VMD Tutorial-Protein Structure Prediction

Protein 3D structure prediction can be done as long as the amino acid sequence of the target gene is available, regardless of species.

Commonly Used Software for Protein Structure Visualization


2.VMD powerful free protein 3D structure visualization software

Swiss-PdbViewer (also known as DeepView) is an application that provides a user-friendly interface and allows simultaneous analysis of multiple proteins. Proteins can be overlaid to infer structural comparisons and compare their active sites or any other relevant parts.

4. Phyre2 homepage (http://www.sbg.bio.ic.ac.uk/phyre2)

Tutorial of Protein Structure Prediction

1. Open the VMD and operation interface

Double-click the VMD icon will pop up three windows, we mainly use the main window to operate, the display window is the interactive interface to observe in real time

2. Open a protein structure

Tap File-New Molecule in the main window - New window pops up - Molecule File Browser (file reading window) - Tap Browse in the file reading window - Automatically open VMD - Installation directory - Enter proteins folder - Select the demo structure bpti.pdb that comes with VMD - Tap Load in the file reading window - Protein structure appears in the display window

3. Using the mouse in VMD

The mouse mode can be switched in the Mouse menu on the main window. The default mouse mode is Rotate Mode (R).

4. To restore the initial position of the structure.

Click Display - Reset View in the main window or click the left mouse button in the display window to activate the window and then click the "=" key.

Other Software Tutorials

1.Homology Modeling

Website: swiss-model

Principle: Similar amino acid sequences correspond to similar protein structures

Requirement: find a known structure with ≥ 30% identity to the target sequence as a template

Result evaluation:

(1) First see if the searched template agrees with your sequence > 30%, if not greater than, re-predict with iTASSER.

(2) If available, then see how high the swissmodel comes with the score.

  • GMQE : confidence range 0-1, larger values indicate better quality
  • QMEAN4: interval -4-0, the closer to 0, the better the match between the protein to be tested and the template protein is assessed. If the swissmodel prediction result is not available or scored badly, re-predict with iTASSER.

2. Folding identification (threading method)

Website: iTASSER

Principle: dissimilar amino acid sequences can also correspond to similar protein structures.

Requirement: This method is generally chosen for proteins that cannot be modeled homologously (<30% agreement).

3. Ab initio calculation method

Website: quark

Principle: The three-dimensional structure of a protein is determined by its own amino acid sequence and is in the lowest free energy state. Simulate all possible poses of the peptide in 3D space and calculate the one with the lowest free energy.

It is extremely computationally intensive and not commonly used.

After the prediction is done, download the corresponding pdb format file, which can be read by the free software VMD, is the 3D structure you predicted.

* For Research Use Only.