| Name of Software
| Description
| Category
|
|
|
LPC
| Analysis of interatomic Contacts in Ligand-Protein complexes.
| Analysis Ligand-Protein interaction
|
|
CSU
| Analysis of interatomic contacts in protein entries.
| Analysis of interatomic contacts in protein.
|
|
PROMOTIF
| PROMOTIF provides details of the location and types of structural motifs in proteins of known structure by analysis of Brookhaven format coordinate files.
| Analyses protein structural motifs
|
|
fpocket
| fpocket is a very fast open source protein pocket (cavity) detection algorithm based on Voronoi tessellation.
| Protein pocket (cavity) detection
|
|
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
|
|
eHiTS
| The eHiTS (electronic High Throughput Screening) software used for performing accurate flexible ligand docking at speed approaching the crude VHTS (virtual high throughput screening methods) methods.
| Flexible ligand docking tool
|
|
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
|
|
HMMER3
| HMMER3 is a new generation of homology search tools based on probabilistic inference. HMMER3 implements a new probabilistic model of local sequence alignment and a new heuristic acceleration algorithm.
| Homology search tools
|
|
Procheck
| PROCHECK checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry.
| Stereochemical analysis
|
|
VEGA ZZ
| VEGA ZZ is the well known VEGA OpenGL package for the molecular software packages.This software is FREE for non-profit academic uses.
| Molecular Modeling software
|
|
AMMP VE
| It is a modern full-featured molecular mechanics, dynamics and modelling program. It can manipulate both small molecules and macromolecules including proteins, nucleic acids and other polymers.
| Molecular Mechanics
|
|
GriDock
| GriDock was designed to perform the molecular dockings of a large number of ligands stored in a single database (SDF or Zip format) in the lowest possible time.
| Molecular dockings
|
|
ESCHER NG
| ESCHER Next Generation (NG) is an enhanced version of the original ESCHER protein-protein automatic docking system.
| Protein-protein and DNA-protein molecular docking
|
|
ORAC 4
| It is a program for running classical simulations of biomolecules. Simulations can be carried out in the NVE, NPT, NHP, and NVT thermodynamic ensembles.
| Molecular dynamics
|
|
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
|
|
Dragon
| Dragon is software which is able to calculate 1481 molecular descriptors. These descriptors can be used to evaluate molecular structure-activity or structure-property relationships, as well as for similarity analysis and high-throughput screening of molecule databases.
| Calculation of molecular descriptors
|
|
DSSP
| The DSSP is software to standardize secondary structure assignment.
| Protein secondary structure
|
| 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
|
|
GROMOS
| GROMOS is a general-purpose molecular dynamics computer simulation package for the study of biomolecular systems.
| Simulation
|
|
MOLARIS
| MOLARIS includes powerful programs POLARIS and ENZYMIX in a unique package. ENZYMIX is a macromolecular simulation program designed to study the functions of proteins ranging from ligand binding to free energy and POLARIS is a fast converging computational software based on the Protein Dipoles-Langevin Dipoles (PDLD) approach.
| Simulation program
|
|
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
|
|
Ascalaph Quantum
| It is an interface for the quantum mechanics packages.
| Quantum mechanism
|
|
Ascalaph Designer
| It is a combines opportunities of Graphics and Quantum.
| Molecular graphics, Molecular model building, Geometry optimization, Quantum chemistry.
|
|
Abalone
| It is a biomolecular modeling program.
| Molecular dynamics simulations
|
