This page provides link to various standalone softwares in the filed related to protein structure prediction, docking, modelling and Structure visualization.
| 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
|
|
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
|
|
DSSP
| The DSSP is software to standardize secondary structure assignment.
| Protein secondary structure
|
|
Naccess
| Naccess is a stand alone program that calculates the accessible area of a molecule from a PDB (Protein Data Bank) format file. It can calculate the atomic and residue accessiblities for both proteins and nucleic acids.
| Solvent Accessible Area Calculations
|
| 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
|
|
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
|
|
[
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
|
|
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
|
|
Abalone
| It is a biomolecular modeling program.
| Molecular dynamics simulations
|
|
Sirius
| Sirius is a component-based visualization framework designed for application in molecular modeling, drug discovery, protein structure analysis, as well as database mining and sequence-based work.
| Molecular modelling
|
| Name of Software
| Description
| Category
|
|
|
PyMOL
| PyMOL is a USER-SPONSORED molecular visualization system on an OPEN-SOURCE foundation.
| Molecular modelling
|
|
QMOL
| Qmol is a program for viewing molecular structures and animating molecular trajectories.
| Molecular graphics
|
|
RasMol
| RasMol is a program for molecular graphics visualisation originally developed by Roger Sayle.
| Molecular graphics
|
|
UCSF Chimera
| 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.
| Molecular modelling
|
|
VMD
| VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
| Molecular modelling
|
|
YASARA
| YASARA is a molecular-graphics, -modeling and -simulation program for Windows, Linux and Mac OS X
| Molecular-graphics, -modeling and -simulation
|
|
SRS 3D
| SRS 3D is a system for displaying 3D structures integrated with sequences and features.
| 3D Viewer
|
|
MolScript
| MolScript is a program for displaying molecular 3D structures, such as proteins, in both schematic and detailed representations.
| Molecular visualization
|
|
MGLTools
| MGLTools is a software developed at the Molecular Graphics Laboratory (MGL) of The Scripps Research Institute for visualization and analysis of molecular structures.
| Molecular visualization
|
|
PocketMol
| PocketMol allows you to view and manipulate Protein Data Bank (pdb) files on a PocketPC. Manipulation includes moving, scaling, and rotating a protein using the stylus. Individual atoms can be selected to view their properties.
| Molecular Visualization
|
