MOLECULAR VISUALIZATION SOFTWARE



MOLECULAR VISUALIZATION SOFTWARE

Important URLS:

















SOFTWARE:

Cn3D

Chime

MolView

Protein Viewer

Swiss PDB

RasMol

Protein Explorer

Kinemage

WebMol

visualization

|Garlic |a free molecular visualization program |

|GeneView II |Interactive GenBank Entry Visualization |

|gff2ps |Converting genomic annotations in GFF format to PostScript |

|ModView |ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments. |

|PyMol |PyMOL is a molecular graphics system with an embedded Python interpreter designed for real-time visualization |

| |and rapid generation of high-quality molecular graphics images and animations. |

|rasmol |RasMol is a free program which displays molecular structure. |

|VEGA |VEGA was developed to create a bridge between most of the molecular software packages, like BioDock, |

| |Quanta/CHARMm, Insight II, MoPac, etc. In this tool have been also implemented some features that are useful to|

| |analyze, display and manage the 3D struct |

|VMD |VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems |

| |using 3-D graphics and built-in scripting |

VMD

|NAMD |NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large |

| |biomolecular systems. |

structure

|Abacus |ABaCUS is a no-frills program developed to investigate the significance of the putative correspondence |

| |between exons and units of protein structure. |

|caRNAsta |Comparative Analysis of RNA structures by Tree Alignment |

|CNS |The 'Crystallography & NMR System' for macromolecular structure anaylsis |

|cove |COVE is an implementation of stochastic context free grammar methods for RNA sequence/structure analysis. |

|Garlic |a free molecular visualization program |

|LIBELLULA |LIBELLULA is a neural network based web server to evaluate fold recognition results |

|MODELLER |a program for homology protein structure modelling by satisfaction of spatial restraints. |

|ModView |ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments. |

|MOPAC7 |a general-purpose semi-empirical molecular orbital package for the study of chemical structures and |

| |reactions. |

|PyMol |PyMOL is a molecular graphics system with an embedded Python interpreter designed for real-time |

| |visualization and rapid generation of high-quality molecular graphics images and animations. |

|RNA GENiE |A web based program for the prediction of rna genes in genomic DNA sequences |

|RnaViz |a user-friendly, portable, GUI program for producing publication-quality secondary structure drawings of RNA|

| |molecules. Drawings |

structural alignments

|Deep View Swiss-PdbViewer |Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyse |

| |several proteins at the same time |

structural biology

|DINO |a realtime 3D visualization program for structural biology data. |

protein structure

|Abacus |ABaCUS is a no-frills program developed to investigate the significance of the putative correspondence |

| |between exons and units of protein structure. |

|Garlic |a free molecular visualization program |

|LIBELLULA |LIBELLULA is a neural network based web server to evaluate fold recognition results |

|MODELLER |a program for homology protein structure modelling by satisfaction of spatial restraints. |

|ModView |ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments. |

protein structure modelling

|MODELLER |a program for homology protein structure modelling by satisfaction of spatial restraints. |

protein structure prediction

|LIBELLULA |LIBELLULA is a neural network based web server to evaluate fold recognition results |

protein/DNA/RNA family clustering

|ModView |ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments. |

protein interaction

|ZDOCK |Protein-protein complex structure prediction software |

protein modelling

|BRAGI |BRAGI is a interactive protein modelling and display program. It was developed for the special purpose to modell |

| |unknown proteins from the structure of a known one |

molecular mechanics

|AMMP |a modern full-featured molecular mechanics, dynamics and modeling program. |

molecular modeling

|Oslet |A molecular modeling and simulation environment in Java, mainly for education. |

|WHAT IF |WHAT IF is a versatile protein structure analysis program that can be used for mutant prediction, structure |

| |verification, molecular graphics, etc |

molecular modelling

|Babel |a program designed to interconvert a number of file formats currently used in molecular modeling |

molecular rendering

|Garlic |a free molecular visualization program |

molecular simulations

|Oslet |A molecular modeling and simulation environment in Java, mainly for education. |

molecular visualization

|Garlic |a free molecular visualization program |

|rasmol |RasMol is a free program which displays molecular structure. |

|VEGA |VEGA was developed to create a bridge between most of the molecular software packages, like BioDock, Quanta/CHARMm, |

| |Insight II, MoPac, etc. In this tool have been also implemented some features that are useful to analyze, display and|

