World Index of BioMolecular Visualization Resources

Free Molecular Visualization and Modeling Software
Caution: Some of free software listed here is Open Source in the strict sense, meaning that all derivatives are required to be free with open source code. If you plan to use the source code (not just the executable program), read the copyright restrictions carefully.

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  AISMIG - An Interactive Server-side Molecule Image Generator:
AISMIG - An Interactive Server-side Molecule Image Generator
AISMIG is a free web-service that enables molecule visualizion without any additional software
like Java or Plug-ins next to a web-browser. You can generate high quality and high resolution
images. It is nice alternative to the standart web-based visualizations techniques because
the user can see and interact with the structure in any case, independend of the software installed
locally. AISMIG is based on PyMol and PovRay.

  AutoDock: Automated docking of flexible ligands to macromolecules:
Designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. The atomic affinity grids can be visualised. This can help, for example, to guide organic synthetic chemists design better binders. Free to academics and educational institutions for non-commercial use. For unix or linux; comes with C++ source code included.

  Avogadro - Free cross-platform molecule viewer and editor:
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. Major features:  
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  BALLView:
BALLView is an extensible tool for visualizing and modeling bio-molecular structures. It provides a variety of different models for molecular visualization, e.g. ball-and-stick models, molecular surfaces, or ribbon models.

In contrast to most existing visualization tools, BALLView also offers rich functionality for molecular modeling and simulation, including molecular mechanics methods (AMBER and CHARMM force fields), continuum electrostatics methods employing a Finite-Difference Poisson Boltzmann solver, and secondary structure calculation. Results of these computations can be exported as publication quality images or as movies. Even unexperienced users have direct access to this functionality through an intuitive graphical user interface, which makes BALLView particularly useful for teaching.

For more advanced users, BALLView is extensible in different ways. Owing to its framework design, extension on the level of C++ code is very convenient. In addition, an interface to the scripting language Python allows the interactive rapid prototyping of new methods.

BALLView is portable and runs on all major platforms (Windows, MacOS X, Linux, most Unix flavors). It is open source software and available free of charge under the GNU Public License (GPL) from our website.

  BioEditor:
Once a macromolecular structure has been determined, the challenge is to communicate that information to a widely diverse audience of scientists, educators and students. Current options include the printed literature and dissemination over the Internet, either via online journals or directly on personal web pages. Printed literature has the advantage of wide acceptance and availability, but presents static images. Web pages can be powerful, but lack a uniform format. Furthermore, any dynamic images that are presented are subject to the whims of the providers of the browsers and plug-ins that are required to view them. At the University of California, San Diego and the Scripps Institute, we are developing the BioEditor as a tool to bridge the gap between the printed literature and current Internet presentation formats. It is a standalone Windows application that can be used to prepare and present structure annotations containing formatted text, graphics, sequence data, and interactive molecular views. BioEditor includes a built-in browser based on Internet Explorer; molecular visualizations are done using the Chime plug-in. The executable includes a help file that has a quick-start tutorial to explain how to use all the components of the software. The web site (http://bioeditor.sdsc.edu) includes a download site and some sample documentaries that you can view to see the potential of BioEditor.  

  Calculator Plugins:



Calculator Plugins are modules of Marvin and JChem applications which perform calculations based on chemical structures.
Separate Calculator Plugins currently cover a range of calculations and physicochemical predictions. The plugin format is open to third party development, within ChemAxon we have ongoing plugin development, currently available plugins:


Free for teaching and academic research through ChemAxon's Academic Package. Introduction, terms and application available from http://www.chemaxon.hu/forum/viewpost570.html#570

Free unlimited structure based prediction implemetation here: http://www.chemaxon.com/demos/try_marvin.html

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  ChemApplet:
A fast Java applet for viewing CAChe chemical sample structures. Provides rotatable and scalable views in space-filling, ball-and-cylinder, cylinder and line styles. Also displays molecular orbitals and isosurfaces. Can work with zip archives of chemical structures and isosurfaces for fast downloads. Rated Top 25% by JARS.

  ChemCraft:
ChemCraft is a graphical program for constructing molecules and visualization of quantum-chemical calculations. It can visualize molecular structures, vibrational modes, molecular orbitals and other properties read from GAMESS, Gaussian output files. Besides these formats, PBD, HIN, XYZ files can be read; the program can also import/export atomic coordinates using Clipboard. ChemCraft allows to construct molecules using a set of molecular fragments, the set can be supplemented with custom fragments. The program produces publication-ready graphical outputs in .BMP, .JPG formats in customizable graphical schemes, which can be supplemented with labels, lines and other designations. Only Windows platform is supported. ChemCraft can be downloaded at our webpage (http://www.chemcraftprog.com); description of the program, demo screenshots are also available at the webpage.

  ChemDraw Net Plugin:
The free ChemDraw Net Plugin (Windows, Macintosh) will allow you to view and manipulate chemical structures, however, the save and print functions are disabled. Search Web databases by structure or substructure, such as the ChemFinder WebServer. View ChemDraw documents that others have placed on the WWW.

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  Chemical and Safety Relational Database:
The software for this resource is open source and is availble for download. A web server outfitted with php and mysql is required to setup your own relational database. The software is OS independent.

This site provides access to a chemical and safety relational database developed in 2003 at Nebraska Wesleyan University. The site is designed specifically for local users but access to the database content is not restricted. This database has many features similar to chemfinder.com and the NIST webbook. The major difference is that the content of the database is determined by local interests and needs and is cross indexed to hazard information (specifically NFPA ratings). For example the database presently contains chemical and safety data for materials used in lab experiments in our first and second year chemistry courses.

The database can be searched by CAS numbers, molecular formula, chemical names, or by specific (NFPA) hazards. Included in the database are files of Chime-pdb files [Chime plugin required for viewing], MSDS's, NFPA ratings (graphic view), and 2D graphics of the molecules. In addition local users can cross-index an unlimited number of web-links to other material (such as IR, NMR, UV-vis and MS spectra, experimental data, potential maps, animations, etc) to each molecule in the database.

  CheVi® - Chemical Visualizer:
CheVi is a 3D chemical visualization package specifically designed to help users gain insight into how ligands and receptors interact. CheVi is able to show the surface of both ligands and receptors color coded based on chemical features. It's also capable of showing the surface difference of the ligand and receptor, interactions lines and much more to give the user valuable information about the chemical nature of the interactions. The tool can work with most 3D file formats: PDB, mol2, SDF, MOL and is ideally suited to be a visualization tool for any docking / screening process. This tool is FREE for all users and it can be downloaded from the CheVi pages on the SimBioSys web-site: http://www.simbiosys.ca/chevi/

  Chime:
For Chime and Chime resources, go to other sections of the World Index of Molecular Visualization Resources.

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  Chimera:

An interactive molecular modeling system developed by the the UCSF Resource for Biocomputing, Visualization, and Informatics. It is free for academic and non-profit use and is available for Windows, Mac OS X, Linux, and other platforms. UCSF Chimera development is funded by the NIH National Center for Research Resources (grant P41-RR01081). Features include:

  CMD Bioscience:
CMD bioscience specializes in the use of novel proprietary computational methods to model and engineer clinically important protein-protein and protein-peptide interactions. Our "Affinity" algorithm is designed to predict protein-protein / protein-peptide binding affinities; it is fast enough for use as a scoring function and will be made freely available to the academic community.

  Cn3D:
Cn3D is an open-source code visualization tool for biomolecular structures, sequences, and sequence alignments. What sets Cn3D apart from other software is its ability to correlate structure and sequence information: for example, a scientist can quickly find the residues in a crystal structure that correspond to known disease mutations, or conserved active site residues from a family of sequence homologs. Cn3D displays structure-structure alignments along with their structure-based sequence alignments, to emphasize what regions of a group of related proteins are most conserved in structure and sequence. Also included are custom labeling features, high-quality OpenGL graphics, and a variety of file exports that together make Cn3D a powerful tool for literature annotation. Cn3D is typically run from a WWW browser as a helper application for NCBI's Entrez system, but it can also be used as a standalone application. Cn3D is available for Windows, Macintosh, and various UNIX platforms.

