Non-Static Structure Visualization

Unlike a nucleotide sequence, which is a relatively static structure, proteins are dynamic entities that change their shape and association with other molecules as a function of temperature, chemical interactions, pH, and other changes in the environment.

Why Visualize?

In each area of bioinformatics, the rationale for using graphics instead of tables or strings of data is to shift the user’s mental processing from reading and mathematical, logical interpretation to faster pattern recognition.

Pattern recognition is an area where humans are much more efficient than computers.

Some Common Tools

100’s of visualization tools have been developed in bioinformatics.

Many are specific to hardware such as microarray devices.

Shareware utilities for PC’s

• PDB Viewer, WebMol, RasMol, Protein Explorer, Cn3D
• VMD, MolMol, MidasPlus, Pymol, Chime, Chimera

 Wireframe used to show individual chains:

Stick view showing atoms and bonds:

Surface View showing surface fields:

Ribbon view of secondary structure:

Other properties that can be visualized:

MolMol supports the display of electrostatic potentials across a protein molecule. MidasPlus (a predecessor of Chimera) allows for the editing of sequences visually to see the effects of point mutations.

The field is wide open.

To definitively characterize the interactions within the proteome, we need more tools. We need new metaphors for managing this complex data. We need tools to reveal dynamic relationships.

Umida Akhmedova, a prominent photojournalist in Uzbekistan, is facing criminal charges of insulting the Uzbek people. The charges stem in part from a 2007 album of photography depicting life in Uzbekistan’s villages. Here is a slide show featuring images from the album. 

Umida Akhmedova, the Uzbek [EN] documentary photographer, has been accused of insult and slander against Uzbek people and traditions, reports Fergana.ru [EN]. The maximum penalty for these charges includes remedial work on two up to three years or detention for up to six months.

According to Umida Akhmedova, captain Nodir Akhmadzhanov, investigator of the Tashkent [EN] city police department, told her that the criminal charges have been filed against all local authors who cooperated with the Gender Program of the Swiss Embassy. Akhmedova is incriminated in the production of “Women and men: from dawn till dusk” photo album [EN - phtos], produced in 2007 under support of Swiss Embassy Gender Program, writes Fergana.ru. There’s no information on other authors against whom the charges were filed.

According to the information received, on December 16, 2009, Ms. Umida Ahmedova was informed by the Mirobod Department of Internal Affairs that she was facing charges of “slander” and “insult” (respectively Articles 139 and 140 of the Uzbek Criminal Code) of the Uzbek people.

Those charges were brought by the Tashkent Prosecutor’s Office, in relation to her book of photographs entitled Women and Men: From Dawn to Dusk, which was published in 2007 and contains 110 photographs reflecting the life and traditions of Uzbek people, as well as to her documentary films Women and Men in Customs and Rituals and Virginity Code. She is facing up to six months’ imprisonment or from two to three years of “correctional work”.

These charges follow an investigation carried out in November 2009 by the Uzbek Agency of Media and Information into several books and films on gender issues that were produced in collaboration with the Gender Programme of the Swiss Embassy in Tashkent.

More pictures can be viewed at http://www.fergana.info/details.php?image_id=1220