Standalone Software
From DrugPedia: A Wikipedia for Drug discovery
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[http://swift.cmbi.kun.nl/gv/dssp/ DSSP] | [http://swift.cmbi.kun.nl/gv/dssp/ DSSP] | ||
| The DSSP is software to standardize secondary structure assignment. | | The DSSP is software to standardize secondary structure assignment. | ||
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| Protein secondary structure | | Protein secondary structure | ||
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Revision as of 04:00, 25 October 2011
Standalone Software |
This page provides link to various standalone softwares in the filed related to protein structure prediction, docking, modelling and Structure visualization.
Standalone softwares related to protein structure analysis
| Name of Software | Description | Category | |
| Analysis of interatomic Contacts in Ligand-Protein complexes. | Analysis Ligand-Protein interaction | ||
| Analysis of interatomic contacts in protein entries. | Analysis of interatomic contacts in protein. | ||
| 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 is a very fast open source protein pocket (cavity) detection algorithm based on Voronoi tessellation. | Protein pocket (cavity) detection | ||
| 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 | ||
| The DSSP is software to standardize secondary structure assignment. | Protein secondary structure | ||
| 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 |
Force field, molecular modeling, docking and Simulation related standalone software
| Name of Software | Description | Category | |
| AMBER (Assisted Model Building and Energy Refinement) is the molecular dynamics software package that simulates the force fields. | Classical force fields | ||
| CHARMM (Chemistry at HARvard Molecular Mechanics) is widely used package for molecular dynamics simulation and analysis force fields. | Classical force fields | ||
| GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics simulation package. | Simulation | ||
| 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 | ||
| Suite of automated docking tools | Protein, ligand docking | ||
| 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 is a computer program used in producing homology models of protein tertiary structures as well as quaternary structures. | Homology modelling of protein tertiary structures | ||
| 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 | ||
| 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 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 Next Generation (NG) is an enhanced version of the original ESCHER protein-protein automatic docking system. | Protein-protein and DNA-protein molecular docking | ||
| 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 software for molecular modeling. | Molecular modeling | ||
| It is a Computational Chemistry Software which is used for molecular modelling and simulations. | Molecular modelling | ||
| SageMD is the software package for the molecular dynamic simulation and a powerful, user friendly molecular visualization tool. | Molecular dynamic simulation | ||
| MOPAC (Molecular Orbital PACkage) is a semiempirical quantum chemistry program. | QSAR | ||
| 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 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 | ||
| GROMOS is a general-purpose molecular dynamics computer simulation package for the study of biomolecular systems. | Simulation | ||
| 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 creates 3D atomic coordinates from molecular connectivity via distance geometry and confomer ensembles using a multi-objective genetic algorithm. | molecular mechanics | ||
| 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 (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 | ||
| 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 | ||
| It is an interface for the quantum mechanics packages. | Quantum mechanism | ||
| It is a combines opportunities of Graphics and Quantum. | Molecular graphics, Molecular model building, Geometry optimization, Quantum chemistry. | ||
| It is a biomolecular modeling program. | Molecular dynamics simulations | ||
| 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 |
Standalone software of Structure visualization
| Name of Software | Description | Category | |
| PyMOL is a USER-SPONSORED molecular visualization system on an OPEN-SOURCE foundation. | Molecular modelling | ||
| Qmol is a program for viewing molecular structures and animating molecular trajectories. | Molecular graphics | ||
| RasMol is a program for molecular graphics visualisation originally developed by Roger Sayle. | Molecular graphics | ||
| 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 is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. | Molecular modelling | ||
| YASARA is a molecular-graphics, -modeling and -simulation program for Windows, Linux and Mac OS X | Molecular-graphics, -modeling and -simulation | ||
| SRS 3D is a system for displaying 3D structures integrated with sequences and features. | 3D Viewer | ||
| MolScript is a program for displaying molecular 3D structures, such as proteins, in both schematic and detailed representations. | Molecular visualization | ||
| 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 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 |