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  Comparison of Five Chemical Drawing Programs:   (English, Hungarian )
This review compares five chemical drawing programs, ISIS/Draw, ChemDraw, ChemWindow, ChemSketch and Chemistry 4-D Draw. ISIS/Draw and ChemSketch are free; the others are commercial software. This review is extensive and detailed, with helpful supplementary information (such as why to use gif rather than jpeg files for the web), and sample output from all 5 programs.

  Computational chemistry, molecular modelling and molecular visualization tools:
Links to a large set of programs for visualization of molecules and molecular modeling in general

  ConSurf Server for the Identification of Functional Regions in Proteins by Surface Mapping of Phylogenetic Information:
ConSurf identifies, in Chime (actually, in Protein Explorer) the most conserved residues, and the hypervariable residues, based on a multiple sequence alignment and phylogenetic tree. It work on any protein for which a 3D structure is available. ConSurf is completely automatic. All you have to provide is the PDB code for a 3D structure. Optionally, you can provide your own multiple sequence alignment. Image at left: enolase -- click on it to see the ConSurf Gallery.
 
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  Deep View:
For Deep View resources, go to the Deep View / Swiss-PDBViewer section.

  DINO - Visualizing Structural Biology:

DINO is a realtime 3D visualization program for structural biology data. It runs under X-Windows and uses OpenGL. Supported architectures are IRIX, Linux (i386 and PPC),OSF1 and SunOS. DINO is distributed in binary form only, but is freely available.

DINO aims to visualize the diversity of structural data in a single program and to allow the user to explore relationships between the data. There are five data-types supported: structure (atomic coordinates and trajectories), surface (molecular surfaces), scalar field (electron densities and electrostatic potentials), topograph (surface topography scans) and geom (geometric primitives such as lines).

The number and size of the data the program can handle is only limited by the amount of RAM present in the system. No artifical limits are set.

Supported input file formats are PDB (coordinates), X-PLOR/CNS (coordinates and electron densities), CHARMM (coordinates, trajectories and scalar fields), CCP4 (electron densities), UHBD (electrostatic potentials), DELPHI (electrostatic potentials), GRASP (electrostatic potentials and surfaces) MSMS (surfaces), MSP (surfaces), MEAD (coordinates and electrostatic potentials) and greyscale TIFF (surface topographs).

Output can be written as TIFF, PNG, PostScript or POV-Ray

  Discovery Studio Visualizer:
A successor to WebLab Viewer Lite and Discovery Studio Viewer.
A visualization utility for small molecules and macromolecules, including ribbon, tube and schematic renderings of protein secondary structure. Mostly a viewer, but has limited editing capabilities. Runs on Windows 2000 and XP, and on Red Hat Enterprise Linux 3.0 and 4.0.
Features (copied from website):
 
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  eMovie: A storyboard-based tool for making molecular movies:
eMovie is a free tool that makes the creation of molecular movies both easy and intuitive via a breakthrough storyboard interface, similar in nature to what is used in the creation of traditional movies. eMovie is a plug-in for PyMOL, a powerful, open source, and multi-platform molecular graphics program. To download eMovie, please visit our download/install page. Through eMovie, the user has the ability to construct an animation of any length out of building blocks like rotations, zooming, color changes, fading of selections, view changes, and even execution of specific PyMOL commands or scripts. Conformation changes and docking actions can be added as well (requires incentive version of PyMOL). Movies can be saved and loaded at a later time, and optionally exported as a ray-traced image sequences to be merged into a traditional movie file (e.g. .mov or .gif) using available external programs.

  Excel Macros for PDB Files:
Excel spreadsheet macros for reading PDB files, manipulating them, and exporting the modified data in PDB format. These "Renumbering Macros" take a number of PDB-Files in a directory (no more than 250, since the size of an EXCEL workbook is limited to 255 worksheets), read the ATOM and HETATM records of each file into an EXCEL worksheet, and extract the sequences, chain and residue labels into separate worksheets. The user can then process (gap) the sequence alignment manually or export it to gap it automatically with programs such as the GCG module PILEUP and reimport the sequence alignment into the EXCEL workbook. Further macros will then change the chain and residue labels of the PDB files according to a common numbering scheme indicated in the header row (for sequence alignments shorter than 250 amino acids) or in the header column (for sequence alignments longer than 250 amino acids) of the alignment and reexport the PDB coordinate files. At the page Renumbering PDB Files don't miss the How To button, which opens a slide show explaining how to use the PDB macros.  

  FirstGlance in Jmol:
FirstGlance in Jmol is a free, open source, browser-based application for viewing macromolecular structures online. It uses the free, open-source Jmol java applet (jmol.org). FirstGlance is an HTML "wrapper" or "user interface" for Jmol. It enables you to see key features of the molecule by clicking on menus or buttons, without learning the (complicated) Jmol menu, or the Jmol command language.

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  FPV: Fast Protein Visualization Using Java 3D:
FPV is a protein visualization software built using Java 3D API. FPV reads PDB files as input. It can load large molecules (e.g. 3000-4000 amino acids) and has a few display modes: spacefill, backbone, bonds, ribbon. It is available with source code.

  Fragmenter:


Fragmenter is the virtual building block creation component of ChemAxon’s Java based chemical software technology.

Fragmenter cleaves molecules to generate fragments which retain their associated cleavage route information.

Using the cleavage route information, the library of fragments generated can be used as building blocks to more easily create small molecule libraries during lead discovery and optimization.


Free for teaching and academic research through ChemAxon's Academic Package. Introduction, terms and application available from http://www.chemaxon.hu/forum/viewpost570.html#570


  Free Molecular Modelling Programs:
A review of free molecular modelling programs the author found to be useful for his work. All entries are complete with feature-list, screenshots and links to the homepages. This is not a complete list of all available free packages but only those which the author thinks are useful.

Update March 2004 (G Mullier): review seems to have moved - now hung off a blog.

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  Free Molecular Visualization Programs for Unix and/or Linux:
A list of freely available molecular visualization programs for unix and unix clones. The list contains links to 36 such programs (February 2002). Some of these programs are free for academic use only. The time-limited trial versions of commercial programs are not included here.

  Free Molecular Visualization Software:
This site lists some molecular visualization freeware packages not yet indexed in the World Index, along with sample images from most of them. There are also links to sites with more extensive lists of molecular visualization freeware.

  Friend, an integrated multiple structure visualization and multiple sequence alignment application.:
Friend is a bioinformatics application designed for simultaneous analysis and visualization of multiple structures and sequences of proteins and/or DNA/RNA. The application provides basic functionalities such as: structure visualization with different rendering and coloring, sequence alignment, and simple phylogeny analysis, along with a number of extended features to perform more complex analyses of sequence structure relationships, including: structural alignment of proteins, investigation of specific interaction motifs, studies of protein-protein and protein-DNA interactions, and protein super-families. It is also useful for functional annotation of proteins, protein modeling, and protein folding studies. Friend provides three levels of usage; 1) an extensive GUI for a scientist with no programming experience, 2) a command line interface for scripting for a scientist with some programming experience, and 3) the ability to extend Friend with user written libraries for an experienced programmer. The application is linked and communicates with local and remote sequence and structure databases.  
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  GABEDIT: A Graphical User Interface for Gamess-US, Gaussian, Molcas, Molpro, MPQC and Q-Chem computational chemistry packages.:
gabedit is a Graphical User Interface for Gamess-US, Gaussian, Molcas, Molpro, MPQC and Q-Chem computational chemistry packages. Gabedit includes an advanced Molecule Builder. Gabedit can graphically display a variety of Gamess-US, Gaussian, Molcas, Molpro, MPQC, Q-Chem and (partially) ADF calculation results, including the following : - Molecular orbitals - Surfaces from the electron density, electrostatic potential, NMR shielding density, and other properties. Surfaces may be displayed in solid, translucent and wire mesh modes. they are can be colorcoded by a separate property. - Contours (colorcoded), Planes colorcoded, Dipole. XYZ axes and the principal axes of the molecule. - Animation of the normal modes corresponding to vibrational frequencies. - Animation of the rotation of geometry, surfaces, contours, planes colorcoded, xyz and the principal axes of the molecule. - Animation of contours, Animation of planes colorcoded. Gabedit can display IR and Raman computed spectra. It can generate a povray file for geometry (including hydrogen's bond), surfaces (including colorcoded surfaces), contours, planes colorcoded. Gabedit can save picture in BMP, JPEG, PNG, PPM and PS format. Gabedit can generate automatically a series of pictures for animation (vibration, geometry convergence, rotation, contours, planes colorcoded).

