Standalone Software

Standalone softwares related to protein structure analysis

Name of Software Description Category


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


Surfnet detects the clefts present on the protein surface. Protein pocket (cavity) detection


Software detects the active sites present on the protein surface. Protein active site detection


Software utilizes energy aspects for finding binding pockets on the protein surface. Protein binding site 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


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


AcconPred is a software package that helps predicting solvent accessibility and contact number of a protein simultaneously. The method is based on a shared weight multi-task learning framework under a novel Conditional Neural Field (CNF) model. Solvent Accessible Area Calculations and prediction.


NetSurfP is a software package that predicts secondary structure and protein surface accessibility. Secondary Structure and Protein Surface Accessibility Prediction.


SANN is a software that predicts solvent accessibility using nearest neighbor method. Solvent Accessibility Prediction.


RNAmap2D is a tool for calculation of contacts and distance maps based on criteria given by user. It also compares pairs or series of contact maps. Structural analysis


ProTSAV ia a meta server which evaluates the quality of a protein and the correctness of the structural model. Structural analysis


KVFinder, a highly versatile and easy-to-use tool for cavity prospection and spatial characterization. Structural analysis

AlloPred uses normal mode analysis and pocket features to predict allosteric pockets on proteins. Structural analysis


MSPocket is an orientation independent program for the detection and graphical analysis of protein surface pockets. The approach is based on the solvent excluded surfaces generated by MSMS

ProTSAV ia a server for determining pocket shape and volume characteristics. Based on POVME algorithm for measuring binding pocket volume

ProTSAV ia a server for predicting protein ligand binding sites. Based on Random forest algorithm.

DrosteP is a tool to evaluate the conservation of pockets detected on the protein surface by CastP. Structural analysis

PocketAnnotate is a pipeline for the annotation of proteins at the level of binding sites. Structural analysis functional annotation

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


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


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

Autodock Vina

It is a Monte Carlo based docking software. Molecular dynamics simulations


It solve the docking problem by putting priority on shape complementarity between receptor and ligand. Genetic Algorithm based docking software for docking small molecules.


It is based on two-dimensional structures of small molecules for fragment-based high-throughput docking. Fragment based docking suite.


DockoMatic is a GUI application that is intended to ease and automate the creation and management of AutoDock jobs for high throughput screening of ligand/receptor interactions. Molecular dynamics simulations


It is a suite of programs to perform flexible protein-ligands docking. Flexibility Induced Through Targeted Evolutionary Description.


It is a program for flexible and induced fit docking. Ensemble-based soft-docking experiment using FlexX-Ensemble


FLIPDock is a molecular docking program that docks a flexible ligand to a flexible receptor. FLIPDock uses two FlexTree data structures to represent a protein-ligand complex. Genetic algorithm based software to performs flexible protein-ligand docking


GalaxyDock GalaxyDock is a protein-ligand docking program that allows flexibility of pre-selected side-chains of ligand using Conformational Space Annealing. Molecular dynamics simulations


GEMDOCK is a program for computing a ligand conformation and orientation relative to the active site of target protein. Generic Evolutionary Method for molecular docking.


It is a Monte Carlo based docking software. Molecular dynamics simulation.


The HYBRID program uses the information present in both the structure of the protein and the bound ligand to enhance docking performance.. Molecular dynamics simulations.


It performs docking for small drug-like molecules to a rigid receptor . Framework for molecular docking with population-based metaheuristics


It is a ACO-based search engine for flexible protein side chains. Stochastic optimization algorithms called ant colony optimization


It is a docking software. Docking program based on active site of target to generate putative poses of molecules.


MPI-Vina is an open-source parallelization of AutoDock Vina, which massively reduces the time of virtual screening by using compute clusters or network of computers. Autodock Vina based


MPI-Vina is an open-source software for the prediction of protein cavities and characterization on molecular dynamics trajectories. Based on Voronoi tessellation algorithm


myPresto is a program suite composed of several molecular simulations for drug development.. Molecular dynamics simulation based

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


RasTop is molecular visualization tool adapted from the program RasMol 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


Swiss-PdbViewer also known as DeepView is an application that allows to visualize and analyze several proteins at the same time. Molecular visualization