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Top : Software : Scientific : Chemistry : Modelling and Visualization

9 Excellent Open Source Configuration Management Applications
This software automates the configuration of machines to a particular state. Like any other tools, they are designed to solve specific problems in certain ways. The goal is to get a system from whatever state it is in, into the desired state. Configuration management software are the tools of choice for many system administrators and devops professionals.

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Final Term
Final Term is a new breed of terminal emulator. Features include semantic text menus, smart command completion, GUI terminal controls and more. Read more


  • Amber
    Assisted Model Building with Energy Refinement: It consists of about 50 programs including sander, pmemd, LEaP, antechamber, ptraj, nmode, and mm_pbsa.
  • Ascalaph
    (commercial) Ascalaph is a general purpose molecular modeling suite that performs quantum mechanics calculations for initial molecular model development, molecular mechanics and dynamics calculations in the gas or in condensed phase. It can interact with external molecular modeling packages (MDynaMix, NWChem, CP2K and PC GAMESS/Firefly).
  • AutoDock
    AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.
  • Avogadro
    Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible rendering and a powerful plugin architecture. Read more
  • Babel
    Babel is a program designed to interconvert a number of file formats currently used in molecular modeling. Babel is capable of assigning hybridization, bond order, and connectivity when these elements are not present in the input file.
  • BALLView
    BALLView is our standalone molecular modeling and visualization application. Furthermore it is also a framework for developing molecular visualization functionality. It is available free of charge for Linux, Windows and MacOS.
  • Bodil
    Bodil is a modular, multi-platform software package for biomolecular visualization and modeling. Bodil aims to provide easy three-dimensional molecular graphics closely integrated with sequence viewing and sequence alignment editing. Functionality of Bodil is implemented in dynamically loaded modules.
  • Brabosphere
    Brabosphere is a program for the 3D visualization of molecular systems and their properties. Its name is derived from the quantum mechanical program package BRABO, for which it acts as a graphical frontend. It can also be used for the analysis and visualization of the data resulting from this type of calculation, so results from some other quantum mechanical applications will also be accepted.
    CACTVS is a distributed client/server system for the computation, management, analysis and visualisation of chemical information of any, even dynamically and ad-hoc defined type.
    CHIMP HIerarchical Modeling Program: a generic tool for the modeling of chemical phenomena. At present, CHIMP has the ability to perform dynamic Monte Carlo simulations on chemical reactions, in particular heterogeneous catalytic reactions.
  • COSMOtherm
    (commercial) COSMOtherm is a program for the quantitative calculation of solvation mixture thermodynamics based on quantumchemistry/COSMO results.
  • ECCE
    The Extensible Computational Chemistry Environment (ECCE, pronounced "etch-ay") provides a sophisticated graphical user interface, scientific visualization tools, and the underlying data management framework enabling scientists to efficiently set up calculations and store, retrieve, and analyze the rapidly growing volumes of data produced by computational chemistry studies. ECCE provides a graphical front-end for setting up, launching, real-time property monitoring, and visualization/analysis for electronic structure calculations using NWChem, GAMESS-UK, Gaussian-03, Gaussian-98, and AMICA. The NWChem molecular dynamics module is also supported with workflow setup, advanced protein rendering, and trajectory visualization.
    Fast Newton-Raphson Torsion Angle Minimizer calculates low-energy conformations of polypeptides and proteins, compatible with distance and dihedral angle constraints obtained typically from NMR experiments.
  • FlexV
    FlexV is a powerful stand-alone tool with easy interfaces and may be used in combination with any kind of molecular modelling software.
  • GoVASP
    (commercial) GoVASP improves the usability of the Vienna Ab-Initio Simulation Package (VASP). GoVASP comprises graphical user interfaces to prepare, perform and monitor VASP calculations and to evaluate and visualize the computed data. The highlight is the surface builder which simplifies the creation of slab models for any kind of surface.Overall GoVASP is ideally suited for VASP beginners and less experienced VASP users.
  • Hybridized Orbital Preview
    Hybridized Orbital Preview (HOPV) is an OpenGL based application that traces selected wave functions and plots electron clouds in 3D space. Rendered models can be rotated and zoomed.
  • ICM Browser
    ICM-Browser provides a biologist or a chemist with direct access to the treasures of structural biology and protein families. It reads PDB files or alignment files directly from the database web-sites and provides rich professional molecular graphics environment with powerful representations of proteins, DNA and RNA, and multiple sequence alignments.
  • ICM-Pro
    (commercial) ICM-Pro is a desktop-modeling environment for a biologist or a chemist interested in molecular structure and function.
  • Kasigra
    Kasigra is for viewing and editing images generated by atomic force microscope Explorer.
  • Kintecus
    Kintecus is a compiler to model the reactions of chemical, biological, nuclear and atmospheric chemical kinetic and equilibrium processes using three input spreadsheet files: a reaction spreadsheet, a species description spreadsheet and a parameter description spreadsheet.
  • KryoMol
    KryoMol is a KDE based program for visualization and analysis of several chemistry related files. Currently KryoMol can cope with: Quantum Chemical Computation logs from Gaussian98/03, GAMESS, ACESII (german version), and NwChem; Molecular Mechanis Logs: Tinker, Macromodel; Other formats as xyz or mol; and 1D NMR spectra and JCAMP-DX spectra.
  • LigandScout
    (commercial) LigandScout allows for sophisticated 3D pharmacophore generation from macromolecule-ligand complexes, pharmacophore overlay and interpolation, and a lightning fast and robust pharmacophore-based alignment algorithm that allows creating consensus pharmacophores and merged feature pharmacophores.
  • Maestro
    (commercial) Maestro is the unified interface for all Schrodinger software.
  • Moviemol
    Moviemol is a program for visualization and animation of molecular structures for SGI workstations. Moviemol typically takes sets of molecular coordinates and displays each of these sets or frames one after the other to create a "movie".
    NAMOT allows users to manipulate molecular models of nucleic acids based on a set of reduced co-ordinates developed at Los Alamos National Laboratory and the Max Planck Institute for Biophysical Chemistry.
  • Pcmodel
    (commercial) Pcmodel is a molecular modeling package with interfaces to many quantum chemistry packages. It has an OpenGL graphics engine for high quality graphics
  • PovChem
    PovChem is a chemical visualization and illustration program with a new graphic interface. It takes molecules in the PDB format, lets you to set up a picture with fine control over details of the illustration - colors, atom and bond radii, view orientation, etc. It will even calculate and display hydrogen bonds.
  • ProtoFit
    ProtoFit is a tool for optimization of surface protonation models from acid-base titration data. The software consists of two parts: ProtoFit, which is the program for model parameter optimization and simulation; and ProtoFit-GUI, a graphical user interface to ProtoFit with data and model visualization capabilities. ProtoFit-GUI provides for easy simulation of titrations and graphical comparison of model with measurements.
  • PyMOL
    PyMOL is a molecular graphics system with an embedded Python interpreter designed for general purpose visualization and for rapid generation of high-quality molecular graphics animations.