  Garlic, Free Molecular Visualization Program, Version 1.2:
Garlic is a free / open source molecular visualization program written for unix and unix clones, like linux. It is released under the terms of GNU GPL (General Public License). Garlic is capable to load and display more than one structure: the maximal number of structures which may be viewed simultaneously is limited by the system RAM. Rotations, translations and other operations are controlled by the numeric keypad rather than by mouse or special hardware (like dials). In addition to planar clipping (slab), garlic offers spherical and cylindrical clipping, as well as spherical and cylindrical color mapping. The only libraries required to compile and run garlic are the standard C library (libc), the standard X11 library (libX11) and the standard C math library (libm). At present (September 20, 2002) all other molecular visualization programs for unix (linux) require more libraries than garlic. The latest version of garlic is capable to create and edit protein structure and to attach a model of membrane to the structure of membrane protein.

  Ghemical:

Ghemical is a computational chemistry software package released under the GNU GPL. It means that full source code of the package is available, and users are free to study and modify the package. Ghemical is written in C++. It has a graphical user interface (which is based on GNOME), and it supports both quantum-mechanics (semi-empirical and ab initio) models and molecular mechanics models (there is an experimental Tripos 5.2-like force field for organic molecules). Also a tool for reduced protein models [1] is included. Geometry optimization, molecular dynamics and a large set of visualization tools are currently available.

Ghemical relies on external code to provide the quantum-mechanical calculations. Semi-empirical methods MNDO, MINDO/3, AM1 and PM3 come from the MOPAC7 package (Public Domain), and are included in the source distribution. The MPQC package (GNU GPL) is used to provide ab initio methods: the methods based on Hartree-Fock theory are currently supported with basis sets ranging from STO-3G to 6-31G**. The MPQC code is not included in the source distribution. In order to use the MPQC-based ab initio methods in Ghemical, you must first compile and install the MPQC program for your system, and then compile Ghemical using some specific settings that link the programs together. Ghemical also contains the OpenBabel package for import and export of many different file formats (as well as other tasks).

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  gOpenMol:
gOpenMol is the graphics interface to the OpenMol set of programs. gOpenMol can also be used for the analysis and display of molecular dynamics trajectories and the display of molecular orbitals, electron densities and electrostatic potentials from programs like the GaussianXX, PC GAMESS and Jaguar. gOpenMol can import, display and analyse a wide range of different input atomic coordinate file formats and binary trajectory file formats. The program has a graphical user interface (GUI) based on the Motif set of widgets. The internal line command interpreter is implemented using the Tool command language (Tcl). gOpenMol can be used for a wide range of analysis and display tasks like the display of isocontour surfaces. Available for linux, Windows, SGI Irix, and other platforms. See also the gOpenMol Gallery.

  GRASS: Graphical Representation and Analysis of Structure Server:
GRASS is designed to facilitate the study of macromolecular function by mapping a number of structural, chemical, and biological properties onto various representations of molecular structure (molecular surfaces, wireframe, CPK spheres, or backbone tracing ribbons). The available properties currently include surface curvature, atomic charges, electrostatic potential, sequence variability, hydrophobicity, temperature factors, and distances from a ligand. The molecular properties and graphics are calculated on our server and sent to be viewed on the user's machine using any of three widely available visualization programs: a Virtual Reality Modeling Language (VRML) viewer, Chime, or Grasp.  

  Hyleos ChemFileBrowser:
ChemFileBrowser is a win32 free sotfware for chemistry designed to visualize and works with SDFile (MDL® format) to exchange and analyse information associated with chemical structure. It includes descriptors calculation like TPSA, molecular weight, HBd and HBa. ChemFileBrowser since version 0.1.6 integrates Chemistry 2D viewer as a free reusable ActiveX control.  
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  iMol - Molecular Viewer for Mac OS X:

iMol is a free molecular viewer for Mac OS X operating system. iMol can load molecules using several file formats: PDB, XYZ, MOL2, HIN, CAR, ALC, BIO. The molecules can be saved as PDB, XYZ or BIO files (the BIO file stores all rendering settings, i.e. colors, lighting, orientation of molecules). iMol can easily handle both small and large molecules, it can load multiple molecules, move and rotate them independently.


   iMol uses OpenGL graphics to display molecules. The molecules can be rendered using various styles: wires, points, Van der Waals spheres, balls and sticks, strands, ribbon, cartoons, spring, tube, ladder. Individual atoms and/or residues can be selected using mouse or a simple selection query. There are several predefined color schemes available (e.g. residuum order, secondary structure, hydrophobicity), as well as custom colors. Also, different materials (e.g. plastic, metal, glass) can be used. Several rendering effects are available, including automatic rotation, motion blur, background gradient, perspective, and stereo projection (both side-by-side and red/blue anaglyph methods). Various rendering parameters can be fine-tuned. Atoms and residues can be labelled using names and numbers. The rendered images may be exported as a bitmap, as a PostScript file, or as a POV-Ray file.

   The program can meaure distances, angles, and torsional angles between atoms. Molecules can be superimposed and the RMSD (Root Mean Square Deviation) between atoms coordinates can be calculated. Additionaly, protein chains can be structurally aligned to detect regions of high structural similarity. iMol can load multimodel PDB files and display them as an animation (e.g. molecular dynamics trajectory). iMol supports QuickTime movie format for rendering the animations. The movies are efficiently compressed for web applications.


   iMol uses OS X Aqua user interface. Different options are placed inside a convienient mobile drawer. The iMol package includes several example files demonstrating full rendering potential and visualization capabilites.

  Interprobe Chemical Services, Software and Databases:
Interprobe Chemical Services supplies molecular modelling software for use with two operating systems: SGI Irix (6.5.x) systems and Microsoft Windows systems (NT4, 95, 98, 2000, XP). The more extensive range of software is for the SGI systems and includes INTERCHEM (general structure modelling including biomolecules, PRESTO (protein sequence analysis), CHEMSPREAD (statistical package for analysing properties of structures), and a range of non-graphical programs; CONVERT (structure file format interconversion), PROTEINS (conversion of PDB files to INTERCHEM formate etc), COMPARISONS (programs for comparing and overlaying structures), ICMECH (molecular mechanics), STRAUSS (stand-alone programs for translating SMILES sttrings), AUTOBUILD (building of small molecule libraries), and structure database searching tools. At present the Windows inventory is limited to INTERCHEM-PC, PRESTO-PC, and PROTEINS-PC. Source code and executables are provided as standard. (N.B. The Windows programs require copies of the Salford Fortran-95 compiler and Clearwin+ graphics tools if the software is to be recompiled).

An ever expanding range of 3D structures derived from the 2D structure catalogues of the so-called "diversity suppliers" is being produced. A total of around 1.25 million "drug-like" structures is available now.

The programs are distributed under a cost-free license to academics and other not-for-profit organisations (i.e. charities). Industrial and government organisations are charged a (relatively) small fee (currently 2500 UK pounds) for a perpetual site license. The databases are distributed for no cost to all users.

 

  Jamberoo (formerly JMolEditor):
Jamberoo (former JMolEditor) is a program for displaying, analyzing, editing, converting, and animating molecular systems. It has intuitive interface and inbuilt help system. Jamberoo can be used also for the analysis to display molecular orbitals, electron densities and electrostatic potentials from the Gaussian. Jamberoo is written in Java, so it is a cross-platform application. System requirements: Java Virtual Machine (JVM) >= 1.5 and Java3d >= 1.4. Jamberoo supports submission of Gaussian jobs to remote computer using the ssh2 protocol. It can monitor submitted jobs and retrieve output files after job completion.

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  jAMVLE: A New Integrated Molecular Visualization Learning Environment:
A new computer-based molecular visualization tool has been developed for teaching, and learning, molecular structure. This java-based ‘jmol Amalgamated Molecular Visualization Learning Environment’ (jAMVLE) is platform-independent, integrated, and interactive. It has an overall graphical user interface that is intuitive and easy to use. Students found that the jAMVLE application stimulated their interest, was a more active learning environment, provided better guidance, and made learning molecular structures fun. The application can be downloaded free from the internet at: wabri.org.au/jamvle.