| |manage the 3D struct |

|VMD |VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using |

| |3-D graphics and built-in scripting |

molecular visualization program

|Garlic |a free molecular visualization program |

modeling

|AMMP |a modern full-featured molecular mechanics, dynamics and modeling program. |

|Kintecus |Run chemical kinetics/fitting of catalyst reactor, and enzyme reactions |

|MMTK-2.2 |molecular modeling tool-kit 2.2 |

|Oslet |A molecular modeling and simulation environment in Java, mainly for education. |

|WHAT IF |WHAT IF is a versatile protein structure analysis program that can be used for mutant prediction, structure |

| |verification, molecular graphics, etc |

Molecular Dynamics high performance simulator

|Gromacs |The World' s fastest Molecular Dynamics - and it' s gpl |

molecular dynamics modeling pdb force field

|MMTK-2.2 |molecular modeling tool-kit 2.2 |

molecular dynamics simulations

|GDIS |a GTK based program for the display and manipulation of isolated molecules and periodic systems |

electron density maps

|Deep View Swiss-PdbViewer |Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyse |

| |several proteins at the same time |

chemical structures

|MOPAC7 |a general-purpose semi-empirical molecular orbital package for the study of chemical structures and reactions. |

bond and atom rendering

|Spock |a full-featured molecular graphics program |

3D structure visualization

|PyMol |PyMOL is a molecular graphics system with an embedded Python interpreter designed for real-time visualization and |

| |rapid generation of high-quality molecular graphics images and animations. |

Cn3D:



Cn3D is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service. Cn3D runs on Windows, Macintosh, and Unix. Cn3D simultaneously displays structure, sequence, and alignment, and now has powerful annotation and alignment editing features.

Below is a relatively simple sample of what Cn3D can do. There are many more examples in the Tutorial, along with instructions to help new users get started!

Chime:



Chime is a free program to show molecular structure in three dimensions. Its images look like RasMol's because Chime is derived, in part, from RasMol. Chime differs from RasMol in that Chime sits directly on a web page (runs inside your browser as a plug-in), whereas RasMol is a standalone program (runs outside your browser, independently). Chime also differs in that most Chime websites show only the molecule(s) provided by the author of the web page you view, whereas RasMol can show any molecule for which you have an atomic coordinate (PDB) file. However, some Chime websites also provide support for showing any molecule of interest, and doing self-directed exploration similar to RasMol, notably Protein Explorer.

Chime's ability to support educational resources has had a large impact on stuctural biochemistry education, as exemplified by the many excellent resources indexed in the World Index of Molecular Visualization Resources.

Chime can be downloaded from the web site of its creators, MDL Information Systems, Inc. See Chime: Browsers, Platforms, Installation, Troubleshooting . The UMass Chime Resources illustrate what Chime is cabable of, document Chime, and make it easier to develop Chime presentations. An ongoing discussion of technical issues about Chime may be seen in the history of the RasMol email list.

MDL® Chime is a plug-in that interactively displays 2D and 3D molecules directly in Web pages. You can rotate, reformat, and save the molecules for use in other programs. You will be required to accept a license agreement when you install the program. To preview the agreement, which explains the permitted and nonpermitted uses of this no-fee software, click on the End User License Agreement link below.

MolView:

Molecular Graphics for the Macintosh



MolView 2.5



MOLVIEW is a collection of tools, which were written to simplify the work with some common ab initio program packages (Gaussian, Molpro, Molcas). There are mainly two areas of application: preparation of inputs for and evaluation of outputs of the ab initio programs. The latter function solely uses the unformatted logfiles. Since the arrangement of the data in these files strongly varies depending on the kind of the job, there is, unfortunately, no guaranty that MOLVIEW's tool work correctly in all cases. Therefore, please be critical of the results produced by MOLVIEW and report errors and suggestions for improvement to the author.

Let me now briefly present the key features of the program. It consists of six tools with different functions.

Protein Viewer:

Prototype Protein Viewer:

Tutorials:

Protein Viewer using Chime:

SwissPDB:

Deep View Swiss PDB Viewer:

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.

Moreover, Swiss-PdbViewer is tightly linked to Swiss-Model, an automated homology modeling server developed within the Swiss Institute of Bioinformatics (SIB) in collaboration between GlaxoSmithKline R&D and the Structural Bioinformatics Group at the Biozentrum in Basel.

Working with these two programs greatly reduces the amount of work necessary to generate models, as it is possible to thread a protein primary sequence onto a 3D template and get an immediate feedback of how well the threaded protein will be accepted by the reference structure before submitting a request to build missing loops and refine sidechain packing.

