quality of biomolecular structures determined via NMR spectroscopy. AQUA was initially developed by Ton Rullmann and Jurgen Doreleijersb Bijvoet Center for Biomolecular Research, Utrecht, The Netherlands.

  • 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.
  • The Cambridge Structural Database (CSD) is the the largest searchable database of experimentally determined crystal structures and is maintained by the the Cambridge Crystallographic Data Center (CCDC).
  • 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.
  • The (Crystallographic Object)-Oriented Toolkit

  • 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.

  • Gaussian performs semiempirical and ab initio molecular orbital (MO), density functional, and molecular mechanics calculations.

  • GaussView is an advanced graphical user interface designed to be used with Gaussian to make calculations easier, quicker, and more efficient. The GaussView interface features include easy Gaussian calculation set up and three dimensional molecular modeling

  • 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.

  • MN-GSM (Minnesota Gaussian Solvation Module) is a module for incorporation of the SMx solvation models and other enhancements into the GAUSSIAN03 code.The executables for this software are only available to MSI users who are staff or students at the University of Minnesota.

  • MODELLER is used for homology or comparative modeling of protein three-dimensional structures. The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms.

  • 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.
  • Molden is a visualization package for viewing the molecular density, molecular orbitals, electron density, chemical structure, etc., from the output files of GAMESS, Gaussian, and MOPAC/AMPAC calculations.With the use of the z-matrix editor initial guesses can be created for input files.

  • Molekel is an advanced interactive 3D-graphics package for molecular sciences. It is a molecular graphics package for visualizing molecular and electronic structure data from the output of various chemistry applications (GAUSSIAN 94/98, GAMESS-US, ADF and many others).

  • MolMol - MOLecule analysis and MOLecule display

  • MolScript is a program for creating schematic or detailed molecular graphics images from molecular 3D coordinates, usually, but not exclusively, protein structures.

  • 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.

  • NWChem provides many methods to compute the properties of molecular and periodic systems by using standard quantum mechanical descriptions of the electronic wave function or density. In addition, NWChem has the capability to perform classical molecular dynamics and free energy simulations.

  • PyMOL is a Python-enhanced molecular graphics program. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. It also has a number of third party plugins available.

  • Q-Chem is a comprehensive ab initio quantum chemistry package. Its capabilities range from the highest performance DFT/HF calculations to high level post-HF correlation methods.

  • Schrödinger provides a complete suite of software solutions with the latest advances in pharmaceutical research and computational chemistry.
  • 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.

  • UCLUST: An exceptionally fast sequence clustering program for nucleotide and protein sequences

  • VMD

    VMD - Visual Molecular Dynamics

  • Xaim is a X11 Motif graphical user interface to several programs based on some aspects of the Theory of Atoms in Molecules developed by Prof. R.F.W. Bader and coworkers.