Download Protein visualization

Jyri Soppela 62947A
Kalle Karhu 63804C
Protein visualization
Introduction
Proteomics is a growing field of science, where numerous scientist groups study protein structures
and function in biosystems. The vast amount of protein data produced is stored in Protein Data
Bank (PDB), where anyone can download information about specific proteins freely. PDB data
includes information about the protein structure, but making this data easily understandable is a
problem. Protein visualization is a field of study that aims to present protein data clearly in
scientific articles, teaching and study. There are numerous applications available, most of them free
for non-profit scientific or educational purposes. The programs have some compatibility problems
and many of them are unstable. However, updates are available often. The programs are capable of
showing the protein macrostructure as a 3D model and giving other crucial information about the
protein functions and structure.
Protein Data Bank
“The mission of the wwPDB(world wide Protein Data Bank) is to maintain a single Protein Data
Bank Archive of macromolecular structural data that is freely and publicly available to the global
community.” (www.wwpdb.org) This pretty much summarizes it: PDB is a communion of several
institutes around the world and it makes protein information universally accessible in a single
format. It has currently 33351 entries, and the number of entries deposited each year has more than
doubled since year 2000. Proteins in PDB have a PDB identification code and can be easily
accessed with that code. A PDB file contains information about the amino acid chain,
macrostructure, the founder and the finding methods. It also gives information about the functions
and classification of proteins. All proteins in PDB are not from humans, as it accepts universally
any protein structures.
Visualization methods
The easiest way to present a protein structure is to build a 3D model of it. Visualization programs
allow user to view and rotate the model and change the model structure to find the desirable
information from it. Common way to visualize proteins are building a wire framework of the amino
acid chain and to present alpha helixes and beta sheets with ribbons to make them stand out.
Depending on the desired information, other visualization methods may be handier. Representing
single atoms as spheres will give a good idea of the protein overall shape, but will give little
information about the amino acid backbone folding. Representing carbon bonds as tubes or
cylinders gives information about both the overall shape and backbone structure, but may prove
confusing and unclear with expecially large proteins. Huge complexes like hemoglobin are usually
best viewed in smaller parts, which is possilbe by making other parts transparent or invisible.
Functional information, like hydrophilic and hydrophobic parts, hydrogen bonds and active sites are
also available in most programs. Distances beetween atoms and bond angles are usally also
available. Some programs allow the tesing of mutations. It is possible to change a amino acid to
another one, but the simulation of the consequences of such a change is incomplete.
Selection of molecular visualization programs
Protein Explorer
Description
Protein Explorer is a software for looking at macromolecular structure and its relation to function. It
is a RasMol-like interface implemented in Chime, but that the Protein Explorer can offer much
greater assistance and automation. Thus, the Protein Explorer can make visual exploration of
protein structure much more accessible to novices, occasional users, or nonspecialists, as well as
making it much more convenient than RasMol, even for experts. Protein Explorer supports nearly
all RasMol commands, plus additional Chime-specific commands. However, Protein Explorer
version 1.71 Beta is much easier to use, and considerably more powerful than RasMol. Much
exploration can be accomplished without learning any of the command language common to
RasMol and Chime. The main goal is for novices to be able to concentrate on the molecular
structure, not on the software required to see it. It can be used on Unix or Windows 95/98/2000/NT
or Power Macintosh machines.
Protein explorer is considered to be one of the best visualization programs for beginners, as there’s
lots and lots of help available in the forms of demo-videos and documents. You’re also obligated to
install the free MDL Chime browser plugin, which requires registeration on their site, which can be
counted as a small downside for the program. However, the user has total control over the
molecular views and is also able to undo last done modifications to the view. User is also able to
create MolSlides and thereby save and restore earlier sessions. This also enables session sharing
over the internet. The Protein Explorer has been awarded in 2003 for revolutionizing teaching of
biology at molecular level by National Science Foundation.
