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Standalone Software

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


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


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

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


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

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