  JChem Base and JChem Cartridge:



JChem Base is a Java tool for the development of applications that allow for the search of mixed structural and non-structural data. JChem Base can integrate a variety of database systems (Oracle, SQL, Access, etc) with web interfaces and fully supports all ChemAxon technology.


Via the JChem Cartridge many JChem functions, such as structure searching or property predictions are directly available from within Oracle's SQL.


The system includes Marvin, a fast substructure, similarity, and exact search engine using 2D hashed fingerprints. Structures are stored in database tables. Structural and non-structural data can be combined. SDF, SMILES, etc. can be imported and exported. There is API with low and high level classes. Key features:

To find out more please visit this implementation: http://www.jchem.com/index.html?content=examples.html or download and evaluate from our website

Free for teaching and academic research through ChemAxon's Academic Package. Introduction, terms and application available from http://www.chemaxon.hu/forum/viewpost570.html#570

  Jmol:   (English, Spanish, Dutch )
Jmol is an open source molecular viewer written in Java. It comes in two forms. There is a Jmol applet which, like Chime, displays the molecule within a web browser. Unlike Chime, you don't have to install a plugin -- Jmol arrives automatically with the web page and displays the molecule. Jmol's second form is a stand-alone application (like RasMol).

Because Jmol is written in Java, Jmol runs on a wide variety of operating systems (Windows, Mac OSX, linux, among others) and in all popular browsers (Internet Explorer, Netscape 4/6/7, Mozilla, Safari, etc.).

Jmol supports the RasMol/Chime scripting language. The Jmol applet provides a migration path for Chime-based web applications. Jmol includes a perl script which will automatically convert many Chime web pages.

The source code and java binaries are available from http://jmol.sourceforge.net and are covered under the GNU Publice Licenses.

  
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  Linux4Chemistry:
The most up-to-date Linux software for chemistry, biochemistry, genetics: molecular modeling, visualization, graphics, computational chemistry calculations, molecular and quantum mechanics, dynamics, kinetics, calcultors, biochemistry and genetics related and evens some drug discovery software

  LPMolecularViewer:
A lightweight ActiveX control that allows you to visualise molecule structure files in 3D in Powerpoint® presentations or in Visual Basic® programs. Windows only (does not work in Apple OS X or linux.) More details here.  

  MAGE:
MAGE (available for Windows, Mac, Unix, Linux, and now Java) is the freeware which first brought powerful macromolecular visualization to personal computers (in 1992). Over a thousand excellent tutorials on molecular structures are available in the form of kinemages (presentations that run in MAGE). MAGE has a number of unique and powerful capabilities not available in RasMol nor Chime. (Here is a brief comparision of MAGE vs. RasMol.)

There is now a capable Java version of Mage which runs on the Web with no plug-ins. The above page (by Martz) comparing Mage and Rasmol is nicely done in general. However, Mage has ribbons, backbone, ball&stick;, etc. representations; kinemages are not scripts but are heirarchical, commented, 3D display lists; and making a simple kinemage is extremely easy, and its exploration is just as open-ended as in RasMol - it's only if you want to make a custom-crafted presentation that it gets "technical". Also, an important use of Mage now is to show all-atom contacts made by Probe (in real time, on Unix).

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  Marvin Applets and JavaBeans:


Marvin Applets and JavaBeans can be applied in web or stand-alone applications for sketching or viewing structures, queries and reactions. Marvin Applets are free for free web sites. MarvinSketch and MarvinView applications are free for academic/home users or for anyone if accessed at the ChemAxon web site. These Java tools are useful in the front end of chemical database systems.
A list of features:
Free for teaching and academic research through ChemAxon's Academic Package. Introduction, terms and application available from http://www.chemaxon.hu/forum/viewpost570.html#570

  MGLTools:
MGLTools is a software for 3D visualization and analysis of molecular structures. It uses Python and OpenGL to deliver cross platform interactive molecular viewer suitable for producing publication-quality images. Short description of its three main applications are shown below.
AutoDockTools
AutoDockTools (ADT)
AutoDockTools is graphical front-end for setting up and running AutoDock - an automated docking software designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.
PMV
Python Molecular Viewer (PMV)
PMV is a powerful molecular viewer that has a number of customizable features and comes with many pluggable commands ranging from displaying molecular surface to running molecular dynamics simulation and energy minimization calculations.
Vision
Vision
Vision is a visual-programming environment in which a user can interactively build networks describing novel combinations of computational methods, and yielding new visualizations of their data without actually writing code.

  Moilin:
Moilin is a molecular modelling program which can be operated in stand alone mode or as part of the Oscail package under PC-Windows. The download includes Mopac and Iconc. The program will also drive Tinker and PC-Gamess both of which are available free to academics. Thus calculations from molecular mechanics (including dynamics movies) to high level dft are possible. Moilin can generate plots of molecular orbitals from Mopac or Gamess. Moilin uses opengl graphics with high resolution hard copy (up to 2400 x 1800). Moilin interacts with the Oscail package which provides access to crystallographic software, file format conversion software, coordination polyhedra and Raster3D photorealism. Downloads include "on-line tutorials" and "on-line" help. Commercial users must obtain permission to use this software.

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  Molecular Workbench:
Molecular Workbench is free, content-oriented molecular modeling software for use in education. Unlike the static ball-and-stick models, the Molecular Workbench software computes and visualizes the motion of ensembles of atoms in real time, in both 2D and 3D.

  Molecule Interactive Collaborative Environment:

The Molecular Interactive Collaborative Environment (MICE) is a Java/Java3D based molecular structure viewer. As a pure Java application, MICE will run without modification on any platform for which Java version 2 and Java3D are available. We have successfully run MICE on Windows 98/NT4.0, Solaris and Linux.

Using a simple form interface, users can users can create custom representations of any molecule in the Protein Databank (PDB), via a network-based scene generator (MSG) that uses MolScript to create VRML representations of the molecule of interest. Once loaded into MICE, the custom view can then be viewed interactively and queried using rudimentary scene interrogation tools.

As well as allowing a user to manipulate and examine a molecule locally, MICE can also share views of molecules across a network. In a collaborative session, multiple users at different geographical locations can view the same representation of the molecule of interest. Any user can take control of the session and alter the view of the molecule, with these changes being seen by all members of the collaboration.

  Molegro Molecular Viewer:
Molegro Molecular Viewer is a free cross-platform application for visualization of molecules and analysis of protein-ligand interactions. Molegro Molecular Viewer is able to visualize most common molecular file formats (PDB, Mol2, SDF) as well as docking results from Molegro Virtual Docker (MVDML).

screenshot of the main user interface
MMV main user interface.

Features at a glance

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  MollyCule - Free, Easy Molecular Visualisation for schools and students.:
Summary:

MollyCule is a free, newly available open source molecular visualisation application - aimed at being 'easy to use' for students and school pupils/teachers - with some interesting features. MollyCule is available for MacOS, Windows, and Linux. MollyCule makes it possible to intuitively generate 3-D animations and nicely illuminated pictures of essays and reports with only a few mouse clicks. It has a plug-in based loosely coupled architecture.


Introduction:

MollyCule http://mollycule.org

MollyCule is mostly intended for school teachers, school pupils and perhaps undergraduate students. It's not really suitable for research-level investigation yet, since it doesn't offer protein visualisation, or the full range of features you'd expect in a research-level package. MollyCule runs on MacOS, Windows and Linux.

Some of the interesting aspects of the project include:

1. "Point and Go" interface. You click on any part of the molecule, and you are 'flown there' automatically in 3D with a nice trajectory. This is much simpler than (rotate/translate/zoom) interaction with models.

2. Plug-in based architecture. Almost everything is a plug-in: the GUI, the file loaders, the interaction mechanism, the JPG/PNG output system, the lighting system... this means anyone can simply and easily add new features without having to modify the main program. You just write the plugin, and put the finished file into the 'plugins' directory. This also means that anyone can distribute their own extensions of MollyCule privately if they wish, without having to branch the software into a new project. This plug-in architecture also provides a way for e.g. teachers to develop plugins to suit their courses, i.e. 'a tour of the hydrocarbons' module that links file-loading, colour highlighting, interaction and visual movement through the molecule together into a single downloadable file.

3. Extremely easy to use for taking nice pictures for essays, practicals etc. There is a focus on flexible, easy to control lighting, easy to adjust colouring, and so on, making it simple to give chemistry pictures the 'feel' that you want without needing to resort to 3-D rendering packages.

