We are using this famous software as driving horse for running calculations to study structures or reaction meachanisms. Available are proven ab-initio methods (HF, post HF methods, DFT) with various basis sets (for example Pople's basis sets, Dunning's correlation consistent basis sets) and semi-empirical methods in the gas phase or using solvation models. Some molecular mechanics force fields can be also applied (Dreiding, UFF, AMBER). ONIOM method is available for the partition of a large system and calculation of the various parts at different levels of theory, for example mixed QM/MM calculations. The software implements molecular dynamics methods, transition state optimization routines etc.
This software implements various quantum mechanical and molecular mechanics methods (MM+, Bio+, OPLS, AMBER). It is very useful because it includes a very friendly molecular modelling environment. A target model can be easily constructed and the program provides a variety of tools for the convenient manipulation of 3D structures (like changing chirality, reflection through planes, easy insertion of a variety of torsional constrains etc), the convenient model build of biological macromolecules (peptides, nucleotides) at a specific conformation (for example a-helix or beta-sheet, A-helix or B-helix form) etc. The molecular models can be optimized or simply used as input structures for calculations with GAUSSIAN software
This software implements the very useful and well established molecular mechanics force fields MM3, MMX, MMFF94, OPLSAA, AMBER. It includes various conformational analysis methods (scan analysis, GMMX, Metropolis Monte Carlo)
Far more than just a visualization program, Maestro also helps researchers organize and analyze data. Maestro's intuitive interface makes setting up calculations easy and straightforward. Computed results are automatically returned and incorporated into projects for further study. Maestro's vast array of visualization options makes it possible to glean insight into molecular properties as well as detailed intermolecular interactions. Maestro is a powerful and versatile molecular modeling environment, and the portal to the most advanced science in computational chemistry. MacroModel combines leading force fields, accurate effective solvation models, and advanced conformational searching methods to provide one of the most complete molecular modeling package suitable for a wide array of research
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems. We use it also extensively for analyzing trajectories and performing measures.
Desmond is a software package developed at D. E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems. 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. Desmond includes code optimized for machines with an NVIDIA GPU. We are using extensively this software for running: a) MD simulations on general-purpose supercomputers and GPUs and b) FEP/MD simulations .
Amber software is a set of molecular mechanical force fields for the simulation of biomolecules and a package of molecular simulation programs. We have used this program recently for running MM-PBSA calculations .
GOLD has won a lot of new users during the last few years because of its good results in impartial tests. Gold uses genetic algorithm to provide docking of flexible ligand and a protein with flexible hydroxyl groups. Otherwise the protein is considered to be rigid. Gold uses a scoring function that is based on favorable conformations found in Cambridge Structural Database and on empirical results on weak chemical interactions.
AUTODOCK uses Monte Carlo simulated annealing and Lamarckian genetic algorithm to create a set of possible conformations. LGA is used as a global optimizer and energy minimization as a local search method. Possible orientations are evaluated with AMBER force field model in conjunction with free energy scoring functions
VMD is used extensively in our lab for visualization, and analysis of biological systems.
PyMol is a comprehensive software package for rendering and animating 3D structures. PyMOL is a commercial product, but most of its source code is freely available under a permissive license. Open source enables open science. This was the vision of the original PyMOL author Warren L. DeLano.
UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated .
