| Name of Software
| Description
| Category
|
|
AMBER
| AMBER (Assisted Model Building and Energy Refinement) is the molecular dynamics software package that simulates the force fields.
| Classical force fields
|
|
CHARMM
| CHARMM (Chemistry at HARvard Molecular Mechanics) is widely used package for molecular dynamics simulation and analysis force fields.
| Classical force fields
|
|
GROMACS
| GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics simulation package.
| Simulation
|
|
Dock
| Dock is a software for 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.
| Molecular docking
|
|
Autodock
| Suite of automated docking tools
| Protein, ligand docking
|
|
MODELLER
| MODELLER is a computer program used in producing homology models of protein tertiary structures as well as quaternary structures.
| Homology modelling of protein tertiary structures
|
|
SYBYL
| SYBYL software for molecular modeling.
| Molecular modeling
|
|
Schrodinger
| It is a Computational Chemistry Software which is used for molecular modelling and simulations.
| Molecular modelling
|
|
SageMD
| SageMD is the software package for the molecular dynamic simulation and a powerful, user friendly molecular visualization tool.
| Molecular dynamic simulation
|
|
MOPAC
| MOPAC (Molecular Orbital PACkage) is a semiempirical quantum chemistry program.
| QSAR
|
|
FlexX
| Fast Flexible Docking Software, FlexX accurately predicts the geometry of the protein-ligand complex, it also used for Virtual high-throughput screening (vHTS).
| Docking Software
|
|
Balloon
| Balloon creates 3D atomic coordinates from molecular connectivity via distance geometry and confomer ensembles using a multi-objective genetic algorithm.
| Molecular mechanics
|
|
TINKER
| The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers.
| Molecular mechanics and dynamics
|
|
BOSS
| BOSS (Biochemical and Organic Simulation System). The BOSS program is a general purpose molecular modeling system that performs molecular mechanics (MM) calculations, Metropolis Monte Carlo (MC) statistical mechanics simulations, and semiempirical AM1, PM3, and PDDG/PM3 quantum mechanics (QM) calculations.
| Molecular modeling
|
|
Ascalaph Graphics
| It is a program for molecular graphics and dynamics, as well as a graphical shell to package of molecular dynamics MDynaMix.
| Molecular graphics and dynamics
|
|
Abalone
| It is a biomolecular modeling program.
| Molecular dynamics simulations
|
|
Autodock Vina
| It is a Monte Carlo based docking software.
| Molecular dynamics simulations
|
|
BetaDock
| It solve the docking problem by putting priority on shape complementarity between receptor and ligand.
| Genetic Algorithm based docking software for docking small molecules.
|
|
DAIM
| It is based on two-dimensional structures of small molecules for fragment-based high-throughput docking.
| Fragment based docking suite.
|
|
DockoMatic
| DockoMatic is a GUI application that is intended to ease and automate the creation and management of AutoDock jobs for high throughput screening of ligand/receptor interactions.
| Molecular dynamics simulations
|
|
FITTED 1.0
| It is a suite of programs to perform flexible protein-ligands docking.
| Flexibility Induced Through Targeted Evolutionary Description.
|
|
Fleksy
| It is a program for flexible and induced fit docking.
| Ensemble-based soft-docking experiment using FlexX-Ensemble
|
|
FLIPDock
| FLIPDock is a molecular docking program that docks a flexible ligand to a flexible receptor. FLIPDock uses two FlexTree data structures to represent a protein-ligand complex.
| Genetic algorithm based software to performs flexible protein-ligand docking
|
|
GalaxyDock
| GalaxyDock GalaxyDock is a protein-ligand docking program that allows flexibility of pre-selected side-chains of ligand using Conformational Space Annealing.
| Molecular dynamics simulations
|
|
GEMDOCK
| GEMDOCK is a program for computing a ligand conformation and orientation relative to the active site of target protein.
| Generic Evolutionary Method for molecular docking.
|
|
GlamDock
| It is a Monte Carlo based docking software.
| Molecular dynamics simulation.
|
|
HYBRID
| The HYBRID program uses the information present in both the structure of the protein and the bound ligand to enhance docking performance..
| Molecular dynamics simulations.
|
|
ParaDockS
| It performs docking for small drug-like molecules to a rigid receptor .
| Framework for molecular docking with population-based metaheuristics
|
|
PLANTS
| It is a ACO-based search engine for flexible protein side chains.
| Stochastic optimization algorithms called ant colony optimization
|
|
Surflex-Dock
| It is a docking software.
| Docking program based on active site of target to generate putative poses of molecules.
|
|
VinaMPI
| MPI-Vina is an open-source parallelization of AutoDock Vina, which massively reduces the time of virtual screening by using compute clusters or network of computers.
| Autodock Vina based
|
|
MDPocket
| MPI-Vina is an open-source software for the prediction of protein cavities and characterization on molecular dynamics trajectories.
| Based on Voronoi tessellation algorithm
|
|
MolSite
| myPresto is a program suite composed of several molecular simulations for drug development..
| Molecular dynamics simulation based
|