4. Menus are always 'on-screen' with sliders and checkboxes, rather than a File/Edit/Tool menubar approach or text boxes. This makes it easy and straightforward for young scientists to 'play around' with the program.

5. Easy to change between full screen interaction (for presentation) and menu based modes. There is also a 'drifter' mode that effectively turns the program into a screensaver, which might make it useful for backdrops to presentations or posters.

There are not many visualisation packages where literally within the first two clicks of the mouse after opening the program, you find yourself gliding across a molecule on an automatically generated 3-D animated flight to the place you're interested in.

Perhaps some other programmers may wish to copy/reproduce some of these features for their own software too. I'd also love it if people considered writing plugins to extend the capabilities of MollyCule.


Project history:

I wrote this package over a few months in 2001 as an undergraduate student, but was discouraged from distributing it then (there was talk of a marketing deal at the time). Marketing fell through; and it was not until recently that I had the free time to dig out the code, tidy it up, and prepare it for distribution. I'm pleased to announce that both the binaries and the source are completely free now for anyone to use under the GPL3 license. Please note that the program re-uses some source code from JMVS for molecule data loaders (under the GPL), and also from PNG/JPEG encoder GPL distributions for output (under license). So, many thanks to the authors of those other programs for sharing their code freely.

  MolMol: MOLecule analysis and MOLecule display:
MOLMOL is a molecular graphics program for display, analysis, and manipulation of three-dimensional structures of biological macromolecules, with special emphasis on nuclear magnetic resonance (NMR) solution structures of proteins and nucleic acids. MOLMOL has a graphical user interface with menus, dialog boxes and on-line help. The display possibilities include conventional presentations, as well as novel schematic drawings, with the option of displaying different presentations in one view. The covalent molecular structures can be modified by addition or removal of individual atoms and bonds; the three-dimensional structure can be manipulated by interactive rotation about individual dihedral angles. Special efforts were made to allow for appropriate display and analysis of sets of (typically 20-40) conformers that are conventionally used to represent the result of a NMR structure determination, using functions for superimposing sets of conformers, calculation of root mean square distance (RMSD) values, identification of hydrogen bonds, checking and displaying violations of NMR constraints, and identification and listing of short distances between pairs of hydrogen atoms. MOLMOL is publicly available at no charge, and runs on UNIX and Windows NT/95/98/2000.

MolMol has been cited by over 500 scientific journal articles (search for "molmol" at highwire.stanford.edu). It ranks among the most popular free visualization programs, including RasMol (>700) and KineMages (>450).

  MolPOV 2:
MolPOV is a graphics file converter for MS Windows that reads Brookhaven Protein Data Bank format files and produces a ready-to-render input file for the Persistence of Vision ray tracer (POV-Ray). The PDB files can be from the Brookhaven PDB itself or from any molecular modeling program that can store structures in the PDB format. A POV setup dialog can be used to edit many of the basic scene features and rendering options. Molecules can be represented with spacefilling spheres, bond cylinders, or balls & sticks. Scene features that can be set in MolPOV include lighting, atom and/or cylinder texture, atom colors and finish, background, camera position, rendering size. POV-Ray input files to produce simple rotational animations can be constructed. In addition, the program allows launching of the POV program to view the rendering immediately.

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  MolScript:
Free license required for academic/not-for-profit use (fee for commercial use). Unix program for molecular visualization. MolScript has been used for probably the majority of published high-resolution macromolecular images. Learning its command language takes some time. It puts out a meta-language image description that must then be rendered with a separate engine, such as Raster3D or POV-Ray.

  MolUSc - Molecules pour un Usage Scolaire:   (French )
MolUSc is a Chime-based web resource in French (MolUSc is the French acronym for Molecules for Scholarly Use). It may be thought of as a simpler Protein Explorer. Its aim is to give students full access to Chime possibilities, without needing to know any RasMol script commands.
In MolUSc all commands are available in easy-access menus. MolUSc allows surface displays, selections from sequences, comparing two molecules... MolUSc works with Netscape Navigator and even better in Internet Explorer. MolUSc can be downloaded and used freely for non commercial purposes.

MolUSc est un programme de manipulation de molecules base sur le plug-in Chime (MolUSc signifie modelisation de Molecules pour un Usage Scolaire). L'objectif de MolUSc est de donner l'acces aux eleves a toutes les possibilites de Chime, au travers d'une interface conviviale, sans avoir a taper d'instructions de commande. MolUSc permet d'afficher des surfaces, de faire des selections a partir des sequences, de comparer deux molecules,... MolUSc fonctionne avec Netscape Navigator mais aussi avec Internet Explorer (meme mieux). MolUSc peut etre telecharge, et utilise librement dans un but educatif et non commercial uniquement.

  MolViewX:
MolviewX is a freeware Macintosh application for OSX that can read several types of coordinate files and display ribbon, CPK, stick, ball&stick;, and surface figures. The interface is completely interactive (i.e. no comand line input). There are countless options that control the display colors and characteristics. The output includes object-oriented PICT, QuickDraw 3D 3DMF files, and VRML files. In addition, there are several analysis tools such as neighbors, distance lines, hydropathy plots, Edmunson wheel plots, B value plots (and color coded stick models), distance plots. In addition, the user can open 2 different structures and even perform 3D alignments on them. Also, subsets of the structure can be stored as MOL files and be read in later.

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  MVM - a Molecular Visualization Program and GUI of ZMM:
MVM is a free molecular viewer that can be used to display protein, nucleic acids, oligosacharides, small and macromolecules. It has an intuitive interface. In addition to being a molecular viewer, it is the user interface of a very powerful molecular mechanics engine (ZMM). ZMM is a molecular modeling program for theoretical studies of systems of any complexity: small molecules, peptides, proteins, nucleic acids, and ligand-receptor complexes. ZMM searches optimal structures in the space of generalized coordinates: torsion angles, bond angles, bond lengths, positions free molecules and ions, and orientation of free molecules. Any generalized coordinate may be kept fixed. Molecules and fragments that are not expected to undergo significant conformational changes may be treated as rigid bodies. ZMM includes a Graphical User Interface (MVM) that is as easy to use as RASMOL or PYMOL. MVM is free and ZMM has a FREE DEMO for DOWNLOAD!  

  Nanocrystallography Visualizations:
Reported structures for several thousand inorganic crystals and small organic compounds. All data on this site have been placed in the public domain by the contributors (http://crystallography.net). Data are in Crystallographic Information File (CIF, not PDB) format. Visualizations of the crystal structures and molecules are in three dimensions using Jmol. CIFs can be downloaded.

  NOC: a program for protein structure visualization, validation, model-building and analyzing:
NOC provides an intelligent and flexible environment for displaying, manipulating, and analyzing small molecules, proteins and their interactions. The program is suitable for most common crystallographic work. Furthermore there are many unique features in NOC.  
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  OpenRasMol Home Page:
RasMol is a program for molecular graphics visualisation originally developed by Roger Sayle. This site is provided for the convenience of users and software developers of open source versions of RasMol. In order to ensure continuing availability of source code and documentation most programs and documents on this site are subject to copyright. This does not prevent you from using the open-source versions of RasMol, from making copies and changes, but prevents the creation of "closed source" versions out of the open source versions. Appropriate copyrights and licenses appear with the relevant sources and documents. See Copyright and NOTICE for applicable Copyright and other Notices.  

  Patmos - a Molecular Screensaver:
click to view large screenshot Patmos is a screensaver that lets you display your favourite molecules on your Windows PCs. As with Santorini it can load XYZ, Gaussian cube or PDB files and will gracefully rotate them in a 3-dimensional view. If your system contains more coordinate frames or models then Patmos plays each frame sequentially as an animation. Settings such as rotation speed, positioning of light source, graphics quality versus CPU usage and much more can be controlled from the "Display Properties | Screensaver" applet in the Windows control panel.

  PDB2MGIF:
PDB to MultiGIF
Visualization of chemical 3D structures on the web comes with problems because the web browser cannot display chemical structures without the help of additional software. If you create a page with a 3D structure of a molecule and the visitor of your page does not use this special viewer software for displaying molecules it cannot get the whole information of the page which should be meditated.