Figure 1: The start of usage and installation has been made extremely beginner friendly
User Notes
The biggest downsides of this program are probably the fact that it isn’t easily expanded and you
have to register to MDL to download it. Other than that, it is very easy to use and there seem to be
lots of databanks available for all kinds of molecules. It took about 5 minutes to get the view I
wanted:
Figure 2: Adenine and Thymine bonding showed in the Protein Explorer environment.
The Internet Explorer environment makes the program very easily accessible and gives a familiar
feeling to the user from the first moments you spend with this program.
Overall, I’d consider Protein Explorer very user friendly, yet a bit limited program for visualizing
smaller molecular structures.
PyMol
Description
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. It is
fully extensible and available free to everyone via the "Python" license. Although still early in
development, PyMOL can already be used to generate molecular images and movies with relative
ease.
The program runs on Linux (or any Unix), MacOS and Windows.
PyMOL is a user-sponsored molecular visualization system on an open-source foundation, so it’s
purely non-commercial as are the other programs presented in the article.
The user interface is designed over Python coding and a visual user interface which can be
controlled by mouse, allowing easy rotation of molecules and selection of single atoms, for an
example.
Figure 3: PyMOL (software-rendering) running under Darwin/XFree86 on an OSX Mac
Figure 4: PyMOL is capable of visualizing very complicated structures.
User Notes
The installation of the program for windows was as simple as any other imaginable program for
windows is, nothing fancy. The actual using however was nowhere near as easy to learn as with
Protein Explorer. I wouldn’t call this program an entry level one, even if there are average manuals
available for it. The ease of use for new users isn’t even intended by the designers since the overall
development has been focused on capabilities. On a contrary to the Protein Explorer presented
before, the PyMOL can be expanded by the user. The click and drag interface is also better than
what Protein Explorer had to offer. Overall, the program is one of the high-end programs of the
open source ones, allowing nearly endless amounts of actions. However, this is not a program for
the beginner and requires somewhat lot of time to fully comprehend.
Biodesigner
Figure 5: Biodesigner has neat options for single atom and backbone visualizations
Description
This is a protein visualization and modelling program by Piotr Rotkiewicz. It includes a sequence
processor and has versatile visualization options for single atoms and polypeptid backbones. It is
possible to construct your own proteins by using the sequence maker, altough this is a slow process.
Biodesigner supports several data types and uses its own file type to store works. It has algorithms
for protein superpositioning and chain refinement.
User Notes
Biodesigner shows great potential, but is way too unstable and prone to malfunctioning. Some of
the program features work poorly and it crashes often. The user interface is pretty simple and fast to
learn, as all the zooming, selecting and rotating f
unctions can be operated by mouse. The visualization options are pretty good, and hyprophobicity
among others can be visualized with coloring options. The documentary is lacking and can only be
found in the program home page. This program has not been updated since 2002, so fixes are not
likely to be available soon.
Chimera
Description
Chimera is a molecular graphics computer application by UCFC, whose previous software was
MidasPlus. Chimera is very extendable and has Python as a “native” language. It is entirely possible
to implement new functions in Python language. Chimera is built so that the core is very simple and
most of the other features are implemented as extensions. Chimera runs on SGI, Compaq/DEC
Alpha, Linux, and Windows platforms.
User Notes
This program had a great documentary an simple tutorials to start with. There were also some
brilliant demos, and it is possible to create your own demos with animation, explanations and text
labels. We found this program most suitable for beginners who demand a lot of features. Compared
to Biodesigner, Chimera was much stabler but still has some minor problems. The extension
possibilities include an easy editor for demos, which could be very useful for teaching purposes.
Other expansion possibilities vary from use to use, but there’s for example H-bond calculator in the
basic features.
Figure 6: Chimera has easily accessible visual manipulation tools.
References
http://pymol.sourceforge.net/
http://www.umass.edu/microbio/chime/pe_beta/pe/protexpl/
http://www.pirx.com/biodesigner/index.shtml
http://www.cgl.ucsf.edu/chimera/