MOLECULAR VISUALIZATION SOFTWARE
Important URLS:
http://www.sdsc.edu/Resources/Software/software.html
http://dmoz.org/Science/Biology/Bioinformatics/Software/
http://people.cryst.bbk.ac.uk/~classlib/bioinf/related-sites.html
http://www.ccl.net/ccl/srs.html
http://www.ccl.net/chemistry/links/software/index.shtml
http://bioinformatics.org/software/index.php3
http://www.rcsb.org/pdb/software-list.html
http://www.umass.edu/microbio/rasmol/othersof.htm
SOFTWARE:
Cn3D
Chime
MolView
Protein Viewer
Swiss PDB
RasMol
Protein Explorer
Kinemage
WebMol
visualization
Garlic
a free molecular visualization program
GeneView
Interactive GenBank Entry Visualization
II
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 publicationquality secondary structure drawings of RNA molecules. Drawings
structural alignments
Swiss-PdbViewer is an application that provides a user
Deep View Swissfriendly interface allowing to analyse several proteins at the
PdbViewer
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 is a interactive protein modelling and display program. It was
BRAGI 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 WHAT IF is a versatile protein structure analysis program that can be
IF
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 was developed to create a bridge between most of the molecular
software packages, like BioDock, Quanta/CHARMm, Insight II, MoPac,
VEGA
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
MMTK2.2
molecular modeling tool-kit 2.2
Oslet
A molecular modeling and simulation environment in Java, mainly for
education.
WHAT IF is a versatile protein structure analysis program that can be
WHAT IF 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
Swiss-PdbViewer is an application that provides a user
Deep View Swissfriendly interface allowing to analyse several proteins at the
PdbViewer
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 is a molecular graphics system with an embedded Python
PyMol interpreter designed for real-time visualization and rapid generation of
high-quality molecular graphics images and animations.
Cn3D:
http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml
Cn3D is a helper application for your web browser that allows you to view 3dimensional 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:
http://www.umass.edu/microbio/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
http://www.enscp.jussieu.fr/labos/MAC/cense/mlv.html
MolView 2.5
http://pro122lin.chemie.hu-berlin.de/Molview/doku/
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:
http://www.alphaworks.ibm.com/tech/ppv?Open&t=0226,l=awb
Tutorials: http://bioinformatics.org/forums/forum.php?forum_id=622
Protein Viewer using Chime:
http://www.life.uiuc.edu/crofts/bioph2/pdb/chime_talk/chime_instructions.html
SwissPDB:
Deep View Swiss PDB Viewer: http://www.expasy.org/spdbv/
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:
http://www.umass.edu/microbio/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 (proteinexplorer.org). 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 (molvisindex.org), 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
(www.umass.edu/microbio/rasmol) pertains to RasMol version 2.6. Herbert Bernstein has
led the OpenRasMol.Org 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 OpenRasMol.Org to find out the latest offerings there,
which will not be listed here.
Protein Explorer:
Version 1.98: http://molvis.sdsc.edu/protexpl/frntdoor.htm
http://www.umass.edu/microbio/chime/explorer/
Version 2.1 Alpha: http://molvis.sdsc.edu/pe_alpha/protexpl/frntdoor.htm
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: http://www.cmpharm.ucsf.edu/cgi-bin/webmol.pl
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: http://www.cmpharm.ucsf.edu/cgi-bin/webmol.pl
WebMol API: http://www.cmpharm.ucsf.edu/~walther/webmol
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
http://www.ks.uiuc.edu/Research/namd/
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.