Standalone Software

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This page provides link to various standalone softwares in the filed related to protein structure prediction, docking, modelling and Structure visualization.  
This page provides link to various standalone softwares in the filed related to protein structure prediction, docking, modelling and Structure visualization.  
</p><br><br><h2> Standalone softwares related to protein structure analysis</h2>
</p><br><br><h2> Standalone softwares related to protein structure analysis</h2>
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| 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.
| 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
| Solvent Accessible Area Calculations
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|}<h2> Force field, molecular modeling, docking and Simulation related standalone software </h2>
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{|  align='center' border='3'
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| &nbsp;&nbsp; <font color='#04B4AE' size='5'>Name of Software</font>
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|  &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<font color='#04B4AE' size='5'>Description
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| &nbsp;&nbsp; <font color='#04B4AE' size='5'>Category</font>
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| <a href="http://ambermd.org/" target=new>AMBER</a>
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| AMBER (Assisted Model Building and Energy Refinement) is the molecular dynamics software package that simulates the force fields.
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| Classical force fields
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| <a href="http://www.charmm.org/" target=new>CHARMM</a>
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| CHARMM (Chemistry at HARvard Molecular Mechanics) is widely used package for molecular dynamics simulation and analysis force fields.
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| Classical force fields
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| <a href="http://www.gromacs.org/" target=new>GROMACS</a>
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| GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics simulation package.
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| Simulation
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| <a href="http://dock.compbio.ucsf.edu/Overview_of_DOCK/index.htm" target=new>Dock</a>
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| 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.
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| Molecular docking
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| <a href="http://autodock.scripps.edu/" target=new>Autodock</a>
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| Suite of automated docking tools
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| Protein, ligand docking
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| <a href="http://www.simbiosys.ca/ehits/index.html" target=new>eHiTS</a>
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| 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.
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| Flexible ligand docking tool
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| <a href="http://salilab.org/modeller/" target=new>MODELLER</a>
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| MODELLER is a computer program used in producing homology models of protein tertiary structures as well as quaternary structures.
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| Homology modelling of protein tertiary structures
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| <a href="http://www.ddl.unimi.it/" target=new>VEGA ZZ</a>
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| VEGA ZZ is the well known VEGA OpenGL package for the molecular software packages.This software is FREE for non-profit academic uses.
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| Molecular Modeling software
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| <a href="http://www.ddl.unimi.it/" target=new>AMMP VE</a>
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| 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.
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| Molecular Mechanics
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| <a href="http://www.ddl.unimi.it/" target=new>GriDock</a>
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| 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.
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| Molecular dockings
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| <a href="http://www.ddl.unimi.it/" target=new>ESCHER NG</a>
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| ESCHER Next Generation (NG) is an enhanced version of the original ESCHER protein-protein automatic docking system.
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| Protein-protein and DNA-protein molecular docking
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| <a href="http://www.ddl.unimi.it/" target=new>ORAC 4</a>
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| It is a program for running classical simulations of biomolecules. Simulations can be carried out in the NVE, NPT, NHP, and NVT thermodynamic ensembles.
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| Molecular dynamics
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| <a href="http://tripos.com/" target=new>SYBYL</a>
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| SYBYL software for molecular modeling.
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| Molecular modeling
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| <a href="http://www.schrodinger.com/" target=new>Schrodinger</a>
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| It is a Computational Chemistry Software which is used for molecular modelling and simulations.
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| Molecular modelling
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| <a href="http://www.sagemd.com/" target=new>SageMD</a>
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| SageMD is the software package for the molecular dynamic simulation and a powerful, user friendly molecular visualization tool.
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| Molecular dynamic simulation
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| <a href="http://openmopac.net/" target=new>MOPAC</a>
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| MOPAC (Molecular Orbital PACkage) is a semiempirical quantum chemistry program.
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| QSAR
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| <a href="http://www.biosolveit.de/FlexX/" target=new>FlexX</a>
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| Fast Flexible Docking Software, FlexX accurately predicts the geometry of the protein-ligand complex, it also used for Virtual high-throughput screening (vHTS).
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| Docking Software
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| <a href="http://www.disat.unimib.it/chm/Dragon.htm" target=new>Dragon</a>
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| 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.
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| Calculation of molecular descriptors
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| <a href="http://www.igc.ethz.ch/GROMOS" target=new>GROMOS</a>
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| GROMOS is a general-purpose molecular dynamics computer simulation package for the study of biomolecular systems.
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| Simulation
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| <a href="http://laetro.usc.edu/programs/index.html" target=new>MOLARIS</a>
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| 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.
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| Simulation program
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| <a href="http://users.abo.fi/mivainio/balloon/" target=new>Balloon</a>
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| Balloon creates 3D atomic coordinates from molecular connectivity via distance geometry and confomer ensembles using a multi-objective genetic algorithm.
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| molecular mechanics
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| <a href="http://dasher.wustl.edu/tinker/" target=new>TINKER</a>
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| The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers.
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| Molecular mechanics and dynamics
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| <a href="http://zarbi.chem.yale.edu/software.html#boss" target=new>BOSS</a>
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| 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.
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| Molecular modeling
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| <a href="http://www.biomolecular-modeling.com/Ascalaph/Ascalaph_Graphics.html" target=new>Ascalaph Graphics</a>
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| It is a program for molecular graphics and dynamics, as well as a graphical shell to package of molecular dynamics MDynaMix.
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| Molecular graphics and dynamics
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| <a href="http://www.biomolecular-modeling.com/Ascalaph/Ascalaph_Quantum.html" target=new>Ascalaph Quantum</a>
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| It is an interface for the quantum mechanics packages.
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| Quantum mechanism
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| <a href="http://www.biomolecular-modeling.com/Ascalaph/Ascalaph_Designer.html" target=new>Ascalaph Designer</a>
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| It is a combines opportunities of Graphics and Quantum.
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| Molecular graphics, Molecular model building, Geometry optimization, Quantum chemistry.
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| <a href="http://www.biomolecular-modeling.com/Abalone/index.html" target=new>Abalone</a>
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| It is a biomolecular modeling program.
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| Molecular dynamics simulations
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| <a href="http://sirius.sdsc.edu/" target=new>Sirius</a>
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| 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.
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| Molecular modelling
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|}<h2> Standalone software of Structure visualization </h2>
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{|  align='center' border='3'
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| &nbsp;&nbsp; <font color='#04B4AE' size='5'>Name of Software</font>
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|  &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<font color='#04B4AE' size='5'>Description
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| &nbsp;&nbsp; <font color='#04B4AE' size='5'>Category</font>
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| <a href="http://pymol.org/" target=new>PyMOL</a>
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| PyMOL is a USER-SPONSORED molecular visualization system on an OPEN-SOURCE foundation.
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| Molecular modelling
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| <a href="http://www.dnastar.com/qmol/" target=new>QMOL</a>
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| Qmol is a program for viewing molecular structures and animating molecular trajectories.
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| Molecular graphics
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| <a href="http://www.rasmol.org/" target=new>RasMol</a>
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| RasMol is a program for molecular graphics visualisation originally developed by Roger Sayle.
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| Molecular graphics
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| <a href="http://www.cgl.ucsf.edu/chimera/index.html" target=new>UCSF Chimera</a>
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| 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.
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| Molecular modelling
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| <a href="http://www.ks.uiuc.edu/Research/vmd/" target=new>VMD</a>
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| VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
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| Molecular modelling
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| <a href="http://www.yasara.org/index.html" target=new>YASARA</a>
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| YASARA is a molecular-graphics, -modeling and -simulation program for Windows, Linux and Mac OS X
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| Molecular-graphics, -modeling and -simulation
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| <a href="http://srs3d.org/About/" target=new>SRS 3D</a>
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| SRS 3D is a system for displaying 3D structures integrated with sequences and features.
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| 3D Viewer
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| <a href="http://www.avatar.se/molscript/" target=new>MolScript</a>
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| MolScript is a program for displaying molecular 3D structures, such as proteins, in both schematic and detailed representations.
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| Molecular visualization
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| <a href="http://mgltools.scripps.edu/" target=new>MGLTools</a>
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| MGLTools is a software developed at the Molecular Graphics Laboratory (MGL) of The Scripps Research Institute for visualization and analysis of molecular structures.
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| Molecular visualization
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| <a href="http://birg.cs.wright.edu/pocketmol/pocketmol.html" target=new>PocketMol </a>
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| 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.
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| Molecular Visualization
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Revision as of 18:49, 24 October 2011