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  • QuteMol
    QuteMol is an open source (GPL), interactive, high quality molecular visualization system. QuteMol exploits the current GPU capabilites through OpenGL shaders to offers an array of innovative visual effects. QuteMol visualization techniques are aimed at improving clarity and an easier understanding of the 3D shape and structure of large molecules or complex proteins.
  • RasMol
    RasMol is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images.
  • Raster3D
    Raster3D is a set of tools for generating high quality raster images of proteins or other molecules. The core program renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing. It uses an efficient software Z-buffer algorithm which is independent of any graphics hardware. Ancillary programs process atomic coordinates from PDB files into rendering descriptions for pictures composed of ribbons, space-filling atoms, bonds, ball+stick, etc. Raster3D can also be used to render pictures composed in other programs such as Molscript in glorious 3D with highlights, shadowing, etc. Output is to pixel image files with 24 bits of color information per pixel.
  • RnaViz
    RnaViz is a user-friendly, portable, GUI program for producing publication-quality secondary structure drawings of RNA molecules. Drawings can be created starting from DCSE alignment files if they incorporate structure information or from mfold ct files.
  • Spartan
    (commercial) Spartan is a potent software tool that applies the power of molecular mechanics and quantum chemical calculations on your chemistry research. With state-of-the-art visualization and sophisticated computational algorithms, Spartan provides pharmaceutical and biotechnology organizations with key data supporting target identification and validation, lead selection and optimization, and process development.
  • Swiss-PdbViewer
    Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface.
  • TkRaster3D
    TkRaster3D is a graphical user interface to the molecular rendering package Raster3D. The interface, written in Tcl/Tk, has been developed at the National Institute of Standards and Technology (NIST), by Hillary S. Gilson.
  • UCSF Chimera
    UCSF Chimera is a highly extensible, interactive molecular graphics program. It is the successor to UCSF Midas and MidasPlus; however, it has been completely redesigned to maximize extensibility and leverage advances in hardware. UCSF Chimera is available free of charge for academic, government, non-profit, and personal use.
  • Viewmol
    Viewmol is an open source graphical front end for computational chemistry programs. It is able to graphically aid in the generation of molecular structures for computations and to visualize their results.
  • Virtual NanoLab
    (commercial) The basic design idea of Virtual NanoLab is to allow users the opportunity to use state-of-the-art atomic scale modelling in a simple and intuitive way. The engine behind the Virtual NanoLab is the Atomistix ToolKit (ATK) which provides modeling techniques ranging from simple force-fields methods to the most advanced non-equilibrium Green?s functions (NEGF) and density functional theory (DFT) methods.
    WMOVIEC is a program for producing computer animations from molecular dynamics simulations, using RCV or COR files.
  • XmMol
    XmMol is a desktop macromolecular visualization and modeling tool designed to be easy to use, configure and enhance. Its graphics are based on X11, and part of its user interface is based on Motif. Thus it provides a way of displaying structures on any X11 server.
  • XVibs
    XVibs is a utility for animating molecular vibrations. Normal modes are read from a file automatically determined to be from Aces2, Gamess, PC Gamess, Gaussian 90/92/95/94/98, ADF, Dalton, Jaguar, MOPAC, or HyperChem. Separate animation files are written for each vibration.
    YASARA is a molecular-graphics, -modeling and -simulation package for Linux and Windows, that finally makes it really easy to answer your questions. With an intuitive user interface and support for affordable shutter glasses, autostereoscopic displays and data gloves, YASARA creates a new level of interaction with the 'artificial reality', that allows you to focus on your goal and forget about the details of the program.
  • YASARA View
    (commercial) YASARA Model contains YASARA View and adds all the functions you need to explore, analyze and model small to macromolecules in a production environment. This includes many features you often miss: unlimited undo/redo, macro recorder, quad-buffered stereo with shutter glasses or the DTI virtual window.
  • YMOL
    Ymol is a molecular visualisation and animation program for the X Window System written from scratch. It can be used to create production quality images, and movies, using either the built in renderer or by exporting the scenes to POVRAY (Persistence of Vision). Ymol contains a programming language of its own, which can be used to create presentations that run non-interactively.

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