Great Free and Open Source Molecular Modeling Software List

Scientists have always been looking for Molecular Modeling software, which enables them to view structure of molecules in 2D and 3D space, rotate them as they wish, undersimagetand molecular patterns, DNA/RNA structures etc. These are highly focused/specialized software with lots of software development costs involved from scientific research companies. Interestingly, there are quite a few Open Source tools that can help one understand the Molecule details, perform molecule modeling etc. This is really encouraging for those who admire and support such open software tools. Please support them if you like! 

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Gabedit

Gabedit is a graphical user interface to computational chemistry packages like Gamess-US, Gaussian, Molcas, Molpro, MPQC, OpenMopac, PCGamess and Q-Chem. It can display a variety of calculation results including support for most major molecular file formats. The advanced "Molecule Builder" allows to rapidly sketch in molecules and examine them in 3D. Graphics can be exported to various formats, including animations.

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Jmol

Jmol is an open-source Java viewer for chemical structures in 3D with features for chemicals, crystals, materials and biomolecules and much more.

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PyMol

PyMOL is a molecular viewer, render tool, and 3D molecular editor developed in the spirit of RasMol and OpenRasMol and intended for visualization of 3D chemical structures including atomic resolution X-ray crystal structures of: proteins, nucleic acids (DNA, RNA, & tRNA), and carbohydrates, as well as small molecule structures of drug leads, inhibitors, metabolites, sugars, nucleoside phosphates, and other ligands including inorganic salts and solvent molecules.

A Virus Visualization

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QuteMol

QuteMol is an open source, interactive, high quality molecular visualization system. QuteMol exploits the current GPU capabilities 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.

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RasMol

RasMol is a program for molecular graphics visualization originally developed by Roger Sayle. RasMol is a molecular graphics program intended for the visualization of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images. RasMol runs on wide range of architectures and operating systems including Microsoft Windows, Apple Macintosh, UNIX and VMS systems.

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Sirius

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. It is equally suited for protein and small molecule construction and visualization.

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Molekel

Molekel is an open-source multi-platform molecular visualization program. It cross-platform, works on Linux, Windows as well as Mac OS! and rendering features etc.

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Are there any better ones?

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