Molecular Modeling and Simulation

LAMMPS

LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a software suite for classical molecular dynamics simulations developed and maintained by Sandia National Labs.

UCLUST

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

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.

QChem

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.

GROMACS

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. It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.

Discovery Studio

Discovery Studio® provides the most advanced software solutions for life science researchers available today. From project conception to lead optimization, Discovery Studio includes a diverse collection of sophisticated software applications to take your research to the next level, all conveniently packaged into a single, easy-to-use Linux- or Windows-based environment.

MN-GSM

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.

ChemBioOffice Ultra; ChemOffice; Chem Office; ChemDraw

This ultimate chemistry & biology suite is designed to meet the needs of both chemists and biologists. ChemBioOffice 2012 includes ChemBioDraw Ultra 13.0, ChemScript 13.0, ChemBio3D Ultra 13.0, Chem3D interfaces to Schrödingers Jaguar and Gaussian, ChemFinder Ultra 13.0, with support for Oracle, ChemBioFinder Ultra 13.0, E-Notebook 13.0, ChemDraw, as well as a collection of databases.

 

Dock

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. A compound that interacts strongly with, or binds, a receptor associated with a disease may inhibit its function and thus act as a drug. Solving the docking problem computationally requires an accurate representation of the molecular energetics as well as an efficient algorithm to search the potential binding modes.

Coot

The (Crystallographic Object)-Oriented Toolkit

Displays maps and models and allows certain model manipulations: idealization, real space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers, Ramachandran plots, model validation and other stuff.

Coot is part of the CCP4 Molecular Graphics Project. The Molecular Graphics Project has a wide remit and crystallographic map fitting is a part of that. The Coot functions have their own interface and some of them will be integrated into CCP4mg in due course.

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