PDB2MultiGIF takes the 3D structure and generates an animated image which can be displayed using any browser. Thus every visitor of your page can get the whole information. It has many controls including size, number of frames, speed and axis of rotation, and if you wish, you can supply your own view as a RasMol script.

Bohne A.
PDB2MultiGIF: a web Tool to Create Animated Images of Molecules
J. Mol. Model. 4 (1998) 344-34

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  Persistence of Vision Raytracer:
POV-Ray is a freeware raytracer available for Windows, Macintosh, Linux, and generic unix platforms. Source code is provided. There are numerous tools which can use POV-Ray to render molecular information (e.g. pdb2pov).

  POLYVIEW:
POLYVIEW - all-in-one for protein sequence/structure analysis
POLYVIEW is a protein structure visualization web server that can be used to generate schematic representations of secondary structures and relative solvent accessibilities, allowing one to highlight selected residues, e.g. polymorphic or involved in protein-protein interactions.
SS along with RSA
2D schemes are dynamically generated and can be easily customized in order to facilitate the visual analysis of patterns of amino acid physico-chemical properties, secondary structure states, relative solvent accessibilities, and trans-membrane domains, all together.
Phys-chem along with TM
Beside the PDB deposited proteins, one can get a custom visualization of a protein structure submitted in the PDB format, or results from protein structure prediction servers in the CASP format, as well as arbitrary sequence profiles. Once submitted together, profiles can be aligned for a comparative analysis.
Aligned profiles PDB
SABLE
PSIPRED
Additional services of POLYVIEW provide user with an automatic interface recognition within a given protein complex, calculation of position specific amino acid conservation scores and generation of 3D animated images, which are ready for presentations and publications.
Polyview 3D Polyview 3D
No plug-ins required! For details and examples, please refer to the POLYVIEW documentation.

  Procreate:
Procreate is a protein visualisation tool that is written using the .NET Framework. It aims to provide a powerful, extensible environment in which users can easily customise the program to view the data exactly how they want. Some of the features include:


Mixed Display Modes Mixed Display Modes Mixed Display Modes Chain Display Mode

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  Protein Data Bank Viewer:
The program is viewer for PDB-Standard files and 3D visualization of the included Atom Structures

  Protein Explorer:

Protein Explorer is free software for visualizing the three-dimensional structures of protein, DNA, and RNA macromolecules, and their interactions and binding of ligands, inhibitors, and drugs. It is arguably the easiest-to-use software of its kind. It is suitable for high school and college students (ages 16 years and older), yet it is also widely used by graduate students and researchers. More about what Protein Explorer does. Protein Explorer makes the power of Chime accessible, offering extensive features both for novices and advanced features for protein structure specialists. Much easier to use, and much more powerful than RasMol. Extensive built-in context-sensitive help, QuickTour, Tutorials. For details, see Snapshots of Protein Explorer in Action, and Protein Explorer for Novices/Protein Explorer, Advanced.

  ProteinShader:

Ribonuclease Inhibitor Retinol-Binding Protein Porin Potassium Channel

ProteinsShader is a molecular visualization program that uses information from Protein Data Bank files to produce illustrative renderings of proteins that approximate what an artist might create using pen and ink. This free platform-independent open-source program is written primarily in Java, but also makes extensive use of the OpenGL Shading Language to modify the graphics pipeline. A graphics card supporting at least OpenGL 2.0 is required (OpenGL 2.0 was finalized on October 22, 2004).

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  ProteinShop:
ProteinShop is an interactive tool for manipulating protein structures. It was designed to quickly create a set of protein configurations using human knowledge and intuition. These configurations can be subjected to local or global optimization.

  Prototype Protein Viewer:
Prototype Protein Viewer (PPV) is an application that allows interactive viewing of linked two-dimensional and three-dimensional representations of biomolecular structures. This application takes advantage of the graphics capabilities of typical personal computers, features that were previously found only on high-end workstations. PPV can load simple Protein Data Bank (PDB) files for interactive viewing of a static structure, and it can import "trajectory" files containing many time steps of a molecular simulation.

This viewer is also an experiment in using DirectX for scientific visualization, which restricts it to computers running Windows 95 and higher. (NT 4.0, Linux, Macintosh will not work; Windows 98, Me, 2000 will work. The current version is limited to PDB files with a single protein chain.).

  PyMOL Molecular Graphics System:
A free and open-source molecular graphics system for visualization, animation, editing, and publication-quality imagery. PyMOL is targeted toward structural biologists, computational chemists, and scientific software developers. It has a graphical user interface, a scriptable command language, and can be extended using Python. Supports Windows, Mac OSX, and Unix. PyMOL functions as a stand-alone package but can serve as an ideal molecular interface and display engine for external software. It is also an effective tool for presenting real-time 3D graphics during seminars and meetings. Provides both OpenGL and ray-traced rendering and supports many different representations including sticks, spheres, cartoons, surfaces, and electron density.

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  Python for Structural Bioinformatics:
Python is an interpreted, interactive, object-oriented programming language. Because of its platform independence and object-oriented nature, it is often compared to Java. Python combines remarkable power with very clear syntax. It has modules, classes, exceptions, very high level data types, and dynamic typing. There are interfaces to many system calls and libraries, as well as to various windowing systems (X11, Motif, Tk, Mac, MFC). Legacy code written in C, C++ or Fortran can easely be made avalaible within a Python interpreter. Python is also usable as an extension language for applications that need a programmable interface. The Python implementation is portable: it runs on many brands of UNIX, on Windows, DOS, OS/2, Mac, Amiga, etc, and it is distributed under an OpenSource license agreement. An active community of users and programmers are constantly contributing new modules, extending the language with novel capabilities.

We have been using Python as a scripting framework to assemble basic components at a high-level. This approach enables the rapid development of custom applications for the visualization and manipulation of molecular data and provides an excellent level of code re-use. Besides being a very powerful "glue" language, its object-oriented nature makes it an appropriate language for the development of components. We have developed a number of Python extensions, also called packages, to deal with different aspects of structural biology. In this course, we will present some of these components and explain how they have been combined to create applications such as PMV: the Python Molecule Viewer and ADT: the AutoDockTools suite. Time permitting , we will also survey other Python-based applications such as MMTK and Chimera.

Full Description.

 

  Qmol:
An OpenGL based viewer for windows (95, 98, NT, 00) supporting the following features:

  QuteMol:
QuteMol is a intuitive real time high quality bio-molecular visualization software. It offers an array of innovative visual effects that are aimed to the creation of hi-res, hi-quality images with a greater clarity and an easier understanding of the 3D shape and structure of the molecule under inspection. QuteMol is portable and runs on all major platforms (Windows, MacOS X, Linux, most Unix flavors).
QuteMol view
A typical realtime rendering of QuteMol with ambient occlusion and a sophisticated edge cueing effect added.
QuteMol view
The 3D shape of very large molecules is difficult to be uderstood without ambient occlusion. Also this example (the 58k atom 1AON) is shown interactively.
QuteMol view
Even for small molecules, our ambient-occlusion adds to the clarity.
qutemol liquorice
Yet another QuteMol rendering featuring a fat liquorice mode and ambient occlusion.
 
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  Ramachandran Plot Explorer 1.0:

The Ramachandran Plot Explorer is designed to make it easy to examine the conformation of a polypeptide - through the interactive Ramachandran plot (phi-psi angles) and chi-angle tool. Simply click on a residue, then drag the marker on the Ramachandran plot.

To see how conformational changes might affect the energetics, I've included real-time calculation of H-bonds, weak H-bonds and steric clashes. This makes it easy to see why (i) certain regions of the Ramachandran plot are forbidden, and (ii) certain sidechain chi angles are favoured, (iii) the core is packed so tightly.

You can also edit (cut/paste/insert) protein sequences and mutate residues, with a simple click of the mouse.

I've worked hard to make an intuitive interface with lots of visual cues and feedback, and I've included what, I think, is a necessary set of navigating tools (sequence-bar, z-slab-bar, snake-measure tool).

There is a 3-point-clamp function, that (i) explores discrete solutions of a loop with fixed anchors and 3 hinge-residues, and (ii) allows the exploration of the phi/psi angles of residues inside the clamp without disturbing the rest of the protein.

This new version uses native widgets (standard file open/save dialogs!) and you can resize the window to your heart's content.

Limited to a single protein.

