VMD (Visual Molecular Dynamics) is a molecular visualization program used to display and analyze molecular structures. Used together with NAMD, VMD can also simulate molecular interactions. It is available for download here, and is supported by all major computer platforms.
Autodock 4 is a molecular docking program used to predict how small molecules, such as drug candidates or enzyme substrates, will interact with a receptor of known 3D-structure. Molecular docking simulations help researchers to screen potential drugs for efficacy against a target protein of choice, and to tailor molecules to better fit a receptor’s binding pocket. For academic research, you can download Autodock here.
Autodock Vina is an open-source program used for molecular docking simulations. It is cited as a significant improvement over the original Autodock 4 in efficiency, binding mode prediction accuracy, and user-friendliness. Autodock Vina is available as a free download for multiple operating systems.
Learn more about molecular docking here.
NAMD (Nanoscale Molecular Dynamics, formerly Not Another Molecular Dynamics program) is a suite of computer software used for molecular dynamics simulations. It was written using the Charm++ parallel programming model, and can be used to simulate large molecular systems. NAMD is used in conjunction with VMD to analyze and visualize interactions between molecules, or other forms of molecular movement.
You can find tutorials for NAMD and its related applications here.
Cactvs is a powerful scripting toolkit and suite of chemoinformatics software. Created by researchers at Xemistry, the cactvs toolkit is useful for substructure matching, in silico reactions, and other forms of computational chemistry. To fully access its diverse functionality, refer to its Tcl manual.
If you are conducting academic research, you may download the core cactvs toolkit for academic and educational use. You can find the latest releases for most operating systems here.
SMILES and SMARTS
Virtually every procedure that uses a digital representation of a molecule, from drug design to analytical chemistry, utilizes substructure searching and a coding language to represent molecules and their properties to a computer. SMILES and SMARTS encode complex chemical structures into a computationally-readable format. Pioneered by Daylight Chemical Information Systems, these languages allow computers to correctly analyze a chemical structure for various applications, such as in silico reaction chemistry.
SMILES (Simplified Molecular Input Line Entry System) is a line notation (typographical method) for representing chemical structures and reactions to a computer.
SMARTS allows a researcher to specify molecular substructures via an extension of the SMILES language rules. Used together, SMILES and SMARTS enable chemists, biologists, and programmers to perform flexible and efficient procedures necessary for computational chemistry.
For a complete documentation of SMILES and SMARTS theory, see the Daylight Theory manual.