Sana's presentation

PROTIEN EXPLORER

Sana Bashir

Protein Explorer

Protein Explorer is a protein visualization software. Strictly speaking, "molecular visualization" means looking at a structure without changing it.

The resulting "model" comes straight from the PDB file.

RasMol

Protein Explorer is a RasMol-derivative software developed by Eric Martz

In 1989, Roger Sayle became interested in the problem of depth perception for computer representations of solid objects. His goal was to write a shadowing program (ray-tracing algorithm) fast enough to allow rotating the shadowed image. He managed to write the second fastest sphere-shadowing program in the world!

This algorithm was implemented in RasMol as well as Protein Explorer

Ray tracing

Ray tracing is a method of generating realistic images by computer, in which the paths of individual rays of light are followed from the viewer to their points of origin.

The algorithm begins by shooting a ray from the eye and through the screen, determining all the objects that intersect the ray, and finding the nearest of those intersections. It then recurses (or repeats itself) by shooting more rays from the point of intersection to see what objects are reflected at that point, what objects may be seen through the object at that point, which light sources are directly visible from that point, and so on.

Ray tracing (continued…)

As the ray travels from the eye, it intersects A, is subsequently reflected to B, then reflected to C, and so on.

Ray tracer calculates the angle at which the ray should bounce off, and then create another ray that will travel from the point of intersection in the calculated direction. Once that ray figures what color it needs to be (by calculating all the intersecting objects, finding the nearest one, and determining the surface color at the point), the first ray is then given that color. This is then propagated back to the pixel through which the original ray was fired.

In this case, D is transparent, and the light is bent both on entering the sphere, and again on exiting it

Ray tracing (continued…)

The ray travels from the eye to where it intersects with sphere A. In order to determine whether there is a shadow at that point, one shadow ray is fired at each light source. The shadow ray from A to the second light source travels uninterrupted, so light reaches the point from that light source. However, sphere B lies between sphere A and light source #1, so the point is in shadow with respect to that light source. The intensity of color at that point on sphere A would represent the fact that only one of the two light sources is shining directly on that point.

Why create Protein Explorer? Need for a software more efficient than RasMol in

the following: maximally informative illustrated introductions to computer renderings such as

clicking on any atom to identify it More powerful rendering options context-triggered help user friendly interface for novice as well as advanced MDL's Chime - a visualizer in the form of a Netscape

Navigator plug-in. Chime uses an adaptation of the rendering and command-language from RasMol. About 16,000 lines of RasMol source code were converted to C++, made reentrant, and built into Chime

Background

Older versions dealt with compatibility issues with Windows, Macintosh OS. As well as problems loading PDB files and running command script files

Beta 1.98 included Protein Comparator, discontinued in later versions. Unable to load PDB files directly from the Protein Data Bank

Background (continued…)

New Version: Can create MolSlides (molecular structures that

user generates). MolSlides display in a web browser, without Protein Explorer, from your computer or from a server, on-line.

MolSlide Manager Compatibility with Netscape 7, Mozilla, Firefox

browsers You don't need to learn any hand-typed

commands to achieve a very high level of visualization power.

Protein Structure Rendering

PE cannot show you a protein if all you have is the amino acid sequence, needs atomic coordinates from the PDB file.

Most macromolecular structures are determined experimentally by X-ray crystallography. However, if 3D structure is not available. A reasonably reliable structure can be predicted by homology modeling.

PE does not support homology modeling  

Protein Explorer enables you to see the relations of 3D molecular structure to function. The image can be simplified by hiding everything except the region of interest. A variety of one-click renderings and color schemes help to visualize the backbone, secondary structure, distributions of hydrophobic vs. hydrophilic residues, noncovalent bonding interactions, and protein comparison

Protein Explorer Functionality

A function of PE that provides side-by-side comparison of two molecules (PDB files) with all the same capabilities as the one-molecule

Currently working on implementing in new version directly via browser.

PE Comparator Function

Same or Different?

Non-covalent bonds In PDB files, you will not see the noncovalent bonds

between neighboring molecules in a protein crystal

At present, PE can display as rods connecting atoms only two subsets of hydrogen bonds: protein backbone-to-backbone h-bonds within chains (but not between chains), and Watson-Crick h-bonds between DNA base pairs. PE presently has no built-in routines to show h-bonds between backbone and sidechain, backbone and water, sidechain and sidechain, sidechain and water, protein and ligand, protein and nucleic acid, non-canonical h-bonds in DNA or RNA, etc. However, manual methods are available to show arbitrary bonds.

How to use?

Go to protienexplorer.org Install MDL Chime Click on quick start button, it will automatically open

up the software with a protein given

Molecular Image: 3D view of protien

Control Panel: control to explore the structure

Message Frame: identity of specific atom,chains, amino acid residues

PE Feature Limitations Visualize a molecule given only a sequence of amino acids and

nucleotides There is visualization but there are no modeling capabilities in PE. Cannot generate new molecular structures or modify old ones Build, mutate bonds in a structure No Docking, It is not possible to load multiple PDB files into Chime,

nor move molecules relative to each other in a single Chime image. Two molecules can be displayed side by side in Protein Comparator, and moved together in synchrony or independently. Two molecules can be aligned and displayed together, but cannot be moved relative to each other.

Saving the state of your PE session is problematic. You can save a command script to play back later, but this is technically challenging. A script recorder is under development to help this situation.

PE Limitations (continued…)

The positions of covalent bonds may be shown incorrectly. Some strong bonds may not be shown as rods (especially involving metals, or between hetero atoms and protein or nucleic acid), or occasionally bond rods may be shown where only noncovalent bonds exist.

Only a very limited subset of hydrogen bonds can be shown easily.

There is no Undo capability yet. Images are not always high enough quality. Cylinders are not available as a cartoon rendering for

alpha helices.

Technical Limitations

PE requires the free but closed-source MDL Chime plug-in

The Sequence and Seq3D displays show nonstandard residues as gaps

There are some rare PDB files that PE does not handle correctly.

When certain states are changed with manually issued commands, or from Chime's menu, related buttons may lose track of the status of the image.

Some records do not appear in MolSlides

Future Implementations

PE-Jmol? In the long term, attempts to port PE to use the Jmol java applet instead of MDL Chime. Jmol is free, has an open-source licence and development team, and operates on a wider range of platforms and browsers than does MDL Chime.

Plan to connect PE to a server that will provide a PDB file suitable for displaying all contacts (including non-covalently bonded atoms) to the asymmetric unit for any crystallographic PDB file.

A mechanism to locate and display all hydrogen bonds, including buttons to show categories such as backbone-backbone, backbone-sidechain, sidechain-sidechain, interchain, water bridges.

References

Protein Explorer 2.79 Beta E. Martz, Protein Explorer: Easy Yet Powerful

Macromolecular Visualization, Trends in Biochemical Sciences 27 (2002) 107-109.

Protein Explorer (Chime) http://www.umass.edu/microbio/chime/pe_beta/pe/protexpl/frntdoor.htm

RasMol & Protein Explorer http://www2.uah.es/biomodel/pe/1/protexpl/pe_v_ras.htm

Chime http://www.umass.edu/microbio/chime/