Now available for Linux, Windows and MacOSX.

  RasMol Home Pages:
There are two main RasMol websites:

  RasMol Home Page~ at UMass:
Featuring RasMol 2.6, authored by Roger Sayle, this site was founded in 1995. Here is the most extensive collection of RasMol resources and reference documents of any in the world. This site is visited by over 5,000 people per week, and RasMol has been downloaded from this site over half a million times. The site includes: The documents at this site pertain to RasMol version 2.6-beta-2a released in 1996. The download site links to RasMol 2.7 which contains the latest enhancements (not documented at the UMass site).
See also RasMol Home Pages.

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  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, Ortex, and XtalView in glorious 3D with highlights, shadowing, etc. Output is to pixel image files with 24 bits of color information per pixel. Distributed as source (tar+gzip), linux RPM, or MSWin binary.

  RasTop:

RasTop brings a friendly graphical user interface to the program RasMol. The result is a unique multi-windows, multi-molecular visualization program where atom manipulations are quick and simple, and do not require any typing on a command line. RasTop is an elegant standalone application for learning and teaching, but can be more than that thanks to its improved rendering quality and ability to restore any session at any given time. The code is available under an open-source license. A French translation is also available at the INRP site thanks to Naoum Salame. Windows and Linux (with Wine) platforms are supported.

  Reactor:


Reactor is the virtual reaction engine of Chemaxon's JChem technology. It supports "smart" reactions (generic reaction equations combined with reaction rules) generating chemically feasible products even in batch mode. The professional version of the tool includes support for multi-step virtual synthesis and filtering of chemically feasible molecules which are not of interest.

Key features:

To find out more about Reactor please visit our public implementation or download JChem Base (containing Reactor) from our web site.

Free for teaching and academic research through ChemAxon's Academic Package. Introduction, terms and application available from http://www.chemaxon.hu/forum/viewpost570.html#570

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  Reveal - a viewer for automated active-site predictions for polypeptides:
The model oriented on localization of areas responsible for ligand binding or protein-protein complex creation is based on characteristics of spatial distribution of hydrophobicity in a protein molecule: It is assumed that hydrophobicity changes from protein interior (maximal) to exterior (close to zero) according to the three-dimensional Gauss distribution (fuzzy oil-drop model). It is generally accepted that the core region is not well described by a spheroid of buried residues surrounded by surfaces residues due to hydrophobic channels that permeate the molecule. Therefore the simple comparison of theoretical (idealized according to Gauss function) and empirical spatial distribution of hydrophobicity in protein gives the opportunity to identify the regions with high deviation versus the ideal model. The viewer 'reveals' regions recognized by high hydrophobicity density discrepancy to be possibly functionally important sites in proteins.  

  Santorini - a Molecular Viewer:

Click to view large screenshot

Santorini is a free molecular viewer for Windows PCs. Supported file formats are XYZ files, Gaussian cube files and PDB files although this at present is restricted to only interpreting the ATOM and HETATM records. If your molecule file contains several coordinate frames of the same set of atoms then Santorini can play the file as an animation. Graphics can be exported as postscript. Santorini can calculate the radial distribution functions of systems employing periodic boundary conditions as well as the isotropic neutron scattering structure factor. Santorini can generate molecular surfaces for XYZ and PDB files.

  Screen:

Screen is a comprehensive high throughput screening tool in JChem. Screen contains a pharmacophore identification engine, chemical and pharmacophore fingerprint generator and a virtual HT screening tool to identify pharmacophoric analogues within small molecule libraries. The pharmacophore mapping tool offers customizable pharmacophore models as well as an optimizer to find the "best" screening metrics and parameter sets:
Free for teaching and academic research through ChemAxon's Academic Package. Introduction, terms and application available from http://www.chemaxon.hu/forum/viewpost570.html#570


To find out more or download JChem to evaluate the Screen tools, please visit the Screen page

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  Software for molecular modeling:

Ascalaph

Ascalaph is a general purpose molecular modeling suite that performs quantum mechanics calculations for initial molecular model development, molecular mechanics and dynamics calculations.

GPL

Features:

  Spock:
Spock is a full-featured molecular graphics program developed by Jon A. Christopher while in the lab of Thomas O. Baldwin of the Department of Biochemistry and Biophysics at Texas A&M; University. Spock has been designed from the ground up to be powerful, flexible and most of all, easy to use. Many of the features of spock are designed to bring molecular modeling programs into the age of the internet. Spock has the features users have come to expect from molecular graphics software including several bond and atom rendering types, and a complete array of backbone "worm" representations. Further, spock can calculate and display molecular and accessible surfaces, and color code these surfaces by properties (such as electrostatic potential). Images can be publication quality, and renderings include cylinders for alpha helices. Unix/irix/linux only. Free for non-profit use; fee for commercial use.

  STING:
STING is a PDB Viewer and Interactive WWW TOOL with emphasis on bi-directional coupling of sequence and 3D information. STING offers a simple and easy way to map single amino acid letter code information in a sequence to its position in 3D and vice versa! Special attention in STING is given to MacroMolecular INTERFACE analysis.

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  STING Millenium:


What is STING Millennium

STING Millennium is a web based suite of programs that starts with visualizing molecular structure and then leads a user through a series of operations resulting in a comprehensive structure analysis:

amino acid sequence and structure positions,with emphasis on bi-directional coupling of sequence and 3D information
pattern search, neighbors identification,
H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface.

In addition, a user can obtain:

sequence to structure relationships,
analysis of a quality of the structure,
nature and volume of atomic contacts of intra and inter chain type,
analysis of amino acid relative conservation at specified position among homologous proteins, and
Accessible Surface Area
relationship of relative conservation to the intra-chain contacts
functional parameters deciphered etc..


Such powerful combination of tools is available from a single site, eliminating needs for time-consuming data parsing. As a real treat, STING Millennium offers to the users a compilation of all these data through Protein Dossier module.

STING Millennium can also be used as an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins previously superimposed, can be displayed simultaneously and then analyzed. A user can compare active sites or any other relevant parts of structural alignment.

STING Millennium has been developed from original STING concept, however, we have completely rewritten all code and made a STING concept much more versatile. In terms of the system design the package is implemented using a variety of programming languages, each one better suited to a specific task:

Chime€ molecular visualization plugin (MDL inc.) to provide the molecular rendering
Sequence window written in Java€ that permits a complete control over the plugin and offers a series of services
A JavaScript interface making the bridge over the Java-plugin communication, which is specific for Netscape€ browsers
The PERL language is used as a wrapper for processing web requests
The C++ classes are used for more intensive programming tasks in structure parameter calculations


STING Millennium MODES:

STING Millennium has several working modes permitting its use with:

A single PDB structure (either from a database or single modeled structure in PDB format)
A structural alignment of several structures (structures previously aligned with CE or PRISM software)
A PDB structure along with a sequence alignment, containing the respective PDB sequence.

This offers a way to visualize sequence conservation/variation and correlate it with structural regions in the target protein. The structure can also have its residues colored by an index that indicates sequence conservation (sequence entropy) promoting a rapid identification of the sites subject to differential selective pressure

STING Millennium MODULES:

Several analytical programs developed by our group are listed under the modules entry in the main menu. They perform several tasks providing a powerful combination of tools to analyze the given PDB structure. These modules are:
HeSSper Graphical Contacts
Ramachandran Plot IFR Contacts
PDB file Text STINGPaint
HORNET PDB Cartoon
SCORPION Protein Dossier
FORMIGA ConSSeq


The HeSSper data base is being re - generated now. For this reason, HESPER option on STING Millennium Modules menu is inactive. As son as the data base is re - generated, this option will become available.

  Structural Alignment Program for Proteins:
STRAP is a work bench for multiple sequence alignments of proteins. It is used to visualize three-dimensional structures, to align several proteins using the amino-acid sequences or the xyz-coordinates of the c-alpha atoms and to highlight residues in the sequence and the 3D-structure. Superimposed proteins are shown in Pymol. STRAP currently integrates the protein viewers Jmol, Pymol, VMD and Rasmol. It is scriptable using java.

