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
|
|
| <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
|
| Name of Software
| Description
| Category
|
|
| <a href="http://ambermd.org/" target=new>AMBER</a>
| AMBER (Assisted Model Building and Energy Refinement) is the molecular dynamics software package that simulates the force fields.
| Classical force fields
|
| <a href="http://www.charmm.org/" target=new>CHARMM</a>
| CHARMM (Chemistry at HARvard Molecular Mechanics) is widely used package for molecular dynamics simulation and analysis force fields.
| Classical force fields
|
| <a href="http://www.gromacs.org/" target=new>GROMACS</a>
| GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics simulation package.
| Simulation
|
| <a href="http://dock.compbio.ucsf.edu/Overview_of_DOCK/index.htm" target=new>Dock</a>
| 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
|
| <a href="http://autodock.scripps.edu/" target=new>Autodock</a>
| Suite of automated docking tools
| Protein, ligand docking
|
| <a href="http://www.simbiosys.ca/ehits/index.html" target=new>eHiTS</a>
| 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
|
| <a href="http://salilab.org/modeller/" target=new>MODELLER</a>
| 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
|
| <a href="http://www.ddl.unimi.it/" target=new>VEGA ZZ</a>
| 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
|
| <a href="http://www.ddl.unimi.it/" target=new>AMMP VE</a>
| 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
|
| <a href="http://www.ddl.unimi.it/" target=new>GriDock</a>
| 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
|
| <a href="http://www.ddl.unimi.it/" target=new>ESCHER NG</a>
| ESCHER Next Generation (NG) is an enhanced version of the original ESCHER protein-protein automatic docking system.
| Protein-protein and DNA-protein molecular docking
|
| <a href="http://www.ddl.unimi.it/" target=new>ORAC 4</a>
| 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
|
| <a href="http://tripos.com/" target=new>SYBYL</a>
| SYBYL software for molecular modeling.
| Molecular modeling
|
| <a href="http://www.schrodinger.com/" target=new>Schrodinger</a>
| It is a Computational Chemistry Software which is used for molecular modelling and simulations.
| Molecular modelling
|
| <a href="http://www.sagemd.com/" target=new>SageMD</a>
| SageMD is the software package for the molecular dynamic simulation and a powerful, user friendly molecular visualization tool.
| Molecular dynamic simulation
|
| <a href="http://openmopac.net/" target=new>MOPAC</a>
| MOPAC (Molecular Orbital PACkage) is a semiempirical quantum chemistry program.
| QSAR
|
| <a href="http://www.biosolveit.de/FlexX/" target=new>FlexX</a>
| 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
|
| <a href="http://www.disat.unimib.it/chm/Dragon.htm" target=new>Dragon</a>
| 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
|
| <a href="http://www.igc.ethz.ch/GROMOS" target=new>GROMOS</a>
| GROMOS is a general-purpose molecular dynamics computer simulation package for the study of biomolecular systems.
| Simulation
|
| <a href="http://laetro.usc.edu/programs/index.html" target=new>MOLARIS</a>
| 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
|
| <a href="http://users.abo.fi/mivainio/balloon/" target=new>Balloon</a>
| Balloon creates 3D atomic coordinates from molecular connectivity via distance geometry and confomer ensembles using a multi-objective genetic algorithm.
| molecular mechanics
|
| <a href="http://dasher.wustl.edu/tinker/" target=new>TINKER</a>
| 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
|
| <a href="http://zarbi.chem.yale.edu/software.html#boss" target=new>BOSS</a>
| 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
|
| <a href="http://www.biomolecular-modeling.com/Ascalaph/Ascalaph_Graphics.html" target=new>Ascalaph Graphics</a>
| 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
|
| <a href="http://www.biomolecular-modeling.com/Ascalaph/Ascalaph_Quantum.html" target=new>Ascalaph Quantum</a>
| It is an interface for the quantum mechanics packages.
| Quantum mechanism
|
| <a href="http://www.biomolecular-modeling.com/Ascalaph/Ascalaph_Designer.html" target=new>Ascalaph Designer</a>
| It is a combines opportunities of Graphics and Quantum.
| Molecular graphics, Molecular model building, Geometry optimization, Quantum chemistry.
|
| <a href="http://www.biomolecular-modeling.com/Abalone/index.html" target=new>Abalone</a>
| It is a biomolecular modeling program.
| Molecular dynamics simulations
|
| <a href="http://sirius.sdsc.edu/" target=new>Sirius</a>
| 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
|
|
| <a href="http://pymol.org/" target=new>PyMOL</a>
| PyMOL is a USER-SPONSORED molecular visualization system on an OPEN-SOURCE foundation.
| Molecular modelling
|
| <a href="http://www.dnastar.com/qmol/" target=new>QMOL</a>
| Qmol is a program for viewing molecular structures and animating molecular trajectories.
| Molecular graphics
|
| <a href="http://www.rasmol.org/" target=new>RasMol</a>
| RasMol is a program for molecular graphics visualisation originally developed by Roger Sayle.
| Molecular graphics
|
| <a href="http://www.cgl.ucsf.edu/chimera/index.html" target=new>UCSF Chimera</a>
| 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
|
| <a href="http://www.ks.uiuc.edu/Research/vmd/" target=new>VMD</a>
| VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
| Molecular modelling
|
| <a href="http://www.yasara.org/index.html" target=new>YASARA</a>
| YASARA is a molecular-graphics, -modeling and -simulation program for Windows, Linux and Mac OS X
| Molecular-graphics, -modeling and -simulation
|
| <a href="http://srs3d.org/About/" target=new>SRS 3D</a>
| SRS 3D is a system for displaying 3D structures integrated with sequences and features.
| 3D Viewer
|
| <a href="http://www.avatar.se/molscript/" target=new>MolScript</a>
| MolScript is a program for displaying molecular 3D structures, such as proteins, in both schematic and detailed representations.
| Molecular visualization
|
| <a href="http://mgltools.scripps.edu/" target=new>MGLTools</a>
| 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
|
| <a href="http://birg.cs.wright.edu/pocketmol/pocketmol.html" target=new>PocketMol </a>
| 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
|
