Biologics, Molecular Dynamics and Small Molecule Docking
Amber | AMBER (Assisted Model Building with Energy Refinement) is a set of molecular mechanical
force fields for the simulation of biomolecules and a package of molecular simulation
programs which includes source code and demos. Installed versions include Amber 12
and 14. Amber is built to run on the CPUs (optionally via MPI) and GPUs (single and multiple). In addition a specially built version of Amber 14 has been implemented, in-house, that incorporates the accelerated RaMD-db originally developed by Donald Hamelberg at Emory. Developer Website Amber on Gemini |
Compound Libraries | Small molecule chemical compound libraries are available for large scale in-silico docking. Currently there are over 5.9 million compounds in our database. The eMolecules database as well as all FDA approved drugs are available. |
Desmond | 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.
The code uses novel parallel algorithms and numerical techniques to achieve high performance
and accuracy on platforms containing a large number of processors, but may also be
executed on a single computer. Developer Website |
Schrodinger Suite | The Schrodinger software suite consists of a number of applications comprised of small-molecule
lead discovery and optimization, quantum mechanics, homology modeling, protein analysis,
protein-protein docking, ligand docking and antibody modeling tools. Developer Website Schrodinger on Gemini |
TINKER | The TINKER molecular modeling software is a complete and general package for molecular
mechanics and dynamics, with some special features for biopolymers. TINKER has the
ability to use any of several common parameter sets, such as Amber (ff94, ff96, ff98,
ff99, ff99SB), CHARMM (19, 22, 22/CMAP), Allinger MM (MM2-1991 and MM3-2000), OPLS
(OPLS-UA, OPLS-AA), Merck Molecular Force Field (MMFF), Liam Dang's polarizable model,
and the AMOEBA (2004, 2009, 2013) polarizable atomic multipole force field. Parameter
sets for other widely-used force fields are under consideration for future releases. Developer Site |