Molecular Dynamics Group, University of Queensland
Molecular Dynamics Group, University of Groningen



Getting Started

Open a terminal window. On a Silicon Graphics machine use the mouse to select the 'Open Unix Shell' under the Desktop Menu. On Linux machines click on the terminal icon, or select 'Terminal' under 'Utilities' in the main menu. You need to be acquainted with UNIX vocabulary. Some UNIX commands you need to know can be found here.

Start by creating a subdirectory where all the files will be stored. This is done with the 'mkdir' command, specifying a name:

mkdir directory_name (e.g. your user name)

Now change to the directory by using 'cd' (or 'chdir'):

cd directory_name

Remember that every time you log off and in, you will first have to change to the directory where you have put your files in.

The starting structure

Modelling studies depend on the quality of the available experimental data. To generate an accurate structural model of Lysozyme we need information on its primary, secondary and tertiary structure. There are several publically available databases that contain primary, secondary and tertiary structural on proteins. Since the number of published sequences and structural information is increasing rapidly to find specific information we have to turn to specific search engines.

Two particularly important databases are:

Go to the ExPASy homepage and have a look around. It is best to open the page in a new window (click the right mouse button on the link and select 'open in new window').

Obtaining a Structure

To obtain a structure of lysozyme, the Protein Data Bank will be used. This database was established at Brookhaven National Laboratories (BNL) in 1971 as an archive for biological macromolecular crystal structures. Initially the archive held seven structures, and each year a few more were deposited. However, in the 1980s the number of deposited structures began to increase dramatically. This was due to the improved technology for all aspects of the crystallographic process (used to determine the three-dimensional structure of proteins), the addition of structures determined by nuclear magnetic resonance (NMR) methods, and changes in the community views about data sharing. In October 1998, the management of the PDB became the responsibility of the Research Collaboratory for Structural Bioinformatics (RCSB). Currently, the PDB contains over 18000 structures based on x-ray data, neutron diffraction data, NMR data and theoretical models.

To find structural information on lysozyme first open the following link in a new window (right click with the mouse, open link in new window):

This is the homepage of the Protein Data Bank (PDB). The PDB is an international repository for publically available information on the structures of biomolecules. If you want to know more about using the PDB you can see the narrated tutorial provided.

To find structures of lysozyme we can just try the text based keyword search option at the top of the page. Type the word lysozyme and click 'Site Search'. This query will return almost 1000 structures, which is the number of entries in the PDB containing the word 'lysozyme'. For simulations high resolution structures are preferred. Refine the search to yield only these structures. To do this, go back to the homepage and select the 'Advanced Search' interface. This gives a customizable search form.

This allows you to restrict the seearch based on various criteria. First select the query type 'Structure Title' in the field 'Structure Summary'. Insert 'Lysozyme' in the box provided and click 'Evaluate Subquerey'

You can then restrict the search just to high resolution X-ray structures by activating a new query field by selecting the '+' and then selecting a new query type 'X-Ray Resolution' in the field 'Materials and Methods'. Search for structures with a resolution between 1.0 A and 1.5 A by typing the appropriate values in the boxes provided and and clicking 'Evaluate Subquerey'. This gives all structures in the databank that fall within this range in resolution. To evaluate the two queries in combination Select 'Evaluate Query' in the lower right hand corner.

This still gives more than 50 structures. We could continue to refine the search by adding more criteria such as the source organism. However, we just need to find the structure with the identifier '1AKI' as this is the structure we will use during these exercises. Use the 'Site Search' at the top of the page and type '1AKI'.

The various 'Display Options' such as 'KiNG' can be used to view the structure.

To download the file containing information on the three dimensional structure go to the option 'Download Files' and select 'PDB text'. A window will appear to save the file. Click 'Save to Disk' to start the download. By default this will download the file to the Desktop. You will need to use the file manager to transfer the file from the desktop to the working directory you created.

Getting Started
MD Theory
MD Practice

©2005 T.A.Wassenaar