This page provides link to various standalone softwares in the filed related to protein structure prediction, docking, modelling and Structure visualization.

</p>

Standalone softwares related to protein structure analysis

   Name of Software                         Description    Category
<a href="http://bip.weizmann.ac.il/oca-bin/lpccsu" target=new>LPC</a> Analysis of interatomic Contacts in Ligand-Protein complexes. Analysis Ligand-Protein interaction
<a href="http://bip.weizmann.ac.il/oca-bin/lpccsu" target=new>CSU</a> Analysis of interatomic contacts in protein entries. Analysis of interatomic contacts in protein.
<a href="http://www.msi.umn.edu/software/promotif/" target=new>PROMOTIF</a> 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
<a href="http://fpocket.sourceforge.net/" target=new>fpocket</a> fpocket is a very fast open source protein pocket (cavity) detection algorithm based on Voronoi tessellation. Protein pocket (cavity) detection
<a href="http://www.ebi.ac.uk/thornton-srv/software/PROCHECK/" target=new>Procheck</a> 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
<a href="http://swift.cmbi.kun.nl/gv/dssp/" target=new>DSSP</a> The DSSP is software to standardize secondary structure assignment. Protein secondary structure
<a href="http://globin.bio.warwick.ac.uk/psipred" target=new>Psipred</a> Psipred is a protein structure prediction software. Protein secondary structure
<a href="http://www.bioinf.manchester.ac.uk/naccess/" target=new>Naccess</a> 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

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