  SweetMollyGrace:
SweetMollyGrace is a suite of freeware tools for automating work of rendering and animating molecules. Imports molecules in PDB, MOL XYZ format (Babel) Generates high quality images of molecules using raytracing tools (Povray and Raster3D). Makes 4 kinds of animation (only rotation around axes) using frames generated by Povray, Raster3D, Rasmol and Qmol. Saves animation in AVI, MPEG, GIF, MOV and FLIC. Generates and views 3D files (without texture) in the following formats: VRML (WRL) Autocad (DXF), 3DStudio (3DS) Wavefront (OBJ) Lightwave (LWO) DirectX (X) and RAW. Imports and manages POV and VRML files generated by Accelrys "ViewerLite 5.0" (not included). Makes and views Postscript (PS) images.  
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  TRITON:
The program TRITON is a graphical tool for modelling protein mutants and assessment of their activities. Protein mutants are modelled based on the wild type structure by homology modelling using the external program MODELLER. Chemical reactions taking place in the mutants' active site are modelled using the semi-empirical quantum mechanic program MOPAC. Semi-quantitative predictions of the mutants' activities can be achieved by evaluating the changes in energies of the system and partial atomic charges of the active site residues during the reaction. The program TRITON offers graphical tools for the preparation of the input data files, for calculation and for the analysis of the generated output data. Implementation ensures the overall integrity of consecutive steps of the modelling of mutants and calculation of reaction coordinates, but the program can also be used simply for combinatorial generation of multiple mutants by homology modelling.  

  Unipro UGENE - Integrated Bioinformatics Tools:

Simple, fast and open source 3D-molecular viewer. Written in fast C++ code and QT library.

Available for Windows, Linux and MacOS X platforms.

Supports PDB and MMDB (starting from March 2009) formats.

 

  VeaR - the geometry-based structural highlighter for polypeptides in limited conformational subspace:
A unified description of protein structure is essential when structural similarity judgment, motif transitions or general folding are considered. In the applied approach, an assumption that all polypeptide chain conformations can be classified as helix-derived coerced invention of a new method of protein structure description based on geometrical parameters: radius of curvature R and dihedral angle between two consecutive peptide bond planes V. Developed basing on the model pentapeptides it helped to determine the general conformational subspace that turned out to be more useful than traditional φ/ψ mapping. The viewer allows to assign colors to the chain according to V/R parameters.

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  VEGA:
VEGA was developed to create a bridge between most of the molecular software packages, like Quanta/CHARMm, Insight II, MoPac, BioDock, etc. Most important features: File format conversion (several formats are implemented, like pdb, cssr, car, mopac, msf, gromos, etc.); calculation of several molecular properties like surface (saved in several format including VRML format), MEP, PSA, volume, dipole, logP (according to Broto's and Crippen's parameters), lipole, etc; trajectory analysis with the calculation of several properties on every frame; charge and atom type attribution trough ATDL language. The available versions are for SGI Irix, Linux, Windows, AmigaOS. A graphical version is also available for Windows with a user-friendly interface.

  VIDA:

VIDA is a graphical interface designed to visualize, manage and manipulate large sets of molecular information. It is capable of handling 100,000s of molecules simultaneously. It supports all standard visualization paradigms, including 2D depiction, both hardware and software stereo, surface selection and manipulation, and many other unique facilities.

VIDA is based on OpenEye's OEChem toolkit and as such handles chemistry properly as well as reading and writing a wide range of formats. The primary features include:

Like all OpenEye software, VIDA is available free of charge for non-commercial 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. Viewmol has originally been developed by Jörg-Rüdiger Hill and Andreas Bleiber in the Quantum Chemistry Group of Humboldt University with contributions by Arne Dummer, Mariann Krossner, Andreas Bünger, and Andries de Man. Viewmol was named an outstanding product in the German/Austrian Academic Software Award 1993.

What can I do with Viewmol ?

What files can Viewmol read ?

Viewmol is currently capable to work with

What files can Viewmol write ?

Viewmol can currently write

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  VMD:
VMD (Visual Molecular Dynamics) is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer. The VMD freeware is ready to run on linux, SGI, and Windows. The VMD source code is open.  

  WebLab (Accelrys) Viewer Lite:
Accelrys stopped offering ViewerLite in 2003, but on 2006 started offering a new version, "Discovery Studio Visualizer", with more features.
A macromolecular visualization utility including ribbon, tube and schematic renderings of protein secondary structure. This is the free version of the commercial WebLab Viewer Pro. The free version lacks many of the features of the latter, such as crystal visualization, animations, script playback, some modeling capabilities, hardware stereo, and sketching of molecular structures. WebLab Viewer Lite gives the highest quality images for printing available in freeware. (Molecular Simulations Inc. was renamed Accelrys Inc. on June 1, 2001.)

  WHAT IF Web Interface:
A free server that does protein model building, checking, repairing, structure validation, graphics, hydrogen bond identification, docking, crystal symmetry, mutation prediction, and many other things.  
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  XCrySDen - (X-Window) Crystalline Structures and Densities:

XCrySDen is a crystalline and molecular structure visualisation program, which aims at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated. It can run on most UNIX platforms, without any special hardware requirements.

XCrySDen has been also ported to MAC OSX (requires X11) and Windows (requires CYGWIN).

XCrySDen also provides a (partial) graphical user interface for CRYSTAL ab initio program, and a visualization system for PWscf and WIEN2k and initio programs.

Molecular (and general) visualising features: XCrySDen possesses more or less all the features that are expected from a modern molecular visualiser:

  1. representation of molecular-models in several display modes (wireframe, sticks, ball-and-sticks, spacefill, ...)
  2. display of forces acting on atoms
  3. real time operations such as rotation, translation and zooming of displayed structure
  4. animations
  5. measurement of distances, angles, and dihedrals
  6. contour-plane and isosurface representation of scalar fields
  7. "arrows" representation of the vector field
  8. setting various attributes, such as colours of atoms and bonds, radii of atoms, thicknesses of bonds and lines, sizes of points, balls and spacefills, just to name a few
  9. and more ...

Crystalline visualising features: In addition to the above described ``standard'' molecular visualising features, XCrySDen comes with an additional set of features that are necessary for visualising crystalline structures. Therefore XCrySDen is able to:

  1. switch between primitive and conventional cell settings
  2. change the number of the displayed unit cells, that is, display smaller or larger portions of a crystal
  3. display the crystal lattice
  4. visualise the Wigner-Seitz cell and Brillouin-zone
  5. k-path selection for band-structure calculations
  6. visualization of Fermi surfaces
  7. and more ...

  XdomView: A Graphical Tool for Protein Domain and Exon Position Visualization:

Enlarged image

XdomView (Version 2.1)
A Chime-based Graphical Tool for Protein Domain and Exon Position Visualization

XdomView is a chime-based visualization tool that maps the domain boundaries of the input PDB chain, obtained from protein structure classification databases (CATH, SCOP, NCBI, 3DEE and DALI) to its tertiary structure. It also runs BLAST2 for the input PDB chain sequence against all protein sequences in the ExInt* database and maps the intron positions and phases of aligned search results on the input protein's 3D structure. Xdom is a useful visualization tool for scientists working on gene and protein evolution and structural modeling and classification.

Contact Details :
Gopalan Vivek
, Dr. Tan Tin Wee, Dr. Shoba Ranganathan
Bioinformatics Centre
Department of Biochemistry
National University of Singapore
*ExInt - Repository of intron positions, phase and protein sequences of all multi-exonic eukaryotic genes available in GenBank 122.

 

  YAPView (Yet Another Protein Viewer):
YAPView is a simple OpenGL-based visualization program for displaying protein structure and folding trajectories. It supports different styles (ribbon, ball and stick, space filling, etc.), individual configuration for each residue, transparency effects, high resolution and postscript output of the rendered 3D images, among other features. YAPView has three aims: 1) To offer a basic, easy-to-use, multiplatform graphical tool for protein visualization. It doesn't try to match more complete and sophisticated visualization tools. 2) To focus in the display of dynamical information (e.g.: folding trajectories). 3) To provide an open and extensible interface allowing the addition of new features through the use of plugins.

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  YASARA View - Yet Another Scientific Artificial Reality Application:


is a molecular graphics and modeling program for Linux and Windows with a very intuitive user interface.

YASARA is powered by PVL (Portable Vector Language), a new development framework that provides performance way above traditional software. PVL allows you to visualize even the largest protein complexes at high frame rates.

Central features:

Click here to download YASARA now for free...

 

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