About the Website

Calculating Diffusion Accessiblity

Protein Data Bank (PDB) file : The location of the PDB file to be uploaded can be entered. Only PDB files with less than twenty thousand atoms will be analyzed. If the protein you wish to analyze has more than the number of atoms allowed, please download the program to run on a Linux machine.

Grid Space : The grid spacing will determine the accuracy of the diffusion accessibility calculation. However, the time needed for the calculation will increase as the gridspace is made finer. If the gridspace is not specified, the program will choose the gridspace automatically. A typical grid spacing is one angstrom.

Graphics : Select if graphics are to be generated. The graphics consist of a movie of the protein rotated about the y-axis and a picture of the protein as it is loaded into PyMol.

Background color : selects the color of the background in the graphics.

Color scheme : selects the color gradient for the protein surface.

1. Red to Blue : red is labeled as most likely binding sites, blue is labeled as least likely binding sites.
2. Blue to Red : blue is labeled as most likely binding sites, red is labeled as least likely binding sites.
3. Green to White : green is labeled as most likely binding sites, white is labeled as least likely binding sites.

1. 3 : three colors used, recommended for Red to Blue and Blue to Red color schemes, the middle color is green.
2. 5 : five colors used, recommended for Red to Blue and Blue to Red color schemes.
3. 10 : ten colors used, recommended for Green to White color scheme.

Run times for PDB files

The real time run for the website is dependent on the PDB file, mainly due to the generation of graphics. Here, several proteins of different sizes were tested for time trials. Time with graphics : running time when graphics are generated. Time without graphics : running time when graphics were not generated.

Output of Diffusion Accessiblity

The output is composed of files and graphics.

Files for visualization : a PDB file with diffusion accessibility calculation in the temperature column.

Output files from programs used : a ".out" file with specific output and details of calculations from the diffusion accessibility program.

Graphics : all graphics are color-coded according to the schemes specified; the first is a moving graphic that depicts the protein rotating about the y-axis; the next picture is of the protein as it is first loaded into PyMol.

Formation of DINO Script

PDB File : Enter the location of the PDB file to be uploaded. The PDB file should be the PDB output file from the diffusion accessibility calculation, such that the calculation is contained in the B-factor column.

MSMS triangulation density : selects the triangulation density for the calculation of the molecular surface. MSMS man page.

1. Normal : rough density; default for the MSMS program; corresponds to 1.0 vertex per square angstrom.
2. Fine : density reasonable for typical graphics machines; corresponds to 2.0 vertices per square angstrom.
3. Very fine : finest density; corresponds to 4.0 vertices per square angstrom.

Output of DINO Script

Output files from programs used : Output files from running the MSMS program.

1. ".xyzr" : output from running pdb2xyzr.
2. ".msms" : output from running msms.

1. ".face" and ".vert" files : generated by running msms. Used in DINO to display the molecular surface.
2. ".dino" : DINO script written to load the PDB file, surface dataset, create the surface object, set temperature gradients, and color the surface according to the temperature column of the PDB file.
3. ".tar.gz" : a compressed file of the PDB file, ".xyzr", ".msms", ".face", ".vert", and ".dino" file. Using all files, and running .dino file, will generate molecular surface and color gradients.