Swiss-PdbViewer can also read electron density maps, and provides various tools to build into the density. In addition, various modeling tools are integrated and command files for popular energy minimization packages can be generated.

Finally, as a special bonus, POV-Ray scenes can be generated from the current view in order to make stunning ray-traced quality images. An example can be found here .

RasMol:



If you are new to RasMol, and if you are using Windows or Macintosh, we strongly recommend that you start with Protein Explorer instead of RasMol. Protein Explorer (PE) is much easier to use, and much more powerful. PE's first image of a molecule is maximally informative (and explained) while RasMol's is an uninformative wireframe display (no explanation). PE has a "select" menu (lacking in RasMol), and you don't need to learn any commands to use PE! PE can show molecular surfaces (not available in RasMol), salt-bridges, and cation-pi interactions (each in one click!). Every color scheme (e.g. polar/nonpolar, lacking in RasMol's Color menu) is accompanied by a color key. Want to find the position of a residue in the amino acid sequence? No problem, use PE's Seq3D clickable sequence display (accessed by clicking Mol Info).

If you are familiar with RasMol, and if you are using Windows or Macintosh, we strongly recommend that you use Protein Explorer instead (). You'll learn a lot more, faster, because of PE's ease of use and greater power. Want to see noncovalent interactions? Try PE's Contact Surface display (one click). Want to see the complete oligomeric form of your molecule? Click on Mol Info, then Probable Quaternary Structure. Want to locate the most evolutinarily conserved residues in a 3D image of your protein? Click on Mol Info in PE and go to the ConSurf Server which will color your protein by conservation and display it in PE. Hate to give up all those RasMol commands you've already learned? No problem, you can enter all of them -- they all work in PE! (But you don't have to learn any!)

Even if you use linux or another flavor of unix, you can still use Protein Explorer on unix.

For those who still wish to use RasMol, links to RasMol resources are below. Beware that maintenance of this site largely stopped in 1999 with the advent of Protein Explorer. Updated lists of resources are available through the World Index of Molecular Visualization Resources (), including ready-to-use tutorials on over 50 proteins and nucleic acids (many with lesson plans).

RasMol users should be aware that the documentation here (umass.edu/microbio/rasmol) pertains to RasMol version 2.6. Herbert Bernstein has led the project which provides RasMol version 2.7, together with an updated Reference Manual, and versions of RasMol for several languages and platforms. RasMol users should please visit to find out the latest offerings there, which will not be listed here.

Protein Explorer:

Version 1.98:



Version 2.1 Alpha:

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.

WebMol:

Java PDB Viewer:

Download WebMol (inludes a stand-alone version (Java application). Options of using WebMol in your Java programs, running WebMol as a browser helper application and the optimization of the performance applying JITs are documented.

WebMol was designed to display and analyze structural information

contained in the Brookhaven Protein Data Bank (PDB). 

It can be run as an applet or as a stand-alone application.

Availability:

CGI interface/ WebMol home:

WebMol API:

To download WebMol, please fill out the Academic License request form.

For installation instructions see the ReadMe.

Graphical features include:

- wireframe representation of structures with full atomic detail

- different color coding schemes

    * atom type

    * secondary structure

    * B-factor

    * chain

    * burial state

    * sequence conservation according to HSSP

- side-by-side stereo view with adjustable separation of the images

- mouse driven zoom, translate and drawing slab manipulations

- selecting focus; i.e. setting point of rotation to a desired position

- selecting residues according to type or burial state and regions within proteins

- animations of rocking motions with adjustable angular range

- variable background colors

Tools

- distance, angle, dihedral angle measurements

- detection of steric conflicts

- peptide bond planarity analysis

- interactive distance matrix plot and other 2D-projection plots

- interactive Ramachandran plot

- dot surface

- numerical calculation of solvent accessible, van der Waals surface area, and volume

- detection of cavities

- axes assignments for secondary structural elements

- secondary structural element packing analysis

- hydrophobic moment vectors of secodary structural elements

- mainchain-mainchain hydrogen bond detection

Input options

- URL, ftp, file, text string

- Format: PDB

Output options

- Postscript

NAMD:

Sacalable Molecular Dynamics



NAMD, recipient of a 2002 Gordon Bell Award, is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using switched fast ethernet. NAMD is file-compatible with AMBER, CHARMM, and X-PLOR and is distributed free of charge with source code. You can build NAMD yourself or download binaries for a wide variety of platforms. Our all-new tutorials show you how to use NAMD for biomolecular modeling.

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